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79 results on '"Génome, populations, interactions, adaptation (GPIA)"'

1. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses

Author: Yannick Gueguen, J. de Lorgeril, Samuel Dupont, C. Salmeron, G. Tanguy, Caroline Montagnani, J.Y. Bou Khalil, Jean-Christophe Auguet, Jean-Michel Escoubas, Bruno Petton, B. La Scola, Eve Toulza, A. Lokmer, Christelle Desnues, Guillaume Mitta, David Pecqueur, Erwan Corre, Laure Guillou, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), 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)-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), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-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), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Observatoire océanologique de Banyuls (OOB), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), ECOlogy of MArine Plankton (ECOMAP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), The present study was supported by: the DHOF program of the UMR5244/IHPE (http://ihpe.univ-perp.fr/en/ihpe-transversal-holobiont/), the Ifremer project HémoMicrobiote, EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future (ANR-10-INBS-02), the ANR projects DECIPHER (ANR-14-CE19–0023) and ENVICOPAS (ANR-15-CE35–0004), the EU funded project VIVALDI (H2020 program, n°678589), by Ifremer, CNRS, Université de Montpellier, Université de Perpignan via Domitia, by the IHU Méditerranée Infection, Marseille, France, by the French Government under the «Investissements d’avenir» program (reference: Méditerranée Infection 10-IAHU-03) and by the Région Provence-Alpes-Côte d’Azur and by the European funding FEDER PRIMI. This study is set within the framework of the 'Laboratoires d’Excellences (LABEX)' TULIP (ANR-10-LABX-41)., ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-14-CE19-0023,DECIPHER,Déchiffrage des maladies multifactorielles: cas des mortalités de l'huître(2014), ANR-15-CE35-0004,ENVICOPAS,Impact des changements environnementaux sur les organismes pathogènes dans les écosystèmes côtiers(2015), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Éco-Anthropologie (EAE), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Adaptation et diversité en milieu marin (AD2M), 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), 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)-Station biologique de Roscoff (SBR), Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Parasitologie fonctionnelle et évolutive (PFE), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Radiopathologie et Thérapies Expérimentales [IRSN, Fontenay-aux-Roses] (PRP-HOM - SRBE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), and 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)
Subjects: Oyster, animal structures, Early-life microbiota, lcsh:QR1-502, Zoology, medicine.disease_cause, Within-host ecosystem, lcsh:Microbiology, 03 medical and health sciences, biology.animal, medicine, Trans-kingdom interactions, Human virome, Microbiome, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Ecological niche, 0303 health sciences, lcsh:Veterinary medicine, biology, 030306 microbiology, Host (biology), Oyster genetic background, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Protist, General Medicine, Pacific oyster, biology.organism_classification, Transplantation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDE]Environmental Sciences, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Crassostrea gigas, lcsh:SF600-1100, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Acln, Hemolymph microbiota dynamics, Research Article
Abstract: Background The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. Results We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 μVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. Conclusion Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transient character. Although it seems that the three microbiome components respond independently to environmental conditions, better characterization of hemolymph-associated viruses could change this picture.
Published: 2020

2. The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

Author: Khalid Belkhir, Henry L. North, Pierre Caminade, Carole M. Smadja, Dany Severac, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Department of Zoology, University of Cambridge, Cambridge, United Kingdom, Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), HLN was funded through an Erasmus Mundus Joint Masters Degree scholarship and an internship stipend from CMS’s research grants. The research leading to these results has received funding from the European Union’s Seventh Framework Programme [FP7/2007-2013] – Marie Curie European Reintegration Grant (ERG), under Grant agreement n°PERG06-GA-2009-251008, as well as from the Agence Nationale pour la Recherche (ANR) under Grant agreement No. 2010BLAN171401-AssortMate., ANR-06-NEUR-0043,Presynaptic-CB1,Récepteurs présynaptique cannabinoïdes de type 1 (CB1): mécanismes et fonctions dans le cortex préfrontal.(2006), SMADJA, Carole, Neurosciences, neurologie et psychiatrie - Récepteurs présynaptique cannabinoïdes de type 1 (CB1): mécanismes et fonctions dans le cortex préfrontal. - - Presynaptic-CB12006 - ANR-06-NEUR-0043 - NEURO - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and University of Cambridge [UK] (CAM)
Subjects: 0106 biological sciences, Reproductive Isolation, DNA Copy Number Variations, Isolation (health care), Subspecies, 010603 evolutionary biology, 01 natural sciences, pool-seq, General Biochemistry, Genetics and Molecular Biology, House mouse, Mice, 03 medical and health sciences, Hybrid zone, Genetic algorithm, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Animals, Mus musculus, Copy-number variation, Selection (genetic algorithm), 030304 developmental biology, reinforcement, 0303 health sciences, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Articles, Reproductive isolation, biology.organism_classification, Europe, speciation, Evolutionary biology, structural rearrangements, hybrid zone, General Agricultural and Biological Sciences, Research Article
Abstract: Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations ofMus musculus musculusthat display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These ‘Choosiness-associated’ CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene,Sp110, that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice—the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Published: 2020

3. The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications

Author: Pierrick Labbé, Mylène Weill, Pascal Milesi, Patrick Makoundou, Khalid Belkhir, Lamine Baba-Moussa, Arnaud Berthomieu, Luc Djogbenou, Benoît S. Assogba, Anna-Sophie Fiston-Lavier, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Abomey Calavi (UAC), Institut Régional de Santé Publique de Ouidah, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), and Institut Régional de Santé Publique Comlan Alfred Quenum [Ouidah] (IRSP)
Subjects: 0301 basic medicine, Insecticides, Life Cycles, Epidemiology, Anopheles gambiae, Artificial Gene Amplification and Extension, Genes, Insect, Disease Vectors, Genome, Mosquitoes, Polymerase Chain Reaction, Larvae, Gene Duplication, Gene duplication, Invertebrate Genomics, Medicine and Health Sciences, Biology (General), Genetics, biology, General Neuroscience, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Chromosome Mapping, Agriculture, Genomics, Amplicon, Phenotype, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Insects, General Agricultural and Biological Sciences, Agrochemicals, Sequence Analysis, Research Article, Arthropoda, DNA Copy Number Variations, QH301-705.5, Locus (genetics), Research and Analysis Methods, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Anopheles, Animals, Molecular Biology Techniques, Sequencing Techniques, Gene, Molecular Biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], General Immunology and Microbiology, Organisms, Biology and Life Sciences, biology.organism_classification, Invertebrates, Insect Vectors, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Genetic Loci, Animal Genomics, Sequence Alignment, Developmental Biology
Abstract: Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides’ target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies. We used an integrative approach, from genome to phenotype level, to investigate the influence of duplication architecture and gene-dosage on mosquito fitness. We found that both heterogeneous (i.e., one susceptible and one resistant ace-1 copy) and homogeneous (i.e., identical resistant copies) duplications segregated in field populations. The number of copies in homogeneous duplications was variable and positively correlated with acetylcholinesterase activity and resistance level. Determining the genomic structure of the duplicated region revealed that, in both types of duplication, ace-1 and 11 other genes formed tandem 203kb amplicons. We developed a diagnostic test for duplications, which showed that ace-1 was amplified in all 173 resistant mosquitoes analyzed (field-collected in several African countries), in heterogeneous or homogeneous duplications. Each type was associated with different fitness trade-offs: heterogeneous duplications conferred an intermediate phenotype (lower resistance and fitness costs), whereas homogeneous duplications tended to increase both resistance and fitness cost, in a complex manner. The type of duplication selected seemed thus to depend on the intensity and distribution of selection pressures. This versatility of trade-offs available through gene duplication highlights the importance of large mutation events in adaptation to environmental variation. This impressive adaptability could have a major impact on vector control in Africa., Author Summary Mutations, whether they affect single nucleotides or large genomic regions, are responsible for the genetic variability that allows species to evolve in response to environmental changes. Duplication represents a class of mutation that results in polymorphism in the copy number of genes. Investigating the phenotypic and fitness consequences of duplications is, however arduous, as it requires contemporary duplications under selection. Organophosphate and carbamate insecticides are used to control the main malaria vector, the mosquito Anopheles gambiae, and resistance to insecticides provides evolutionary biologists with ongoing adaptation to manmade modifications of the environment. Recent studies have revealed an intriguing complexity of resistance alleles at the ace-1 locus (encoding the target of these insecticides), in particular different duplications involving various numbers and types (susceptible or resistant) of copies of this gene. We used an integrative approach, from genomic to phenotypic levels, to show that the various genomic architectures of these adaptive alleles result in different evolutionary trade-offs whose selection depends on insecticide distribution and intensity. However, this versatility also provides a high adaptability to An. gambiae, which may have a major impact on malaria vector control in Africa.
Published: 2016

4. Iron(II) complexes are suitable catalysts for the isomerization of trifluoromethylated allylic alcohols. Synthesis of trifluoromethylated dihydrochalcones

Author: Sylvain Gaillard, Dominique Cahard, Jean-Luc Renaud, Xiaoyang Dai, Vincent Bizet, Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Laboratoire de chimie moléculaire et thioorganique (LCMT), Centre National de la Recherche Scientifique (CNRS)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), and Normandie Université (NU)
Subjects: Allylic rearrangement, [CHIM.ORGA]Chemical Sciences/Organic chemistry, 010405 organic chemistry, Chemistry, Organic Chemistry, chemistry.chemical_element, Dihydrochalcone, 010402 general chemistry, Ring (chemistry), 01 natural sciences, Biochemistry, Medicinal chemistry, 0104 chemical sciences, Catalysis, Inorganic Chemistry, chemistry.chemical_compound, Environmental Chemistry, Physical and Theoretical Chemistry, Platinum, Isomerization, ComputingMilieux_MISCELLANEOUS
Abstract: We demonstrated that iron(II) complexes can substitute platinum metals as well as iron(0) carbonyls for the isomerization of γ-trifluoromethylated allylic alcohols into β-trifluoromethylated ketones. In particular, iron(II)-tetra(isonitrile) complexes were employed for the synthesis of a series of trifluoromethylated dihydrochalcones variously decorated on each aromatic ring.
Published: 2013

5. From the laboratory to the wild: salinity-based genetic differentiation of the European sea bass (Dicentrarchus labrax) using gene-associated and gene-independent microsatellite markers

Author: François Bonhomme, Erick Desmarais, Costas S. Tsigenopoulos, Jacques Lagnel, Nolwenn Quéré, Bruno Guinand, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche sur l'Education, les apprentissages et la didactique (CREAD EA 3875), Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Brest (UBO)-Institut Brestois des Sciences de l'Homme et de la Société (IBSHS), Université de Brest (UBO), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Génome, populations, interactions, adaptation (GPIA), 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), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226, Université de Brest (UBO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Brestois des Sciences de l'Homme et de la Société (IBSHS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: 0106 biological sciences, 0303 health sciences, Candidate gene, Ecology, Locus (genetics), Aquatic Science, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Minisatellite, Evolutionary biology, Microsatellite, Dicentrarchus, 14. Life underwater, Sea bass, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Allele frequency, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Local adaptation
Abstract: International audience; Convincing evidence reporting adaptive variation for physiologically and/or ecologically important traits in marine taxa is often derived from studies comparing field and laboratory observations and based on candidate-gene markers, mainly allozymes, responding to habitat selection. Likewise, patterns of genetic differentiation between sea and lagoon populations of the euryhaline European sea bass (Dicentrarchus labrax) were shown to correlate with changes in allele frequencies recorded during experimental salinity challenges, suggesting potential role for local adaptation. However, there has been criticism of these past approaches, causing a need for further investigation. We reinvestigated this correlation in European sea bass using a set of 20 micro- and one minisatellite markers, some of which are associated with candidate genes. We used rigorous experimental settings to demonstrate that only one single gene-associated marker consistently reported significant genetic differentiation between fish raised in seawater compared to fish acclimated to freshwater (locus EIF3E; F ST = 0.060; p = 0.007, n = 268). A few other loci were shown to be false positive and did not respond to selection. Furthermore, a field study of sea–lagoon differentiation in wild European sea bass (n = 144) using the same loci reported marginally significant genetic differentiation at locus EIF3E (F ST = 0.0114, p = 0.068). This locus was identified as putatively under selection. Two other microsatellite loci associated with genes (DLA0070 and DLA0060, respectively) were found to significantly participate to sea–lagoon differentiation and deviate from neutral expectation. The evidence for sea–lagoon local adaptation in sea bass remains faint if not highly elusive.
Published: 2015

6. Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee, Apis mellifera

Author: Matthew T. Webster, Sylvain Glémin, Andreas Wallberg, Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: Cancer Research, Genome evolution, lcsh:QH426-470, Genome, Insect, Gene Conversion, Genomics, Biology, Genome, Linkage Disequilibrium, Chromosomal crossover, Evolution, Molecular, Molecular evolution, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Animals, Ectopic recombination, Gene conversion, Selection, Genetic, Genetik, Molecular Biology, Phylogeny, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, Recombination, Genetic, Natural selection, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Bees, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Meiosis, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Evolutionary biology, Research Article
Abstract: Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how recombination rates vary across the genomes of most species and the molecular and evolutionary determinants of this variation. The honeybee, Apis mellifera, has extremely high rates of meiotic recombination, although the evolutionary causes and consequences of this are unclear. Here we use patterns of linkage disequilibrium in whole genome resequencing data from 30 diploid honeybees to construct a fine-scale map of rates of crossing over in the genome. We find that, in contrast to vertebrate genomes, the recombination landscape is not strongly punctate. Crossover rates strongly correlate with levels of genetic variation, but not divergence, which indicates a pervasive impact of selection on the genome. Germ-line methylated genes have reduced crossover rate, which could indicate a role of methylation in suppressing recombination. Controlling for the effects of methylation, we do not infer a strong association between gene expression patterns and recombination. The site frequency spectrum is strongly skewed from neutral expectations in honeybees: rare variants are dominated by AT-biased mutations, whereas GC-biased mutations are found at higher frequencies, indicative of a major influence of GC-biased gene conversion (gBGC), which we infer to generate an allele fixation bias 5 – 50 times the genomic average estimated in humans. We uncover further evidence that this repair bias specifically affects transitions and favours fixation of CpG sites. Recombination, via gBGC, therefore appears to have profound consequences on genome evolution in honeybees and interferes with the process of natural selection. These findings have important implications for our understanding of the forces driving molecular evolution., Author Summary Evolution results from changes in allele frequencies in populations. The main forces that cause such changes are natural selection and random genetic drift. However, an additional process, GC-biased gene conversion (gBGC), associated with meiotic recombination, affects the probability that alleles are passed from one generation to the next. The honeybee, Apis mellifera, has extremely high recombination rates—more than 20 times to those observed in humans. However, the reason for this is unknown and the effects of such high recombination rates on evolution are not well understood. Here we use patterns of genetic variation in the genomes of 30 honeybees to infer variation in the rate of recombination across the genome. We find that recombination rates and levels of genetic variation are strongly correlated, which is indicative of a pervasive impact of natural selection on genetic variation. We also infer a major role of DNA methylation in determining recombination rates in genes. Patterns of genetic variation appear to be strongly skewed due to the effects of gBGC, suggesting that recombination generates a bias in transmission of alleles during meiosis. This process seems to be interfering with the efficacy of selection at removing deleterious alleles and favouring beneficial ones. Recombination therefore has a huge impact on genetic variation and evolution in honeybees and appears to play a dominant role in genome evolution.
Published: 2015

7. Range-wide population structure of European sea bass Dicentrarchus labrax

Author: Bart Hellemans, Erika Souche, Luca Bargelloni, Tomaso Patarnello, Eoin MacAoidh, Jann T. Martinsohn, François Bonhomme, Filip Volckaert, Massimiliano Babbucci, Dimitry A. Chistiakov, Bruno Guinand, Department of Comparative Biomedicine and Food Science, Universita degli Studi di Padova, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Génétique moléculaire, évolutive et médicale, IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), Laboratory of Animal Diversity and Systematics, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and 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)
Subjects: Mediterranean climate, Evolution, [SDV]Life Sciences [q-bio], Introgression, Zoology, SNP, Locus (genetics), adaptation, Biology, Marine fish, Mediterranean sea, Behavior and Systematics, somatolactin, 14. Life underwater, Sea bass, Adaptation, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Ecology, DNA microsatellite, Somatolactin, biology.organism_classification, Taxon, marine fish, Microsatellite, Dicentrarchus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: The euryhaline European sea bass Dicentrarchus labrax L., inhabiting the coasts of the eastern Atlantic Ocean and Mediterranean Sea, has had many opportunities for differentiation throughout its large natural range. However, evidence for this has been incompletely documented geographically and with an insufficient number of markers. Therefore, its full range was sampled at 22 sites and individuals were genotyped with a suite of mapped markers, including 14 microsatellite loci (N = 536) and 46 neutral or gene-linked single nucleotide polymorphisms (SNPs; N = 644). We confirm that the Atlantic and Mediterranean basins harbour two distinct lineages. Within the Atlantic Ocean no pattern was obvious based on the microsatellite and SNP genotypes, except for a subtle difference between South-eastern and North-eastern Atlantic sea bass attributed to limited introgression of alleles of Mediterranean origin. SNP genotypes of the Mediterranean lineage differentiated into three groups, probably under the influence of geographical isolation. The Western Mediterranean group showed genetic homogeneity without evidence for outlier loci. The Adriatic group appeared as a distinct unit. The Eastern Mediterranean group showed a longitudinal gradient of genotypes and most interestingly an outlier locus linked to the somatolactin gene. Overall, the spatial pattern fits those observed with other taxa of between-basin segregation and within-basin connectivity, which concurs well with the swimming capabilities of European sea bass. Evidence from a few outlier loci in this and other studies encourages further exploration of its regional connectivity and adaptive evolution. ispartof: Biological Journal of the Linnean Society vol:116 issue:1 pages:86-105 status: published
Published: 2015

8. Geographic and within-population variation in the globeflower–globeflower fly interaction: the costs and benefits of rearing pollinators’ larvae

Author: Åsa M. Hemborg, Sébastien Ibanez, Bernard Godelle, Laurence Després, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Botany, University of Cape Town, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: 0106 biological sciences, flower size, Pollination, conflict, Population Dynamics, chiastocheta flies, seed predators, egg aggregation, 01 natural sciences, yucca moths, Predation, Pollinator, Anthomyiidae, density-dependent competition, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Mutualism (biology), education.field_of_study, Geography, biology, Ecology, Larva, Seeds, France, competition, mutualism, Trollius europaeus, Population, cooperation, Flowers, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, Trollius-europaeus, evolution, Animals, pollination mutualism, Symbiosis, education, Ecology, Evolution, Behavior and Systematics, Population Density, Sweden, Analysis of Variance, Diptera, Interspecific competition, stability, biology.organism_classification, Predatory Behavior, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, oviposition, Ranunculaceae, 010606 plant biology & botany
Abstract: International audience; Interspecific interactions can vary within and among populations and geographic locations, and this variation can influence the nature of the interaction (e.g. mutualistic vs. antagonistic) and its evolutionary stability. Globeflowers are exclusively pollinated by flies, whose larvae feed only on their seeds. Here we document geographic variability in costs and benefits in globeflowers in sustaining their pollinating flies throughout the range of this arctic-alpine European plant over several years. A total of 1,710 flower heads from 38 populations were analysed for their carpel, egg and seed contents. Individual and population analyses control for the confounding influences of variation in both: (1) population traits, such as fly density and egg distribution among flower heads; and (2) individuals traits, such as carpel and egg numbers per flower head. Despite considerable variation in ecological conditions and pollinator densities across populations, large proportions (range 33-58%) of seeds were released after predation, with a benefit-to-cost ratio of 3, indicating that the mutualism is stable over the whole globeflower geographical range. The stability of the mutualistic interaction relies on density-dependent competition among larvae co-developing in a flower head. This competition is revealed by a sharp decrease in the number of seeds eaten per larva with increasing larval number, and is intensified by non-uniform egg distribution among globeflowers within a population. Carpel number is highly variable across globeflowers (range 10-69), and flies lay more eggs in large flowers. Most plants within a population contribute to the rearing of pollinators, but the costs are greater for some than for others. Large globeflowers lose more seed to pollinator larvae, but also release more seed than smaller plants. The apparent alignment of interests between fly and plants (positive relationship between numbers of seed released and destroyed) is shown to hide a conflict of interest found when flower size is controlled for.
Published: 2006

9. A Comparison of Rarefaction and Bayesian Methods for Predicting the Allelic Richness of Future Samples on the Basis of Currently Available Samples

Author: Kevin J. Dawson, François Bonhomme, Khalid Belkhir, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), and Rothamsted Research
Subjects: 0106 biological sciences, CONSERVATION, Bayesian probability, Population, DIVERSITY, Sample (statistics), Biology, Bioinformatics, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Bayes' theorem, Gene Frequency, BOTTLENECKS, Statistics, Genetics, Quantitative Biology::Populations and Evolution, NEUTRAL ALLELES, education, Molecular Biology, Bayesian average, Alleles, Genetics (clinical), 030304 developmental biology, 0303 health sciences, education.field_of_study, Genetic Variation, Bayes Theorem, Bayesian statistics, Genetics, Population, SIZE, Sampling distribution, Sample Size, GENETIC-MARKERS, POPULATIONS, Rarefaction (ecology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Monte Carlo Method, Biotechnology
Abstract: International audience; Rarefaction methods have been introduced into population generics (from ecology) for predicting and comparing the allelic richness of future samples (or sometimes populations) on the basis of currently available samples, possibly of different sizes. Here, we focus our attention on one such problem: Predicting which population is most likely to yield the future sample having the highest allelic richness. (This problem can arise when we want to construct a core collection from a larger germplasm collection.) We use extensive simulations to compare the performance of the Monte Carlo rarefaction (repeated random subsampling) method with a simple Bayesian approach we have developed-which is based on the Ewens sampling distribution. We found that neither this Bavesian method nor the (Monte Carlo) rarefaction method performed uniformly better than the other. We also examine briefly some of the other motivations offered for these methods and try to make sense of them from a Bayesian point of view.
Published: 2006

10. A transcriptomic approach of salinity response in the euryhaline teleost, Dicentrarchus labrax

Author: C. Long Ky, François Bonhomme, Isabelle Boutet, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Station IFREMER de Palavas-les-Flots, and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: Gills, Male, 0106 biological sciences, Transcription, Genetic, Sea bass, Fresh Water, Sodium Chloride, Suppression subtractive hybridisation, 01 natural sciences, Transcriptome, Osmoregulation, Carbonic Anhydrases, 0303 health sciences, education.field_of_study, Carbonic anhydrase, Cell Cycle, Metalloendopeptidases, General Medicine, Euryhaline, Water-Electrolyte Balance, Adaptation, Physiological, 6. Clean water, Intestines, Biochemistry, Female, Dicentrarchus, Fish Proteins, Genetic Markers, Molecular Sequence Data, Population, Biology, 010603 evolutionary biology, Acclimatization, 03 medical and health sciences, Genetics, Animals, Seawater, Amino Acid Sequence, RNA, Messenger, 14. Life underwater, education, 030304 developmental biology, Base Sequence, Gene Expression Profiling, MRNA expression, mRNA expression, biology.organism_classification, Salinity, Fishery, Bass, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Euryhaline teleosts possess the capacity to osmoregulate under various environmental conditions (freshwater to hypersaline water). This physiological capacity is generally monitored using enzyme activity assays (Na+/K+-ATPase...), hormones quantification (prolactine, growth hormone) or their mRNAs expression. To date, few studies addressed the genetic correlates of adaptation to varying salinity at a molecular level in such fish. In the sea bass Dicentrarchus labrax, genetic differentiation was observed at specific allozyme loci between lagoon- and open-sea populations. In the present study, we investigated transcriptomic response of D. labrax to salt- and freshwater acclimation in two organs involved in osmoregulation, gill and intestine. By using suppression subtractive hybridisation, we characterised 586 partial cDNA sequences encoding proteins potentially involved in the metabolism of sea bass acclimated to salt- or freshwater under experimental conditions. Using these results, we first characterised complete genomic sequence of a carbonic anhydrase and then analysed mRNA expression of genes potentially involved in osmoregulation mechanisms (Na+/K+-ATPase, carbonic anhydrase, angiotensin-converting enzyme and claudin-3), cell-cycle regulation (secretagogin) and immune system (nephrosin) in gill and intestine of wild fish from open sea and lagoons. Our analyses indicate a strong tissue- and environmental-dependant expression pattern for all the genes studied. A transcriptomic approach such as described in the present paper provides thus a first description of genes involved in metabolic or structural functions important for coping with environmental salinity variations in a euryhaline fish like the common sea bass D. labrax. It should be supplemented by proteomics to check the direct involvement of the gene products at the protein level, and by polymorphism analyses if one is to understand population or individual fluctuations in acclimation to salinity variation. (c) 2006 Elsevier B.V. All rights reserved.
Published: 2006

11. Marker-based investigation of inbreeding depression in the endangered species Brassica insularis

Author: Thomas Bataillon, Sylvain Glémin, Agnès Mignot, L. Vimond, Joëlle Ronfort, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Bioinformatics Research Center (BiRC), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genetic Markers, epistasis, 0106 biological sciences, molecular markers, Outbreeding depression, Rare species, Genetic purging, Brassica, Biology, lethal equivalent, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Inbred strain, Genetics, Inbreeding depression, Inbreeding, Alleles, Genetics (clinical), Brassica insularis, 030304 developmental biology, Lethal equivalent, 0303 health sciences, Models, Genetic, Inbreeding coefficients, Molecular markers, Epistasis, Genetic, Genetics, Population, Genetic marker, inbreeding coefficients, Epistasis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microsatellite Repeats, inbreeding depression
Abstract: Correspondance: glemin@univ-montp2.fr; International audience; Various methods have been proposed to estimate inbreeding depression and to assess its consequences for natural populations. As an alternative to controlled crosses, the use of molecular markers has allowed direct investigation of inbreeding depression in natural populations, but usually suffers from low statistical power. Here, we investigated the effect of inbreeding depression on survival in two populations of the rare species Brassica insularis, using both controlled crosses and a marker-based approach. We compare the respective merits of the two approaches for studying inbreeding depression. We also use information from the molecular markers to dissect in detail patterns of inbreeding depression in this species. A posteriori, we find that combining the approaches was not necessary to obtain simple point estimates of inbreeding depression. However, using molecular markers may give insight into the genetic basis of inbreeding depression, such as the occurrence of epistatic interactions among deleterious alleles or purging.
Published: 2006

12. Within-host evolution and virulence in microparasites

Author: Bernard Godelle, Jean-Baptiste André, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Instituto Gulbenkian de Ciência [Oeiras] (IGC), and Fundação Calouste Gulbenkian
Subjects: 0106 biological sciences, Statistics and Probability, Population, Virulence, Deleterious mutations, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Host-Parasite Interactions, 03 medical and health sciences, Parasitic Diseases, Animals, Parasites, Selection, Genetic, Suboptimality, education, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Models, Genetic, General Immunology and Microbiology, Transmissibility, Applied Mathematics, General Medicine, Biological Evolution, Multilevel selection, Transmissibility (vibration), 3. Good health, Modeling and Simulation, Mutation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Microparasite
Abstract: International audience; An important aspect of microparasite biology is the fact that infections are populations of thousands of microbes. As any population, infections are hence subject to two main types of changes: demographic and evolutionary. Here we analyse the consequences of within-host evolutionary changes. We build an epidemiological model where infections are regularly invaded by locally favored mutations affecting various infectious traits (virulence, transmissibility and clearance). Our results are the following. In durable infections, where within-host evolution is an important matter, a drop of transmissibility is only slightly deleterious to the infection, while a reduction of infection lifespan is very costly. In consequence, locally favored mutations reducing transmissibility reach a larger frequency, or even the complete fixation, and the suboptimality accumulated in infections owing to within-host evolution affects more their transmission than their duration. Conversely, taking an infection at random and observing the events of within-host evolution, one is more likely to observe reductions of infection length than reductions of transmissibility, because the mutations affecting transmissibility are often already present in infections. We then discuss the interpretation of these results in terms of deleterious mutations, and we also emphasize that the management of within-host evolution could be used as a novel therapeutic approach to the treatment of infection.
Published: 2006

13. Fitness landscapes support the dominance theory of post-zygotic isolation in the musselsMytilus edulisandM. galloprovincialis

Author: Patrice David, Nicolas Bierne, François Bonhomme, Pierre Boudry, Marta Szulkin, Génome, populations, interactions, adaptation (GPIA), 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), Laboratoire de Génétique et Pathologie (LGP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, Hybrid zone, animal structures, Genotype, Mytilus edulis, Introgression, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Linkage Disequilibrium, General Biochemistry, Genetics and Molecular Biology, Dobzhansky Muller incopatibilities, 03 medical and health sciences, hybrid breakdown, Negative epistasis, Animals, Inbreeding, 14. Life underwater, Selection, Genetic, post-zygotic isolation, 030304 developmental biology, General Environmental Science, Mytilus, Genetics, 0303 health sciences, Models, Genetic, General Immunology and Microbiology, Directional selection, fungi, General Medicine, Mussel, biology.organism_classification, negative epistasis, Dobzhansky-Muller incopatibilities, Post zygotic isolation, Evolutionary biology, Hybridization, Genetic, Epistasis, hybrid zone, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Research Article, Hybrid breakdown
Abstract: We studied the genetic basis of post-zygotic isolation in the marine musselsMytilus edulisandMytilus galloprovincialis. Evidence was obtained for a high number of recessive Dobzhansky–Muller substitutions in the genome of these two mussel taxa. We analysed the segregation of unlinked diagnostic markers in the progeny of two backcrosses and an F2cross, 36 h and 200 days after fertilization. Directional selection favouringM. galloprovincialisgenotypes was observed in both kinds of cross. In the F2, epistatic interactions between each pair of chromosome fragments mapped by the markers were identified in addition. Our results imply that homozygous–homozygous interactions are required for breakdown of coadaptation, in accordance with the dominance theory of post-zygotic isolation. Endogenous post-zygotic selection distributed over many loci throughout the genome provides the missing factor explaining the astonishing persistence and strength of barriers to neutral introgression in such a dispersive taxon asMytilus.
Published: 2006

14. Phylogenetic relationships among monogenean gill parasites (Dactylogyridea, Ancyrocephalidae) infesting tilapiine hosts (Cichlidae): Systematic and evolutionary implications

Author: Antoine Pariselle, Erick Desmarais, Laurent Pouyaud, Marty Deveney, GAMET, IRD, UR081 (GAMET), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), and PIRSA Aquaculture
Subjects: Systematic, Systematics, food.ingredient, rDNA, Zoology, Morphology (biology), DNA, Ribosomal, Host-Parasite Interactions, 030308 mycology & parasitology, 03 medical and health sciences, food, Genus, cichlid fishes, systematic, DNA, Ribosomal Spacer, West Africa, RNA, Ribosomal, 18S, Genetics, Animals, Parasite hosting, Sarotherodon, phylogenetic analyses, Molecular Biology, Phylogenetic analyses, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, biology, Tilapia, Cichlids, biology.organism_classification, Biological Evolution, Oreochromis, Platyhelminths, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Monogenea, Cichlid fishes
Abstract: We studied the systematics of 14 species of monogenean (Ancyrocephalidae) gill parasites from West African tilapiine hosts (Cichlidae) using both morphological and genetic data. With these tools, we were able to: (i) confirm the validity of the previously described morphological parasite species and of the genus Scutogyrus; (ii) propose that some stenoxenous species (i.e., parasite species with more than one host) may be composed of sister species (e.g., Cichlidogyrus tilapiae); (iii) state that the use of the morphology of the haptoral sclerites is more suitable to infer phylogenetic relationships than the morphology of the genitalia (which seems to be more useful to resolve species-level identifications, presumably because of its faster rate of change). These results imply that: (i) the specificity of these monogenean parasites is greater than initially supposed (what were thought to be stenoxenous species may be assemblages of oioxenous sister species); (ii) related species groups (i.e., "tilapiae," "halli," and "tiberianus") have to be, as genus Scutogyrus, validated within the 54 ancyrocephalid species described from 18 species of tilapiine hosts in West Africa, (iii) the group "tilapiae," due to its morphology and host range, have to be considered as being the most primitive; (iv) the occurrence of lateral transfers and parallel speciation processes are necessary to describe the repartition of the newly described parasite groups on the three host genera studied (Tilapia, Oreochromis, and Sarotherodon). (c) 2005 Elsevier Inc. All rights reserved.
Published: 2006

15. A Model-Based Approach for Detecting Coevolving Positions in a Molecule

Author: Julien Y. Dutheil, Tal Pupko, Nicolas Galtier, Alain Jean-Marie, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Tel Aviv University [Tel Aviv], Algorithmes et Performance des Réseaux (APR), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: 0106 biological sciences, RNA structure prediction, Protein Conformation, Markov models, Biology, Markov model, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, Set (abstract data type), 03 medical and health sciences, symbols.namesake, Protein structure, Escherichia coli, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Computer Simulation, Selection, Genetic, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Independence (probability theory), 030304 developmental biology, 0303 health sciences, intramolecular and intermolecular interaction, Base Sequence, Models, Genetic, Markov chain, Phylogenetic tree, correlated substitutions, Substitution (logic), Genetic Variation, Bayes Theorem, Markov Chains, Pearson product-moment correlation coefficient, RNA, Ribosomal, symbols, [SDV.IMM]Life Sciences [q-bio]/Immunology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Biological system, Coevolution
Abstract: International audience; We present a new method for detecting coevolving sites in molecules. The method relies on a set of aligned sequences(nucleic acid or protein) and uses Markov models of evolution to map the substitutions that occurred at each site onto thebranches of the underlying phylogenetic tree. This mapping takes into account the uncertainty over ancestral states andamong-site rate variation. We then build, for each site, a ‘‘substitution vector’’ containing the posterior estimates of thenumber of substitutions in each branch. The amount of coevolution for a pair of sites is then measured as the Pearsoncorrelation coefficient between the two corresponding substitution vectors and compared to the expectation under the nullhypothesis of independence. We applied the method to a 79-species bacterial ribosomal RNA data set, for which extensivestructural characterization has been done over the last 30 years. More than 95% of the intramolecular predicted pairs of sitescorrespond to known interacting site pairs.
Published: 2005

16. Evolution of Mutualism Between Globeflowers and their Pollinating Flies

Author: Jean-Baptiste Ferdy, Laurence Després, Bernard Godelle, Department of Botany and Agricultural Biochemistry, University of Vermont [Burlington], Conservatoire Botanique National du Bassin Parisien (CBNBP), Muséum national d'Histoire naturelle (MNHN), Ecologie Systématique et Evolution (ESE), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Laboratoire d'Ecologie Alpine (LECA), and Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])
Subjects: 0106 biological sciences, Statistics and Probability, Avian clutch size, Pollination, Trollius europaeus, cooperation, Parasitism, chiastocheta flies, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, yucca moths, anthomyiidae, 03 medical and health sciences, Pollinator, Anthomyiidae, Animals, Plant Physiological Phenomena, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Mutualism (biology), 0303 health sciences, General Immunology and Microbiology, biology, Ecology, Diptera, Applied Mathematics, fungi, food and beverages, General Medicine, biology.organism_classification, Biological Evolution, fitness, speciation, Sympatric speciation, Fertilization, Modeling and Simulation, trollius-europaeus, Pollen, Seed-parasitic pollinators, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, oviposition, General Agricultural and Biological Sciences
Abstract: International audience; Plant/seed-eater pollinators mutualisms involve a plant pollinated by an insect whose larvae develop by eating a fraction of host-plant seeds. The outcome of the interaction therefore depends on the number of ovules fertilized by adult visits and the number of seeds destroyed by larvae. Among the very few cases of such mutualisms reported so far is the globeflower-globeflower flies mutualism, which is unique in that it involves several congeneric fly species (Chiastocheta genus) coexisting within a single host-plant species, Trollius europaeus. These species exhibit contrasted oviposition behaviors resulting in a more or less beneficial outcome for the plant. We designed an adaptive dynamics model to investigate how morphological traits of globeflower could affect the evolution of oviposition in its pollinating flies. Three fly traits (flower age at oviposition, clutch size and the level of avoidance of already parasitized flowers) and one plant trait (closed or open corolla) were examined. Whatever the shape of the flower, evolutionary branching occurs between early and late ovipositing flies, driven by strong competition among larvae within a fruit. Once this branching occurred, the closed shape of the corolla is likely to offer a better protection to eggs of early but not of late ovipositing flies. The difference in egg survival results in higher competition among early larvae and thus selects for decreased clutch size in early flies. This can be seen as a first step in the evolution of a mutualistic behavior. The prediction of our model fits field observations of fly behavior, giving theoretical support to the hypothesis of fly sympatric speciation within its host plant. Moreover, flower closed globe shape can be positively selected in globeflowers as it results in a reduction of parasitism strength. This last evolution therefore leads to a stable mutualism between globeflowers and globeflower flies. (C) 2002 Elsevier Science Ltd. All rights reserved.
Published: 2002

17. Fitness difference between cryptic salinity-related phenotypes of sea bass (Dicentrarchus labrax)

Author: Guinand, Bruno, Quéré, Nolwenn, Cerqueira, Frédérique, Desmarais, Erick, Bonhomme, François, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche sur l'Education, les apprentissages et la didactique (CREAD EA 3875), Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Brest (UBO)-Institut Brestois des Sciences de l'Homme et de la Société (IBSHS), Université de Brest (UBO), Labex CEMEB, Université Montpellier 2 - Sciences et Techniques (UM2), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Université de Brest (UBO)-Université de Rennes 2 (UR2), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Brestois des Sciences de l'Homme et de la Société (IBSHS)
Subjects: lcsh:SH1-691, insulin-like growth factor 1, phenotype, SH1-691, expression de genes, factor de crecimiento similar a la insulina 1, lubina, lcsh:Aquaculture. Fisheries. Angling, growth hormone receptor, [SDE]Environmental Sciences, Aquaculture. Fisheries. Angling, gene expression, fenotipo, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, sea bass, ComputingMilieux_MISCELLANEOUS, receptor de la hormona del crecimiento
Abstract: The existence of cryptic salinity-related phenotypes has been hypothesized in the “euryhaline” sea bass (Dicentrarchus labrax). How differential osmoregulation costs between freshwater and saltwater environments affect fitness and phenotypic variation is misunderstood in this species. During an experiment lasting around five months, we investigated changes in the whole body mass and in the expression of growth-related genes (insulin-like growth factor 1 [IGF-1]; growth hormone receptor [GHR]) in the intestine and the liver of sea bass thriving in sea water (SSW), successfully acclimated to freshwater (SFW), and unsuccessfully acclimated to freshwater (UFW). Albeit non-significant, a trend toward change in body mass was demonstrated among SSW, UFW and SFW fish, suggesting that SSW fish were a mixture of the other phenotypes. Several mortality peaks were observed during the experiment, with batches of UFW fish showing higher expression in the osmoregulatory intestine due to down-regulation of genes in the liver and significant up-regulation of GHR in the intestine compared with SFW fish. Energy investment toward growth or ion homeostasis hence partly mediates the fitness difference between cryptic SFW and UFW phenotypes. The use of a genetic marker located within the IGF-1 gene showed no genotype-phenotype relationship with levels of gene expression. En la especie “eurihalina” de la lubina (Dicentrarchus labrax) se ha planteado la existencia de fenotipos crípticos relacionados con la salinidad. En esta especie los costes diferenciales de osmoregulación a la adaptación en de agua dulce y salada son aún desconocidos. Durante un experimento de aproximadamente 5 meses, se investigó los cambios en la masa corporal y en la expresión de genes relacionados con el crecimiento (factor de crecimiento similar a la insulina 1 [IGF-1]; receptor de la hormona del crecimiento [GHR]) en el intestino y el hígado de lubina en individuos que prosperan en agua de mar (SSW), individuos aclimatados con éxito con el agua dulce (SFW), e individuos no aclimatados al agua dulce (UFW). Aunque no es significativa, se observa una tendencia de cambio en la masa corporal entre individuos SSW, UFW y SFW. Estos resultados sugieren que los individuos SSW son una mezcla de los otros fenotipos. Se observaron varios picos de mortalidad durante el experimento, con lotes de peces UFW que presentan una expresión génica más elevada en el intestino osmoregulador, debido a la regulación a la baja de genes en el hígado y regulación hacia arriba en la GHR del intestino cunado se compara con los peces SFW. Por lo tanto, la inversión de energía hacia el crecimiento o la homeostasis iónica explica en parte la diferencia de adaptación entre los crípticos fenotipos SFW y UFW. El uso de un marcador genético localizado dentro del gen de IGF-1 no demuestra relación genotipo-fenotipo con los niveles de expresión génica.
Published: 2014
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18. Interpretation of Variation Across Marker Loci as Evidence of Selection

Author: Renaud Vitalis, Kevin J. Dawson, Pierre Boursot, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Station Biologique de la Tour du Valat, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Long Ashton Research Station, Department of Agricultural Science (I.A.C.R.), University of Bristol [Bristol], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)
Subjects: Genetic Markers, 0106 biological sciences, Population, Locus (genetics), Haploidy, Biology, marqueur, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Joint probability distribution, Genetics, Animals, MESH: marker, education, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [STAT.AP]Statistics [stat]/Applications [stat.AP], 0303 health sciences, Genetic diversity, education.field_of_study, Models, Statistical, Polymorphism, Genetic, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Natural selection, Models, Genetic, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, Estimator, Conditional probability distribution, Models, Theoretical, Genetics, Population, Evolutionary biology, Outlier, Drosophila, variation, Research Article
Abstract: Population structure and history have similar effects on the genetic diversity at all neutral loci. However, some marker loci may also have been strongly influenced by natural selection. Selection shapes genetic diversity in a locus-specific manner. If we could identify those loci that have responded to selection during the divergence of populations, then we may obtain better estimates of the parameters of population history by excluding these loci. Previous attempts were made to identify outlier loci from the distribution of sample statistics under neutral models of population structure and history. Unfortunately these methods depend on assumptions about population structure and history that usually cannot be verified. In this article, we define new population-specific parameters of population divergence and construct sample statistics that are estimators of these parameters. We then use the joint distribution of these estimators to identify outlier loci that may be subject to selection. We found that outlier loci are easier to recognize when this joint distribution is conditioned on the total number of allelic states represented in the pooled sample at each locus. This is so because the conditional distribution is less sensitive to the values of nuisance parameters.
Published: 2001

19. Effects of Colonization Processes on Genetic Diversity: Differences Between Annual Plants and Tree Species

Author: Stéphanie Mariette, Pierre-Henri Gouyon, Frédéric Austerlitz, Bernard Godelle, Nathalie Machon, Unité de recherches forestières (BORDX PIERR UR ), Institut National de la Recherche Agronomique (INRA), ProdInra, Migration, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7), and Austerlitz, Frederic
Subjects: Nuclear gene, Population genetics, [SDV.GEN] Life Sciences [q-bio]/Genetics, Biology, medicine.disease_cause, Trees, Gene flow, Evolution, Molecular, Pollen, Genetic variation, Genetics, medicine, Colonization, MESH: Genetic Variation, MESH: Models, Genetic, MESH: Evolution, Molecular, ComputingMilieux_MISCELLANEOUS, VARIABLE GENETIQUE, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Models, Statistical, Models, Genetic, Ecology, Genetic Variation, GENETIQUE, MESH: Trees, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], human activities, MESH: Models, Statistical, Research Article, Woody plant
Abstract: Tree species are striking for their high within-population diversity and low among-population differentiation for nuclear genes. In contrast, annual plants show much more differentiation for nuclear genes but much less diversity than trees. The usual explanation for this difference is that pollen flow, and therefore gene flow, is much higher for trees. This explanation is problematic because it relies on equilibrium hypotheses. Because trees have very recently recolonized temperate areas, they have experienced many foundation events, which usually reduce within-population diversity and increase differentiation. Only extremely high levels of gene flow could counterbalance these successive founder effects. We develop a model to study the impact of life cycle of forest trees, in particular of the length of their juvenile phase, on genetic diversity and differentiation during the glacial period and the following colonization period. We show that both a reasonably high level of pollen flow and the life-cycle characteristics of trees are needed to explain the observed structure of genetic diversity. We also show that gene flow and life cycle both have an impact on maternally inherited cytoplasmic genes, which are characterized both in trees and annual species by much less diversity and much more differentiation than nuclear genes.
Published: 2000

20. Effect of bacterial symbionts Xenorhabdus on mortality of infective juveniles of two Steinernema species

Author: Nathalie Le Brun, Mathieu Sicard, Jean-Baptiste Ferdy, Vanya Emelianoff, Catherine Moulia, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: NEMATOPHILA, Nematoda, media_common.quotation_subject, Zoology, Xenorhabdus, Insect, [SDE.BE.IO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.io, Microbiology, 03 medical and health sciences, Aposymbiotic, Species Specificity, Symbiosis, CARPOCAPSAE, Animals, Parasite hosting, 030304 developmental biology, media_common, 0303 health sciences, General Veterinary, biology, 030306 microbiology, fungi, General Medicine, biology.organism_classification, Enterobacteriaceae, Infectious Diseases, Nematode, Insect Science, Parasitology, Bacteria
Abstract: International audience; Steinernema species are entomopathogenic nematodes associated with Xenorhabdus bacteria. The life cycle of these associations is composed of two stages: (1) a free stage in the soil, where infective juveniles (IJs), which carry bacteria in their guts, search for new insect hosts; and (2) a parasitic stage, where the IJs infect insects, release their Xenorhabdus symbionts and reproduce in order to produce new IJs. Previous studies clearly showed benefits to the association for several Steinernema species during the parasitic stage. Nevertheless, no study has so far explored, during the free stage, the existence of costs or benefits to the association for different Steinernema. Here, we compared the survival of both symbiotic and aposymbiotic IJs in two nematode species: (1) Steinernema carpocapsae-exhibiting IJs that carry a high number of Xenorhabdus cells in their guts; and (2) its closely relative species, S. scapterisci-exhibiting IJs, that carry very few Xenorhabdus cells in their guts. We showed that the bacterial symbionts were costly for S. carpocapsae by increasing IJs' mortality but not for S. scapterisci. This difference in cost induced by bacteria to IJs during the free stage could be correlated with the difference in the numbers of bacteria carried by IJs of each nematode species.
Published: 2006

21. Isomérisation rédox : une réaction économe en atome à fort potentiel d'innovation

Author: Bizet, Vincent, Cahard, Dominique, Gaillard, Sylvain, Renaud, Jean-Luc, Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Laboratoire de chimie moléculaire et thioorganique (LCMT), Centre National de la Recherche Scientifique (CNRS)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), and Normandie Université (NU)
Subjects: [CHIM.ORGA]Chemical Sciences/Organic chemistry, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2013

22. Reference-Free Population Genomics from Next- Generation Transcriptome Data and the Vertebrate- Invertebrate Gap

Author: Etienne Loire, Nicolas Faivre, José Melo-Ferreira, Nicolas Bierne, Nicolas Galtier, Aurélien Bernard, Vincent Cahais, Benoit Nabholz, Khalid Belkhir, Paulo C. Alves, Marion Ballenghien, Joao M. Lourenco, Philippe Gayral, Sylvain Glémin, Miguel Carneiro, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO), Universidade do Porto = University of Porto, Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto (FCUP), Universidade do Porto = University of Porto-Universidade do Porto = University of Porto, Génome, populations, interactions, adaptation (GPIA), 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), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université de Tours-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Universidade do Porto, Universidade do Porto-Universidade do Porto, Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), CIBIO, Centro de Investigação em Biodiversidade de Recursos Genéticos, Universidade do Porto [Porto], Centro de Investigacao em Biodiversidade e Recursos Genéticos (CIBIO), CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Faculdade de Ciências da Universidade do Porto, Biologie, Ingénierie et Imagerie de la Greffe de Cornée (EA 2521, JE2521, IFR143), and Université Jean Monnet [Saint-Étienne] (UJM)
Subjects: 0106 biological sciences, Evolutionary Genetics, Cancer Research, Population genetics, 01 natural sciences, Emydidae, Population genomics, Génétique des populations, Ostrea, Natural Selection, Genome Evolution, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, education.field_of_study, Population size, High-Throughput Nucleotide Sequencing, Genomics, Turtles, Reticulitermes, Vertebrates, Drosophila, Research Article, Modèle animal, Méthodologie, Evolutionary Processes, lcsh:QH426-470, Genotype, Invertébré, Population, Isoptera, Biology, 010603 evolutionary biology, Polymorphism, Single Nucleotide, génomique, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Humans, Population animale, Urochordata, Adaptation, education, Molecular Biology, Lièvre, Ecology, Evolution, Behavior and Systematics, Taille du groupe, 030304 developmental biology, Génie génétique, Genetic diversity, Evolutionary Biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Base Sequence, Genome, Human, Genetic Drift, Étude de cas, Genomic Evolution, Comparative Genomics, L10 - Génétique et amélioration des animaux, Hares, Invertebrates, Ostreidae, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Metagenomics, Evolutionary biology, Genomic Profile, Mammifère, U30 - Méthodes de recherche, Genome Expression Analysis, Transcriptome, Population Genetics, Reference genome
Abstract: In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity., Author Summary The analysis of genomic variation between individuals of a given species has so far been restricted to a small number of model organisms, such as human and fruitfly, for which a fully sequenced, well-annotated reference genome was available. Here we show that, thanks to next-generation high-throughput sequencing technologies and appropriate genotype-calling methods, de novo population genomic analysis is possible in absence of a reference genome. We characterize the genomic level of neutral and selected polymorphism in five non-model animal species, two vertebrates and three invertebrates, paying particular attention to the treatment of multi-copy genes. The analyses demonstrate the influence of population size on genetic diversity in animals, the two vertebrates (hare, turtle) and the social insect (termite) being less polymorphic than the two marine invertebrates (oyster, tunicate) in our sample. Interestingly, genomic indicators of the efficiency of natural selection, both purifying and adaptive, did not vary in a simple, predictable way across organisms. These results prove the value of a diversified sampling of species when it comes to understand the determinants of genome evolutionary dynamics.
Published: 2013

23. Variation in gene expression along a salinity gradient in wild populations of the euryhaline black-chinned tilapia Sarotherodon melanotheron

Author: Mbaye Tine, Bruno Guinand, Jean-Dominique Durand, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Salinity, food.ingredient, Population, Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, food, Botany, Animals, education, Gene, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, education.field_of_study, Principal Component Analysis, Brackish water, Gene Expression Profiling, Tilapia, Euryhaline, 6. Clean water, Up-Regulation, Gene expression profiling, Gene Expression Regulation, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: This study evaluated variation in expression of 11 genes within and among six wild populations of the black-chinned tilapia Sarotherodon melanotheron distributed along a salinity gradient from 0 to 100. Previous laboratory studies had shown that expression of these genes was sensitive to water salinity; the current study confirmed that a number of them also varied in expression in wild populations along the salinity gradient. Principal component analysis (PCA) first distinguished two, not mutually exclusive, sets of genes: trade-off genes that were highly expressed at one or other extreme of the salinity gradient and stress genes that were up-regulated at the two salinity extremes (i.e. a U-shaped expression pattern). The PCA clearly partitioned the populations into three groups based on their gene expression patterns and their position along the salinity gradient: a freshwater (GL; 0) population, four brackish and seawater (GB, HB, SM, SF; ranging from 20 to 50) populations and a hypersaline (SK, 100) population. Individual variation in gene expression was significantly greater within the populations at the extreme compared to intermediate salinities. These results reveal phenotypically plastic regulation of gene expression in S. melanotheron, and greater osmoregulatory and plasticity costs at extreme salinities, where fitness-related traits are known to be altered.
Published: 2012

24. SNP Detection from De Novo Transcriptome Sequencing in the Bivalve Macoma balthica: Marker Development for Evolutionary Studies

Author: Eric Pante, Khalid Belkhir, Audrey Rohfritsch, Pascale Garcia, Nicolas Bierne, Vanessa Becquet, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and 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)
Subjects: 0106 biological sciences, Population genetics, lcsh:Medicine, Sequence assembly, DNA sequences, 01 natural sciences, Linkage Disequilibrium, Transcriptomes, Gene flow, Marine Conservation, Transcriptome, Macoma balthica, Genome Sequencing, lcsh:Science, Genetics, 0303 health sciences, Multidisciplinary, biology, Gene Ontologies, Marine Ecology, RNA sequencing, Genomics, Hybrid Zones, Genome Scans, Adaptation, Physiological, Mitochondria, Transcriptome analysis, Research Article, Genetic Markers, Gene Flow, Evolutionary Processes, Genetic loci, Marine Biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Polymorphism, Single Nucleotide, 010603 evolutionary biology, DNA sequencing, Evolution, Molecular, 03 medical and health sciences, Hybrid zone, Genome Analysis Tools, Animals, Selection, Genetic, Adaptation, Biology, Hybridization, 030304 developmental biology, Evolutionary Biology, Gene Expression Profiling, lcsh:R, Molecular Sequence Annotation, Comparative Genomics, 15. Life on land, biology.organism_classification, Bivalvia, Genetic divergence, Haplotypes, lcsh:Q
Abstract: International audience; Hybrid zones are noteworthy systems for the study of environmental adaptation to fast-changing environments, as they constitute reservoirs of polymorphism and are key to the maintenance of biodiversity. They can move in relation to climate fluctuations, as temperature can affect both selection and migration, or remain trapped by environmental and physical barriers. There is therefore a very strong incentive to study the dynamics of hybrid zones subjected to climate variations. The infaunal bivalve Macoma balthica emerges as a noteworthy model species, as divergent lineages hybridize, and its native NE Atlantic range is currently contracting to the North. To investigate the dynamics and functioning of hybrid zones in M. balthica, we developed new molecular markers by sequencing the collective transcriptome of 30 individuals. Ten individuals were pooled for each of the three populations sampled at the margins of two hybrid zones. A single 454 run generated 277 Mb from which 17K SNPs were detected. SNP density averaged 1 polymorphic site every 14 to 19 bases, for mitochondrial and nuclear loci, respectively. An An external file that holds a picture, illustration, etc. Object name is pone.0052302.e001.jpg scan detected high genetic divergence among several hundred SNPs, some of them involved in energetic metabolism, cellular respiration and physiological stress. The high population differentiation, recorded for nuclear-encoded ATP synthase and NADH dehydrogenase as well as most mitochondrial loci, suggests cytonuclear genetic incompatibilities. Results from this study will help pave the way to a high-resolution study of hybrid zone dynamics in M. balthica, and the relative importance of endogenous and exogenous barriers to gene flow in this system.
Published: 2012

25. Use of OmpU porins for attachment and invasion of Crassostrea gigas immune cells by the oyster pathogen Vibrio splendidus

Author: Nicole Lautredou-Audouy, Rafael Diego Rosa, Sylvie Kieffer-Jaquinod, Marylise Duperthuy, Edwin Garzón, Julien de Lorgeril, Bernard Romestand, Audrey Caro, Frédérique Le Roux, Patrice Got, Delphine Destoumieux-Garzón, Paulina Schmitt, Evelyne Bachère, Laboratoire de Microbiologie, UMR INRA 1082, AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), MRI-Montpellier RIO Imaging, 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), Génome, populations, interactions, adaptation (GPIA), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Microbiologie, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Oyster, Hemocytes, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Host–pathogen interaction, Green Fluorescent Proteins, invertebrate, Porins, Virulence, Human pathogen, host-pathogen interaction, Polymerase Chain Reaction, Statistics, Nonparametric, Microbiology, 03 medical and health sciences, Tandem Mass Spectrometry, biology.animal, Animals, Crassostrea, oxidative burst, Adhesins, Bacterial, innate immunity, ComputingMilieux_MISCELLANEOUS, Vibrio, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Analysis of Variance, 0303 health sciences, Microscopy, Confocal, Multidisciplinary, Innate immune system, biology, Superoxide Dismutase, 030306 microbiology, Intracellular parasite, mollusk, Biological Sciences, Flow Cytometry, Actin cytoskeleton, biology.organism_classification, Immunity, Innate, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, Host-Pathogen Interactions, Electrophoresis, Polyacrylamide Gel, France, Chromatography, Liquid
Abstract: OmpU porins are increasingly recognized as key determinants of pathogenic host Vibrio interactions. Although mechanisms remain incompletely understood, various species, including the human pathogen Vibrio cholera , require OmpU for host colonization and virulence. We have shown previously that OmpU is essential for virulence in the oyster pathogen Vibrio splendidus LGP32. Here, we showed that V. splendidus LGP32 invades the oyster immune cells, the hemocytes, through subversion of host-cell actin cytoskeleton. In this process, OmpU serves as an adhesin/invasin required for β-integrin recognition and host cell invasion. Furthermore, the major protein of oyster plasma, the extracellular superoxide dismutase Cg -EcSOD, is used as an opsonin mediating the OmpU-promoted phagocytosis through its RGD sequence. Finally, the endocytosed bacteria were found to survive intracellularly, evading the host defense by preventing acidic vacuole formation and limiting reactive oxygen species production. We conclude that ( i ) V. splendidus is a facultative intracellular pathogen that manipulates host defense mechanisms to enter and survive in host immune cells, and ( ii ) that OmpU is a major determinant of host cell invasion in Vibrio species, used by V. splendidus LGP32 to attach and invade oyster hemocytes through opsonisation by the oyster plasma Cg -EcSOD.
Published: 2011

26. Charge density and electrostatic potential analyses in paracetamol

Author: Benoit Guillot, Christian Jelsch, Nour-Eddine Ghermani, François Bonhomme, Nouzha Bouhmaida, Mat Sci Lab, Fac Sci Semlalia, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Cristallographie, Résonance Magnétique et Modélisations (CRM2), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Laboratoire Structures, Propriétés et Modélisation des solides (SPMS), and Institut de Chimie du CNRS (INC)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Electron density, Static Electricity, 02 engineering and technology, 010402 general chemistry, Crystallography, X-Ray, 01 natural sciences, Molecular physics, General Biochemistry, Genetics and Molecular Biology, Computational chemistry, Electric field, Atom, [CHIM.CRIS]Chemical Sciences/Cristallography, [CHIM]Chemical Sciences, Acetaminophen, Ions, Molecular Structure, Chemistry, Hydrogen bond, Electric potential energy, Charge density, Hydrogen Bonding, General Medicine, Maxwell stress tensor, 021001 nanoscience & nanotechnology, 0104 chemical sciences, 0210 nano-technology, Multipole expansion, Dimerization
Abstract: International audience; The electron density of monoclinic paracetamol was derived from high-resolution X-ray diffraction at 100 K. The Hansen– Coppens multipole model was used to refine the experimental electron density. The topologies of the electron density and the electrostatic potential were carefully analyzed. Numerical and analytical procedures were used to derive the charges integrated over the atomic basins. The highest charge magnitude (À1.2 e) was found for the N atom of the paracetamol molecule, which is in agreement with the observed nucleophilic attack occurring in the biological media. The electric field generated by the paracetamol molecule was used to calculate the atomic charges using the divergence theorem. This was simultaneously applied to estimate the total electrostatic force exerted on each atom of the molecule by using the Maxwell stress tensor. The interaction electrostatic energy of dimers of paracetamol in the crystal lattice was also estimated.
Published: 2008

27. Physiological and behavioural responses of Gammarus pulex exposed to acid stress

Author: Fabien Aujoulat, Vincent Felten, Olivier Geffard, Jeanne Garric, Guy Charmantier, Mireille Charmantier-Daures, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Biologie des écosystèmes aquatiques (UR BELY), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), and Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Physiology, Health, Toxicology and Mutagenesis, Longevity, Zoology, 010501 environmental sciences, Biology, Toxicology, 01 natural sciences, Biochemistry, Locomotor activity, Freshwater ecosystem, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Hemolymph, Animals, Amphipoda, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Acid stress, Behavior, Animal, Ecology, 010604 marine biology & hydrobiology, Respiration, Sodium, Cell Biology, General Medicine, Hydrogen-Ion Concentration, biology.organism_classification, Gammarus pulex, Pulex, Breathing, Osmoregulation, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Acids, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Locomotion, Water Pollutants, Chemical, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Physiological and behavioural responses of the acid-sensitive amphipod Gammarus pulex exposed to a wide range of acid conditions (pH 4.1, 5.1, 6.0) under laboratory conditions were investigated. An exposure of 38 h to acid conditions caused significant decreases in survival rate, osmolality, haemolymph Na+ concentration, ventilatory and locomotor activity compared to organisms exposed to a circumneutral medium (pH 7.9). We highlighted the interest of using individual response distribution, since drastic effects can be detected in organisms exposed to pH 6.0, in particular for osmolality: The response can be divided into two groups, unimpacted and impacted organisms. Moreover this representation permitted to evaluate the health level of individual organisms through the determination of threshold values. Significant correlations between mean pH and mean physiological/behavioural responses were observed. The relationships between individual responses permitted not only to compare endpoints, but also to show that affected organisms were impacted by ionoregulation failure, hypoventilation and low locomotor activity. The energetic reallocation in favour of maintenance functions, such as osmoregulation, is discussed. The results of this study indicate that the values of haemolymph Na+ concentration, osmolality and locomotor activity in G. pulex could be effective ecophysiological/behavioural markers to monitor freshwater ecosystems and to assess the health of organisms or populations.
Published: 2008

28. Physiological and behavioural responses of Gammarus pulex (Crustacea: Amphipoda) exposed to cadmium

Author: Guy Charmantier, Alain Geffard, Philippe Rousselle, Jeanne Garric, Olivier Geffard, Marina Coquery, Raphaël Mons, Vincent Felten, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), 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), Laboratoire d'écotoxicologie, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Milieux aquatiques, écologie et pollutions (UR MALY), Biologie des écosystèmes aquatiques (UR BELY), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), and Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Time Factors, Health, Toxicology and Mutagenesis, 010501 environmental sciences, 01 natural sciences, Toxicology, Eating, Hemolymph, MIC, QELY, ComputingMilieux_MISCELLANEOUS, Cadmium, Behavior, Animal, 6. Clean water, Osmoregulation, SURVIVAL, GAMMARUS PULEX, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Sodium-Potassium-Exchanging ATPase, Amphipoda, CEMAGREF, chemistry.chemical_element, Zoology, Aquatic Science, Biology, Motor Activity, Lethal Dose 50, CADMIUM, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Chlorides, Ecotoxicology, Animals, PHYSIOLOGY, 0105 earth and related environmental sciences, 010604 marine biology & hydrobiology, Osmolar Concentration, Sodium, BEHAVIOUR, BELY, biology.organism_classification, ECO, Crustacean, Survival Analysis, Gammarus pulex, Pulex, chemistry, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Water Pollutants, Chemical, CHI, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: The aim of this study was to investigate the effects of cadmium on physiological and behavioural responses in Gammarus pulex. In a first experiment, cadmium LC50s for different times were evaluated in 264 h experiment under continuous mode of exposure (LC50(96 h)=82.1 microgL(-1), LC50(120 h)=37.1 microgL(-1), LC50(168 h)=21.6 microgL(-1), LC50(264 h)=10.5 microgL(-1)). In a second experiment, the physiological and behavioural responses of the amphipod exposed to cadmium (0, 7.5 and 15 microgL(-1)) were investigated under laboratory conditions. The mortality and the whole body cadmium concentration of organisms exposed to cadmium were significantly higher than in controls. Concerning physiological responses, cadmium exposure exerted a significant decrease on osmolality and haemolymph Ca(2+) concentration, but not on haemolymph Na(+) and Cl(-) concentrations, whereas the Na(+)/K(+)-ATPase activity was significantly increased. Behavioural responses, such as feeding rate, locomotor and ventilatory activities, were significantly reduced in Cd exposed organisms. Mechanism of cadmium action and consequent energetic reallocation in favour of maintenance functions (i.e., osmoregulation) are discussed. The results of this study indicate that osmolality and locomotor activity in G. pulex could be effective ecophysiological/behavioural markers to monitor freshwater ecosystem and to assess the health of organisms.
Published: 2008

29. Genetically based resistance to summer mortality in the Pacific oyster (Crassostrea gigas) and its relationship with physiological, immunological characteristics and infection processes

Author: Stephane Pouvreau, Isabelle Boutet, Arnaud Huvet, Thierry Burgeot, F. Geret, Lionel Degremont, A. Van Wormhoudt, Jean-Louis Nicolas, Helene Bacca, Joel Haure, Pierre Boudry, Jeanne Moal, Tristan Renault, Edouard Bedier, Béatrice Gagnaire, F. Le Roux, Jean-Francois Samain, Viviane Boulo, Christophe Lambert, Philippe Soudant, Maryse Delaporte, Katherine Costil, Patrick Soletchnik, Michel Ropert, Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Génétique et Pathologie (LGP), Laboratoire Environnement Ressources des Pertuis Charentais (LER/PC), Laboratoire Laboratoire Environnement Ressources Morbihan Pays de Loire (LER/MPL), Laboratoire Environnement Ressources de Normandie (LERN), 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), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Biologie des organismes marins et écosystèmes (BOME), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), 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 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), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Université européenne de Bretagne - European University of Brittany (UEB), Laboratoire d'Écotoxicologie, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Régions of Basse-Normandie, Bretagne, Pays de la Loire, Poitou-Charentes, Conseil Général du Calvados, National Morest project funded by Ifremer, Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire Environnement Ressources des Pertuis Charentais (LERPC), LITTORAL (LITTORAL), Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-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 Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Écotoxicologie (LEX), Biogéochimie et Ecotoxicologie (BE), Institut Universitaire Européen de la Mer (IUEM), and 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: Oyster, Hemocytes, media_common.quotation_subject, Genetic selection, Aquatic Science, Stress, 03 medical and health sciences, Animal science, biology.animal, 14. Life underwater, Mollusca, Pacific Oyster, 030304 developmental biology, media_common, 0303 health sciences, biology, Ecology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Reproduction, fungi, Resistant oyster, Temperature, food and beverages, ROS, 04 agricultural and veterinary sciences, Pacific oyster, Bivalvia, biology.organism_classification, Ostreidae, Summer mortality, Crassostrea gigas, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Crassostrea, Respiration rate
Abstract: International audience; Summer mortality of Pacific oysters is known in several countries. However no specific pathogen has been systematically associated with this phenomenon. A complex combination of environmental and biological parameters has been suggested as the cause and is now starting to be identified. A high genetic basis was found for survival in oysters when a first generation (G1) was tested in three sites during summer. This paper presents a synthesis on physiological characteristics of two selected groups (‘R' and ‘S', from families selected for resistance and susceptibility to summer mortality respectively), of the second and third generations. R and S showed improvement or reduction of survival compared with the control in both field and laboratory trials confirming the high heritability of survival of juveniles
Published: 2007

30. Mark-recapture cloning: a straightforward and cost-effective cloning method for population genetics of single-copy nuclear DNA sequences in diploids

Author: Bierne, Nicolas, Tanguy, Arnaud, Faure, Matthieu, Faure, Baptiste, David, Elise, Boutet, Isabelle, Boon, E., Quéré, Nolwenn, Plouviez, Sophie, Kemppainen, P., Jollivet, Didier, Moraga, Dario, Boudry, Pierre, David, P., Génome, populations, interactions, adaptation (GPIA), 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), 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), Laboratoire de Génétique et Pathologie (LGP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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), Department of Marine Ecology, Tjarno Marine Biological Laboratory, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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 Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), and 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)
Subjects: Population genetics, DNA polymorphism, [SDE]Environmental Sciences, Sequence, high throughput allele recognition, population genetics, sequence, High throughput allele recognition
Abstract: International audience; We describe a simple protocol to reduce the number of cloning reactions of nuclear DNA sequences in population genetic studies of diploid organisms. Cloning is a necessary step to obtain correct haplotypes in such organisms, and, while traditional methods are efficient at cloning together many genes of a single individual, population geneticists rather need to clone the same locus in many individuals. Our method consists of marking individual sequences during the polymerase chain reaction (PCR) using 5'-tailed primers with small polynucleotide tags. PCR products are mixed together before the cloning reaction and clones are sequenced with universal plasmid primers. The individual from which a sequence comes from is identified by the tag sequences upstream of each initial primer. We called our protocol mark-recapture (MR) cloning. We present results from 57 experiments of MR cloning conducted in four distinct laboratories using nuclear loci of various lengths in different invertebrate species. Rate of capture (proportion of individuals for which one or more sequences were retrieved) and multiple capture (proportion of individuals for which two or more sequences were retrieved) empirically obtained are described. We estimated that MR cloning allowed reducing costs by up to 70% when compared to conventional individual-based cloning. However, we recommend to adjust the mark:recapture ratio in order to obtain multiple sequences from the same individual and circumvent inherent technical artefacts of PCR, cloning and sequencing. We argue that MR cloning is a valid and reliable high-throughput method, providing the number of sequences exceeds the number of individuals initially amplified.
Published: 2007

31. Growth hormone and Prolactin-1 gene transcription in natural populations of the black-chinned tilapia Sarotherodon melanotheron acclimatised to different salinities

Author: M. Tine, Jean-Dominique Durand, Jacques Panfili, François Bonhomme, J. de Lorgeril, Khady Diop, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut de recherche pour le développement (IRD [Sénégal]), Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), and 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)
Subjects: 0106 biological sciences, Transcription, Genetic, Physiology, 030310 physiology, Acclimatization, Fresh Water, adaptation, Growth hormone, 01 natural sciences, Biochemistry, Gene expression, 0303 health sciences, Ecology, Tilapia, Sarotherodon melanotheron, Africa, Western, gambia, Osmoregulation, variation, Fish Proteins, medicine.medical_specialty, food.ingredient, growth, Zoology, Biology, 010603 evolutionary biology, 03 medical and health sciences, food, Internal medicine, medicine, Animals, Seawater, 14. Life underwater, Molecular Biology, Gene, 030304 developmental biology, Brackish water, 010604 marine biology & hydrobiology, mRNA expression, saloum, Prolactin, estuaries, Salinity, Endocrinology, Gene Expression Regulation, Growth Hormone, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, osmoregulation
Abstract: International audience; The effects of salinity on the expression of genes coding for growth hormone (GH) and prolactin-1 (PRL1) were studied in various natural populations of the black-chinned tilapia Sarotherodon melanotheron from West Africa. Individuals were sampled in June 2005 in six locations in Senegal and the Gambia, at various salinities between 0 and 101. The poorest condition factors were recorded in the most saline sampling site and the best growth in the fish from a marine environment. The pituitary GH mRNA levels were significantly higher in fish adapted to seawater, whereas the PRL1 mRNA levels were highest in fish adapted to fresh- and brackish water. These results show that the PRL1 mRNA levels seem to reflect relatively well the differences in environmental salinity, in contrast to those of GH, which would tend instead to reflect the individual growth in each environment. However, no relation could be found between growth in the hypersaline areas and the expression profile of GH. Although the fish analysed were morphologically identical, the expression of genes coding for GH and PRL1 showed large differences between individuals. This inter-individual variation in gene expression remains poorly understood.
Published: 2007

32. Increasing genomic information in bivalves through new EST collections in four species: development of new genetic markers for environmental studies and genome evolution

Author: Sergio Jarque, François Bonhomme, Benjamin Piña, Michael Kube, Sylvie Lapegue, Jean-Francois Samain, Pierre Boudry, Isabelle Boutet, Arnaud Huvet, Dario Moraga, Arnaud Tanguy, Carole Dossat, M. Leonor Cancela, Didier Jollivet, Viviane Boulo, Sven Klages, Eleftherios Zouros, Adelino V.M. Canario, Ricardo B. Leite, Jeanne Moal, Richard Reinhardt, Pascal Favrel, Nicolas Bierne, Evelyne Bachère, Eric Bazin, Carlos Saavedra, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Instituto de Acuicultura de Torre la Sal (IATS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), IBMB-CSIC, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Max Planck Institute for Molecular Genetics (MPIMG), Max-Planck-Gesellschaft, Laboratoire de Génétique et Pathologie (LGP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], 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), Physiologie et Ecophysiologie des Mollusques Marins (PE2M), 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 diversité en milieu marin (AD2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Department of Biology, University of Crete [Heraklion] (UOC), Centro de Ciências do Mar [Faro] (CCMAR), Universidade do Algarve (UAlg), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), 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), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), and 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)
Subjects: 0106 biological sciences, Genetic Markers, Genome evolution, animal structures, Evolution, Context (language use), Genomics, Biology, Environment, 01 natural sciences, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, Genetics, Animals, 14. Life underwater, 030304 developmental biology, Gene Library, Expressed Sequence Tags, 0303 health sciences, Expressed sequence tag, Genome, cDNA library, ESTs, 010604 marine biology & hydrobiology, General Medicine, Molluscs, biology.organism_classification, Mytilus, Bivalvia, [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp, Evolutionary biology, Genetic marker, Tandem Repeat Sequences, Crassostrea, Microsatellite Repeats
Abstract: The generation of EST information is an essential step in the genomic characterisation of species. In the context of the European Network Marine Genomics, a common goal was to significantly increase the amount of ESTs in commercial marine mollusk species and more specifically in the less studied but ecologically and commercially important groups, such as mussel and clam genera. Normalized cDNA libraries were constructed for four different relevant bivalves species (Crassostrea gigas, Mytilus edulis, Ruditapes decussatus and Bathymodiolus azoricus), using numerous tissues and physiological conditions. In this paper, we present the analysis of the 13,013 expressed sequence tags (ESTs) generated. Each EST library was independently assembled and 1300-3000 unique sequences were identified in each species. For the different species, functional categories could be assigned to only about 16 to 27% of ESTs using the GO annotation tool. All sequences have been incorporated into a publicly available database and form the basis for subsequent microarray design, SNP detection and polymorphism analysis, and the placement of novel markers on genetic linkage maps. © 2007 Elsevier B.V. All rights reserved., The research presented in this paper was funded by the European Commission through the Marine Genomics Network of Excellence (GOCE-CT-2004-505403). C.S. wishes to acknowledge additional funding from the “Ramón y Cajal” Program and grants AGL2003–04143 and AGL2006–08944 from the Spanish government.
Published: 2007

33. Geographical and within-population variation in the globeflower-globeflower fly interaction: the costs and benefits of rearing pollinator's larvae

Author: Laurence, Després, Sébastien, Ibanez, Asa M, Hemborg, Bernard, Godelle, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Botany, University of Cape Town, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: 0106 biological sciences, flower size, mutualism, conflict, cooperation, chiastocheta flies, [SDV.BID]Life Sciences [q-bio]/Biodiversity, seed predators, egg aggregation, 010603 evolutionary biology, 01 natural sciences, yucca moths, anthomyiidae, Trollius-europaeus, evolution, Animals, pollination mutualism, Ecosystem, Ecology, Evolution, Behavior and Systematics, density-dependent competition, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Diptera, 010604 marine biology & hydrobiology, Feeding Behavior, Larva, Seeds, Pollen, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, oviposition, Ranunculaceae, competition
Abstract: International audience; Interspecific interactions can vary within and among populations and geographical locations, and this variation can influence the nature of the interaction (e.g. mutualistic versus antagonistic) and its evolutionary stability. Globeflowers are exclusively pollinated by flies whose larvae feed only on their seeds. Here we document geographical variability in costs and benefits in globeflowers in sustaining their pollinating flies throughout the range of this arctic-alpine European plant over several years. A total of 1,710 flower heads from 38 populations were analysed for their carpel, egg and seed contents. Individual and population analyses control for the confounding influences of variation in both: (1) population traits, such as fly density and egg distribution among flower heads; and (2) individuals traits, such as carpel and egg numbers per flower head. Despite considerable variation in ecological conditions and pollinator densities across populations, large proportions (range 33-58%) of seeds are released after predation, with a benefit-to-cost ratio of 3, indicating that the mutualism is stable over the whole globeflower geographical range. The stability of the mutualistic interaction relies on density-dependent competition among larvae co-developing in a flower head. This competition is revealed by a sharp decrease in the number of seeds eaten per larva with increasing larval number, and is intensified by non-uniform egg distribution among globeflowers within a population. Carpel number is highly variable across globeflowers (range 10-69), and flies lay more eggs in large flowers. Most plants within a population contribute to the rearing of pollinators, but some pay more than others. Large globeflowers lose more seed to pollinator larvae, but also release more seed than smaller plants. The apparent alignment of interests between fly and plant (positive relationship between numbers of seeds released and destroyed) is shown to hide a conflict of interest found when flower size is controlled for.
Published: 2007

34. Genomic reticulation indicates mixed ancestry in Southern-Hemisphere #Mytilus$ spp. mussels

Author: Borsa, Philippe, Daguin, Claire, Bierne, Nicolas, Écosystémique des communautés récifales et de leurs usages dans le Pacifique insulaire (CoReUS), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Génome, populations, interactions, adaptation (GPIA), 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), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: antitropical distribution, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, introgression, nuclear DNA, geographical structure, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, hybridization, intron length polymorphism
Abstract: International audience; Previous surveys of allozyme variation in smooth-shell Mytilus spp. mussels have reported the presence in the Southern Hemisphere of both Mytilus edulis and Mytilus galloprovincialis mussels. In the present study, nuclear DNA markers mac-1 and Glu-5'/Glu-3', both diagnostic for Northern-Hemisphere M. edulis and M. galloprovincialis, were used to further characterize the nuclear genomes of M. edulis from Kerguelen and M. galloprovincialis from Tasmania. Genomic reticulation was observed, with typical M. edulis allelomorphs fixed in both populations at locus mac-1 whereas, at locus Glu-5'/Glu-3', allelomorphs characteristic of M. galloprovincialis were present in Kerguelen and nearly fixed in Tasmania. Kerguelen mussels had a genome of mixed M. edulis and M. galloprovincialis ancestry without evidence of barriers to merging as shown by Hardy-Weinberg and linkage equilibrium. Tasmanian mussels possessed a predominantly M. galloprovincialis genomic background introgressed by M. edulis allelomorphs at locus mac-1. Genetic drift superimposed on ancient hybridization and introgression may explain the genomic reticulation observed in both Kerguelen and Tasmanian mussels. There was no evidence of a recent introduction of Northern-Hemisphere M. galloprovincialis or M. edulis to Kerguelen or Tasmania.
Published: 2007

35. The effect of environmental salinity on the proteome of the sea bass (Dicentrarchus labrax L.)

Author: Ky, C.L., De Lorgeril, Julien, Hirtz, Christophe, Sommerer, Nicolas, Rossignol, Michel, Bonhomme, François, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université Montpellier 1 (UM1), Unité de Recherche Protéomique (PROTEOMIQUE), Institut National de la Recherche Agronomique (INRA), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Laboratoire de Physiologie et Endocrinologie Oro-Faciale, and Université de Montpellier (UM)
Subjects: Fish Proteins, Gills, Male, Salinity, Proteome, Receptors, Prolactin, Acclimatization, Sea bass, Fresh Water, REAL TIME PCR, Sodium Chloride, Mass Spectrometry, Two dimensional gel electrophoresis, Aromatase, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], SALINITY, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, Electrophoresis, Gel, Two-Dimensional, Seawater, RNA, Messenger, MALDI TOF mass spectrometry, Intestinal Mucosa, [SDV.GEN]Life Sciences [q-bio]/Genetics, MALDI-TOF MASS SPECTROMETRY, BIOLOGIE MOLECULAIRE, Real time PCR, SEA BASS, Bass, Female, TWO-DIMENSIONAL GEL ELECTROPHORESIS
Abstract: International audience; The European sea bass, Dicentrarchus labrax L., tolerates a range of salinities from freshwater to hyper-saline. To study differences in protein expression, fish were reared in both freshwater and seawater. After 3-month acclimation, gill and intestine epithelia were collected and the soluble protein extracted. In all, 362 spots were differentially expressed in the gills and intestines of fishes reared in seawater compared to those from freshwater. Fifty differential protein spots were excised from a colloidal Coomassie-stained gel. Nine separate protein spots were identified unambiguously by mass spectrometry and database searching. Among the six proteins over-expressed in gill cells in seawater, five were cytoskeleton proteins and one was the aromatase cytochrome P450. In gill cells under freshwater conditions, the two over-expressed proteins identified were the prolactin receptor and the major histocompatibility complex class II β-antigen. In intestinal cells under freshwater conditions, the Iroquois homeobox protein Ziro5 was upregulated over ninefold. The expression of these proteins, their possible direct or indirect roles in the adaptation of D. labrax to salinity, and their correspondences with a previous study are discussed.
Published: 2007

36. A cDNA microarray for Crassostrea virginica and C. gigas

Author: Paul S. Gross, Jonas S. Almeida, Jean Michel Escoubas, David J. McKillen, Yian A. Chen, Isabelle Boutet, Robert W. Chapman, Arnaud Tanguy, Arnaud Huvet, Viviane Boulo, Gregory W. Warr, Z. John Liu, Hal Trent, Evelyne Bachère, Paul Lang, Charles E. Cunningham, Ximing Guo, Matthew J. Jenny, Sylvain De Guise, Dario Moraga, Pauline M. Cupit, Annalaura Mancia, Hollings Marine Laboratory, National Institute of Standards and Technology [Gaithersburg] (NIST), Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), South Carolina Department of Natural Resources, Marine Resources Research Institute, Biochemistry and Molecular Biology, Medical University of South Carolina [Charleston] (MUSC), Department of Statistics, Texas AM University, Department of Fisheries and Wildlife, Oregon State University (OSU), Ecologie microbienne des insectes et interactions hôte-pathogène (EMIP), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University (AU), Department of Biology [New Mexico], The University of New Mexico [Albuquerque], Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Haskin Shellfish Research Laboratory (HSRL), Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of Pathobiology, University of Connecticut (UCONN), Program in Biomathematics and Biostatistics, The University of Texas Health Science Center at Houston (UTHealth), Department of Biochemistry and Molecular Biology, 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), 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), 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 Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), 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 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), and 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)
Subjects: 0106 biological sciences, Oyster, animal structures, Microarray, Crassostrea virginica, Gene Expression, 01 natural sciences, Applied Microbiology and Biotechnology, bivalve, 03 medical and health sciences, Species Specificity, biology.animal, Complementary DNA, Animals, 14. Life underwater, Crassostrea, heterologous hybridization, Crassostrea gigas, microarray, oyster, Gene, Gene Library, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, Genetics, 0303 health sciences, biology, Gene Expression Profiling, 010604 marine biology & hydrobiology, fungi, Reproducibility of Results, food and beverages, Pacific oyster, biology.organism_classification, Fishery, Gene expression profiling, [SDE]Environmental Sciences, Eastern oyster
Abstract: International audience; The eastern oyster, Crassostrea virginica, and the Pacific oyster, C. gigas, are species of global economic significance as well as important components of estuarine ecosystems and models for genetic and environmental studies. To enhance the molecular tools available for oyster research, an international group of collaborators has constructed a 27,496-feature cDNA microarray containing 4460 sequences derived from C. virginica, 2320 from C. gigas, and 16 non-oyster DNAs serving as positive and negative controls. The performance of the array was assessed by gene expression profiling using gill and digestive gland RNA derived from both C. gigas and C. virginica, and digestive gland RNA from C. ariakensis. The utility of the microarray for detection of homologous genes by cross-hybridization between species was also assessed and the correlation between hybridization intensity and sequence homology for selected genes determined. The oyster cDNA microarray is publicly available to the research community on a cost-recovery basis.
Published: 2007

37. Molecular and morphological relationships between two closely related species, Turbinaria ornata and T. conoides (Sargassaceae, Phaeophyceae)

Author: François Bonhomme, Valérie Stiger, Audrey Rohfritsch, Claude Payri, Génome, populations, interactions, adaptation (GPIA), 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), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Écophysiologie et de Biotechnologie des Halophytes et des Algues Marines (LEBHAM), Université de Brest (UBO), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: 0106 biological sciences, Rubisco, sister species, Turbinaria conoides, 01 natural sciences, Biochemistry, Turbinaria, 03 medical and health sciences, Monophyly, Algae, Botany, Turbinaria ornata, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Sister species, biology, 010604 marine biology & hydrobiology, Conoides, biology.organism_classification, elongation factor, Brown algae, intergenic mitochondrial region, Elongation factor, [SDE]Environmental Sciences, Sargassaceae, Intergenic mitochondrial region, ITS
Abstract: International audience; We employed four markers (two chloroplastic, one mitochondrial and one nuclear) to investigate whether Turbinaria ornata and Turbinaria conoides, two morphologically similar brown algae, are distinct species. The molecular data revealed reciprocal monophyly, thus confirming the two algae as discrete species. Nevertheless, taxonomical ambiguities remain. T. conoides is more morphologically variable than T. ornata. We identified an atypical T. conoides morphotype whose blade possesses intramarginal teeth, a morphological characteristic of the T. ornata group that is normally absent within T. conoides. The molecular data indicate, nonetheless, that this morphotype belongs genetically to the T. conoides group. Thus, the results cast doubt upon the validity of using intramarginal teeth for species diagnosis.
Published: 2007

38. Mitochondrial DNA and population size - Response

Author: Bazin, E., Glémin, Sylvain, Galtier, Nicolas, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp
Abstract: Letter; International audience
Published: 2006

39. Impact of mating systems on patterns of sequence polymorphism in flowering plants

Author: Sylvain Glémin, Eric Bazin, Deborah Charlesworth, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institute of Evolutionary Biology, and University of Edinburgh
Subjects: 0106 biological sciences, Genome evolution, Population genetics, selection, Outcrossing, Flowers, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, sequence polymorphism, Evolution, Molecular, 03 medical and health sciences, Effective population size, Species Specificity, Molecular evolution, selfing, mating system, Selection, Genetic, 030304 developmental biology, General Environmental Science, Genetics, 0303 health sciences, Genetic diversity, Polymorphism, Genetic, General Immunology and Microbiology, Reproduction, Selfing, Genetic Variation, General Medicine, selﬁng, 15. Life on land, Plants, Mating system, recombination, Genetics, Population, [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp, Pollen, General Agricultural and Biological Sciences, effective population size, Research Article
Abstract: A fundamental challenge in population genetics and molecular evolution is to understand the forces shaping the patterns of genetic diversity within and among species. Among them, mating systems are thought to have important influences on molecular diversity and genome evolution. Selfing is expected to reduce effective population size,Ne, and effective recombination rates, directly leading to reduced polymorphism and increased linkage disequilibrium compared with outcrossing. Increased isolation between populations also results directly from selfing or indirectly from evolutionary changes, such as small flowers and low pollen output, leading to greater differentiation of molecular markers than under outcrossing. The lower effective recombination rate increases the likelihood of hitch-hiking, further reducing within-deme diversity of selfers and thus increasing their genetic differentiation. There are also indirect effects on molecular evolutionary processes. LowNereduces the efficacy of selection; in selfers, selection should thus be less efficient in removing deleterious mutations. The rarity of heterozygous sites in selfers leads to infrequent action of biased conversion towards GC, which tends to increase sequences' GC content in the most highly recombining genome regions of outcrossers. To test these predictions in plants, we used a newly developed sequence polymorphism database to investigate the effects of mating system differences on sequence polymorphism and genome evolution in a wide set of plant species. We also took into account other life-history traits, including life form (whether annual or perennial herbs, and woody perennial) and the modes of pollination and seed dispersal, which are known to affect enzyme and DNA marker polymorphism. We show that among various life-history traits, mating systems have the greatest influence on patterns of polymorphism.
Published: 2006

40. Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome

Author: François Bonhomme, Erick Desmarais, Khalid Belkhir, John Carlos Garza, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), and National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)
Subjects: Retroelements, LTR retrotransposons, Molecular Sequence Data, Retrotransposon, mouse genome, Genome, Transposition (music), Mice, 03 medical and health sciences, chemistry.chemical_compound, Retrovirus, Tandem repeat, Genetics, Animals, Indel, Molecular Biology, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, simple tandem repeats, Base Sequence, biology, Phylogenetic tree, Simple tandem repeats, Mouse genome, 030302 biochemistry & molecular biology, Terminal Repeat Sequences, food and beverages, DNA, biology.organism_classification, Rats, Mutagenesis, Insertional, RMER10, [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp, chemistry, Nucleic Acid Conformation, Sequence Alignment
Abstract: International audience; Solitary LTR loci are the predominant form of LTR retrotransposons in most eukaryotic genomes. They originate from recombination between the two LTRs of an ancestral retrovirus and are therefore incapable of transposition. Despite this inactivity, they appear to have a substantial impact on the host genome. Here we use the murine RMER10 LTR family as an example to describe how such elements can reshape regions of the genome through multiple mutations on an evolutionary time scale. Specifically, we use phylogenetic analysis of multiple copies of RMER10 in rodent species, as well as comparisons of orthologous pairs in mouse and rat, to argue that insertions of members of this family have locally induced the emergence of tandem repeat loci as well as many indels. Analysis of structural aspects of these sequences (secondary structures and transcription factors signals) may explain why RMER10 can become endogenous "mutagenic" factors through induction of replication fork blockages and/or error-prone repair of aberrant DNA structures. This hypothesis is also consistent with features of other interspersed repeated elements.
Published: 2006

41. Mouse SNPs for evolutionary biology: Beware of ascertainment biases

Author: Boursot, Pierre, Belkhir, Khalid, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: GENOME, InformationSystems_GENERAL, HOUSE MOUSE, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MathematicsofComputing_GENERAL, PATTERNS, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, GeneralLiterature_MISCELLANEOUS
Abstract: Editorial Material; International audience
Published: 2006

42. A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus musculus domesticus

Author: Ruth Rottscheidt, Christian R. Voolstra, Tobias Heinen, François Bonhomme, Diethard Tautz, Sonja Ihle, John F. Baines, Bettina Harr, Werner Müller, Institute for Genetics, Department of Evolutionary Genetics, German Research Centre for Biotechnology, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: 0106 biological sciences, Locus (genetics), MAP Kinase Kinase 7, adaptation, Biology, 010603 evolutionary biology, 01 natural sciences, Polymerase Chain Reaction, House mouse, selective sweep, 03 medical and health sciences, Mice, Gene expression, Animals, Northern blot, RNA, Messenger, Allele, Selection, Genetic, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, Genetics, 0303 health sciences, Polymorphism, Genetic, Sequence Analysis, DNA, biology.organism_classification, mus musculus, Blotting, Northern, Up-Regulation, Fixation (population genetics), [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp, Mutation, gene expression, Hybridization, Genetic, Selective sweep, microarray, Signal Transduction
Abstract: International audience; Changes in gene expression are known to occur between closely related species, but it is not yet clear how many of these are due to random fixation of allelic variants or due to adaptive events. In a microarray survey between subspecies of the Mus musculus complex, we identified the mitogen-activated protein-kinase-kinase MKK7 as a candidate for change in gene expression. Quantitative PCR experiments with multiple individuals from each subspecies confirmed a specific and significant up-regulation in the testis of M. m. domesticus. Northern blot analysis shows that this is due to a new transcript that is not found in other tissues, nor in M. m. musculus. A cis-trans test via allele specific expression analysis of the MKK7 gene in F1 hybrids between domesticus and musculus shows that the expression change is mainly caused by a mutation located in cis. Nucleotide diversity was found to be significantly reduced in a window of at least 20 kb around the MKK7 locus in domesticus, indicative of a selective sweep. Because the MKK7 gene is involved in modulating a kinase signalling cascade in a stress response pathway, it seems a plausible target for adaptive differences between subspecies, although the functional role of the new testis-specific transcripts will need to be further studied.
Published: 2006

43. Phylogeographic support for horizontal gene transfer involving sympatric bruchid species

Author: Alvarez, Nadir, Benrey, Betty, Hossaert-McKey, Martine, Grill, Andrea, McKey, Doyle, Galtier, Nicolas, Laboratoire d'Entomologie Evolutive, Université de Neuchâtel (UNINE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), 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), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: BOMBYX-MORI, [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp, lcsh:Biology (General), SEQUENCES, ORIGIN, Research, [SDV]Life Sciences [q-bio], COLEOPTERA, MITOCHONDRIAL GENES, EUKARYOTES, lcsh:QH301-705.5, EVOLUTION
Abstract: Background We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric. The bruchid beetles Acanthoscelides obtectus, A. obvelatus, A. argillaceus and Zabrotes subfasciatus develop on various bean species in Mexico. Whereas A. obtectus and A. obvelatus develop on Phaseolus vulgaris in the Mexican Altiplano, A. argillaceus feeds on P. lunatus in the Pacific coast. The generalist Z. subfasciatus feeds on both bean species, and is sympatric with A. obtectus and A. obvelatus in the Mexican Altiplano, and with A. argillaceus in the Pacific coast. In order to assess the phylogenetic position of these four species, we amplified and sequenced one nuclear (28S rRNA) and two mitochondrial (cytb, COI) genes. Results Whereas species were well segregated in topologies obtained for COI and 28S rRNA, an unexpected pattern was obtained in the cytb phylogenetic tree. In this tree, individuals from A. obtectus and A. obvelatus, as well as Z. subfasciatus individuals from the Mexican Altiplano, clustered together in a unique little variable monophyletic unit. In contrast, A. argillaceus and Z. subfasciatus individuals from the Pacific coast clustered in two separated clades, identically to the pattern obtained for COI and 28S rRNA. An additional analysis showed that Z. subfasciatus individuals from the Mexican Altiplano also possessed the cytb gene present in individuals of this species from the Pacific coast. Zabrotes subfasciatus individuals from the Mexican Altiplano thus demonstrated two cytb genes, an "original" one and an "infectious" one, showing 25% of nucleotide divergence. The "infectious" cytb gene seems to be under purifying selection and to be expressed in mitochondria. Conclusion The high degree of incongruence of the cytb tree with patterns for other genes is discussed in the light of three hypotheses: experimental contamination, hybridization, and pseudogenisation. However, none of these seem able to explain the patterns observed. A fourth hypothesis, involving recent horizontal gene transfer (HGT) between A. obtectus and A. obvelatus, and from one of these species to Z. subfasciatus in the Mexican Altiplano, seems the only plausible explanation. The HGT between our study species seems to have occurred recently, and only in a zone where the three beetles are sympatric and share common host plants. This suggests that transfer could have been effected by some external vector such as a eukaryotic or viral parasite, which might still host the transferred fragment. Reviewers This article was reviewed by Eric Bapteste, Adam Eyre-Walker and Alexey Kondrashov.
Published: 2006

44. History of the Crested Lark in the Mediterranean region as revealed by mtDNA sequences and morphology

Author: Jean-Marie Pons, Bernard Godelle, Alban Guillaumet, Pierre-André Crochet, Génome, populations, interactions, adaptation (GPIA), 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), Origine, structure et évolution de la biodiversité, Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, Mediterranean climate, Morphology, Galerida cristata, Maghreb, Cytochrome b, Allopatric speciation, Crested Lark, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, Birds, 03 medical and health sciences, Mediterranean sea, Genetics, Animals, 14. Life underwater, Clade, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Sahara, 030304 developmental biology, 0303 health sciences, Ecology, Nucleic Acid Hybridization, Cytochromes b, biology.organism_classification, Gibraltar Strait, Phylogeography, Biological dispersal, Taxonomy (biology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The Crested Lark has a very complex taxonomy, partly as a result of a strong variation in plumage ground color seemingly linked with environmental factors. However, large variations in body size and bill shape further complicate the situation in the Maghreb. In this paper, we first present a set of hypotheses to explain patterns of morphological variation around the Mediterranean Sea. A phylogeographical analysis covering all major biogeographical areas in the species' range is then performed to test these scenarios. Three mtDNA groups with distinct geographical distribution were identified. The randonii clade (= G. (c.) randonii) is endemic from central Maghreb and is phylogenetically basal relative to cristata and senegallensis. These two latter groups are much more widespread. The cristata clade is found in NW Morocco, throughout Europe and W Asia and in NE Africa, while senegallensis regroups the populations sampled in the Western Sub-Saharan Africa and in NE Maghreb (E Algeria, Tunisia). A combination of genetic and paleoenvironmental evidences supports a scenario of allopatric differentiation of these two lineages outside the Maghreb, with subsequent range expansion leading to their secondary presence in the Maghreb. However, the alternative hypothesis of differentiation in two, or even three separate Maghreb refuges cannot be completely dismissed with the present data. Interestingly, the Sahara desert and the Gibraltar Strait did not act as permanent barriers to dispersal in this species. In addition, the populations in the Maghreb are consistently longer-billed than their closest relatives, suggesting a role for natural selection or phenotypic plasticity.
Published: 2006

45. Effects of coancestry on accuracy of individual assignments to population of origin: examples using Great Lakes lake trout (Salvelinus namaycush)

Author: Laura Main, Mary K. Burnham-Curtis, Kristi B. Filcek, Kevin S. Page, Kim T. Scribner, Bruno Guinand, Department of Fisheries and Wildlife, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Minnesota Department of Natural Resources, National Forensics Laboratory, and U.S. Fish and Wildlife Service
Subjects: 0106 biological sciences, lake trout, Trout, Population, inbreeding, Locus (genetics), Plant Science, Biology, 010603 evolutionary biology, 01 natural sciences, Animal Population Groups, Linkage Disequilibrium, Statistics, Nonparametric, assignment test, 03 medical and health sciences, Genetics, Animals, Computer Simulation, Allele, education, Allele frequency, Phylogeny, 030304 developmental biology, Salvelinus, 0303 health sciences, education.field_of_study, Models, Genetic, General Medicine, gene correlations, Ecological genetics, biology.organism_classification, coancestry, Evolutionary biology, Insect Science, Microsatellite, Animal Science and Zoology, Great Lakes Region, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Inbreeding
Abstract: International audience; Methods for assigning individuals to population of origin are widely used in ecological genetics, resources management, and forensics. Characteristics of genetic data obtained from putative source populations that enhance accuracy of assignment are well established. How non-independence within and among unknown individuals to be classified [i.e., gene correlations within individual (inbreeding) and gene correlations among individuals within group (coancestry)] affect assignment accuracy is poorly understood. We used empirical data for six microsatellite loci and offspring from full-sib crosses of hatchery strains of lake trout (Salvelinus namaycush; Salmonidae) representing known levels of coancestry (mean θ = 0.006 and 0.06) within families to investigate how gene correlations can affect assignment. Additional simulations were conducted to further investigating the influence of allelic diversity (2, 6 or 10 alleles per locus) and inbreeding (F = 0.00, 0.05, and 0.15) on assignment accuracy for cases of low and high inter-population variance in allele frequency (mean F st = 0.01 and 0.1, respectively). Inbreeding had no effect on accuracy of assignments. In contrast, variance in assignment accuracy across replicated simulations, and for each empirical case study increased with increasing coancestry, reflecting non-independence of probabilities of correct assignment among members of kin groups. Empirical estimates of assignment error rates should be interpreted with caution if appreciable levels of coancestry are suspected. Additional emphasis should be placed on sampling designs (spatially and temporally) that define or minimize the potential for sampling related individuals.
Published: 2006

46. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics

Author: Julien Y. Dutheil, Eric Bazin, Sylvain Gaillard, Vincent Ranwez, Khalid Belkhir, Sylvain Glémin, Nicolas Galtier, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Source code, Theoretical computer science, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Concatenation, Computational biology, Biology, lcsh:Computer applications to medicine. Medical informatics, 010603 evolutionary biology, 01 natural sciences, Biochemistry, Evolution, Molecular, Set (abstract data type), 03 medical and health sciences, Structural Biology, Animals, Humans, Amino Acid Sequence, MAXIMUM-LIKELIHOOD, Molecular Biology, lcsh:QH301-705.5, Phylogeny, 030304 developmental biology, media_common, 0303 health sciences, Object-oriented programming, Sequence, Models, Statistical, Sequence Homology, Amino Acid, Hierarchy (mathematics), Applied Mathematics, Computational Biology, Computer Science Applications, Maximum parsimony, Genetics, Population, lcsh:Biology (General), lcsh:R858-859.7, Programming Languages, Algorithms, Software, Distance matrices in phylogeny
Abstract: Background A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/ouput methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications. Results We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus. Conclusion Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website http://kimura.univ-montp2.fr/BioPP.
Published: 2006

47. Population size does not influence mitochondrial genetic diversity in animals

Author: Nicolas Galtier, Sylvain Glémin, Eric Bazin, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: 0106 biological sciences, Conservation genetics, Genetic Markers, Mitochondrial DNA, Ecology (disciplines), CONSERVATION, Biodiversity, Adaptation, Biological, Biology, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, Evolution, Molecular, 03 medical and health sciences, Molecular evolution, SELECTION MODEL, Animals, Body Size, 14. Life underwater, Selection, Genetic, Ecosystem, 030304 developmental biology, Population Density, Recombination, Genetic, 0303 health sciences, Genetic diversity, Multidisciplinary, Polymorphism, Genetic, Population size, Genetic Variation, NEUTRAL MOLECULAR VARIATION, DNA, Biological Evolution, Invertebrates, EVOLUTION, POLYMORPHISM, Isoenzymes, Genes, Mitochondrial, Genetics, Population, DRIFT, Evolutionary biology, Mutation, Vertebrates, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Neutral theory of molecular evolution, human activities
Abstract: International audience; Within-species genetic diversity is thought to reflect population size, history, ecology, and ability to adapt. Using a comprehensive collection of polymorphism data sets covering 3000 animal species, we show that the widely used mitochondria) DNA (mtDNA) marker does not reflect species abundance or ecology: mtDNA diversity is not higher in invertebrates than in vertebrates, in marine than in terrestrial species, or in small than in large organisms. Nuclear loci, in contrast, fit these intuitive expectations. The unexpected mitochondria( diversity distribution is explained by recurrent adaptive evolution, challenging the neutral theory of molecular evolution and questioning the relevance of mtDNA in biodiversity and conservation studies.
Published: 2006

48. Mutation hot spots in mammalian mitochondrial DNA

Author: Khalid Belkhir, Yoan Radondy, Eric Bazin, David Enard, Nicolas Galtier, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: 0106 biological sciences, MTDNA SEQUENCES, Mutation rate, Mitochondrial DNA, RECOMBINATION, Hot spot (veterinary medicine), Biology, AFRICAN, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, 03 medical and health sciences, chemistry.chemical_compound, Open Reading Frames, Species Specificity, Genetics, DIVERGENCE, Coding region, Animals, Humans, CONTROL REGION, PHYLOGENETIC ANALYSIS, Letters, MAXIMUM-LIKELIHOOD, Gene, Genetics (clinical), 030304 developmental biology, Mammals, 0303 health sciences, Polymorphism, Genetic, Phylogenetic tree, Models, Genetic, GENE, EVOLUTION, [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp, chemistry, GENOME VARIATION, Mutation, DNA, Recombination
Abstract: International audience; Animal mitochondrial DNA is characterized by a remarkably high level of within-species homoplasy, that is, phylogenetic incongruence between sites of the molecule. Several investigators have invoked recombination to explain it, challenging the dogma of maternal, clonal mitochondrial inheritance in animals. Alternatively, a high level of homoplasy Could be explained by the existence of mutation hot spots. By using an exhaustive mammalian data set, we test the hot spot hypothesis by comparing patterns of site-specific polymorphism and divergence in several groups of closely related species, including hominids. We detect significant co-occurrence of synonymous polymorphisms among closely related species in various mammalian groups, and a correlation between the site-specific levels of variability within humans (on one hand) and between Hominoidea species (on the other hand), indicating that mutation hot spots actually exist in mammalian mitochondrial coding regions. The whole data, however, cannot be explained by a simple mutation hot spots model. Rather, we show that the site-specific Mutation rate quickly varies in time, so that the same sites are not hypermutable in distinct lineages. This Study provides a plausible mutation model that potentially accounts for the peculiar distribution of mitochondrial sequence variation in mammals without the need for invoking recombination. It also gives hints about the proximal causes of mitochondrial site-specific hypermutability in humans.
Published: 2006

49. A new perspective on isochore evolution

Author: Adam Eyre-Walker, Nicolas Galtier, Laurent Duret, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), 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)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), 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), Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, National Evolutionary Synthesis Center, Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), and 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)
Subjects: 0106 biological sciences, MAMMALIAN GENOMES, [SDV]Life Sciences [q-bio], Recombination rate, Gene Conversion, VERTEBRATES, RECOMBINATION, GC-CONTENT EVOLUTION, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Birds, Evolution, Molecular, 03 medical and health sciences, Genetics, HUMAN GENOME, Animals, Gene conversion, 030304 developmental biology, Mammals, 0303 health sciences, Models, Genetic, Mechanism (biology), Perspective (graphical), SUBSTITUTION, General Medicine, BIASED GENE CONVERSION, COMPOSITIONAL EVOLUTION, GC Rich Sequence, EQUILIBRIUM, Evolutionary biology, DRIVES, Human genome, Isochores
Abstract: International audience; The genomes of mammals and birds show dramatic variation in base composition over large scales, the so called isochore structure of the genome. The origin of isochores is still controversial: various neutral and selectionist models have been proposed – and criticized – since the discovery of isochores in the 1970s. The availability of complete mammalian genomes has yielded new opportunities for addressing this question. In particular, it was recently proposed that (i) the isochore structure is declining in many mammalian groups, and that (ii) GC-content is influenced by local recombination rate, possibly via the mechanism of GC-biased gene conversion. In this article we review the existing support for these two hypotheses, and discuss how they can be combined to provide a new perspective on isochore evolution.
Published: 2006

50. Characterization of a defensin from the oyster Crassostrea gigas. Recombinant production, folding, solution structure, antimicrobial activities, and gene expression

Author: Gueguen, Yannick, Herpin, Amaury, Aumelas, André, Garnier, Julien, Fievet, Julie, Escoubas, Jean-michel, Bulet, Philippe, Gonzalez, Marcelo, Lelong, Christophe, Favrel, Pascal, Bachere, Evelyne, Génome, populations, interactions, adaptation (GPIA), 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), Atheris Laboratories, Departamento de Tecnología Electrónica, Universidade de Vigo, Centre hépato-biliaire (CHB), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Departamento de Literatura Española e Hispanoamericana, Universidad de Salamanca, Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Département d'Astrophysique, de physique des Particules, de physique Nucléaire et de l'Instrumentation Associée (DAPNIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paul-Valéry - Montpellier 3 (UPVM), Departamento de Optica y Fisica Aplicada, Universidad de Valladolid [Valladolid] (UVa)-Facultad de Ciencias, Laboratorio de Bioinformática y Expresión Génica, Laboratoire de psychologie cognitive (LPC), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Biochimie et biophysique des systèmes intégrés (BBSI), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Universidate de Vigo, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Université Paul-Valéry - Montpellier 3 (UM3), Universidad de Santiago de Chile [Santiago] (USACH), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), and Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)
Subjects: MESH: Gene Expression, gene Expression, MESH: Protein Folding, MESH: Protein Structure, Secondary, molecular sequence data, MESH: Amino Acid Sequence, Microbiology, recombinant proteins, Protein Structure, Secondary, MESH: Defensins, MESH: Gram-Positive Bacteria, MESH: Recombinant Proteins, MESH: Protein Structure, Tertiary, biomolecular, protein folding, MESH: Gram-Negative Bacteria, MESH: Nuclear Magnetic Resonance, Biomolecular, Escherichia coli, MESH: Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Crassostrea, protein structure, Nuclear Magnetic Resonance, Biomolecular, MESH: Molecular Sequence Data, Oyster, MESH: Escherichia coli, fungi, gram-negative bacteria, Protein Structure, Tertiary, amino acid sequence, animals, nuclear magnetic resonance, MESH: Crassostrea, Defensin, gram-positive bacteria, Crassostrea gigas, Genomic library, defensins
Abstract: International audience; In invertebrates, defensins were found in arthropods and in the mussels. Here, we report for the first time the identification and characterization of a defensin (Cg-Def) from an oyster. Cg-def mRNA was isolated from Crassostrea gigas mantle using an expressed sequence tag approach. To gain insight into potential roles of Cg-Def in oyster immunity, we produced the recombinant peptide in Escherichia coli, characterized its antimicrobial activities, determined its solution structure by NMR spectroscopy, and quantified its gene expression in vivo following bacterial challenge of oysters. Recombinant Cg-Def was active in vitro against Gram-positive bacteria but showed no or limited activities against Gram-negative bacteria and fungi. The activity of Cg-Def was retained in vitro at a salt concentration similar to that of seawater. The Cg-Def structure shares the so-called cystine-stabilized alpha-beta motif (CS-alphabeta) with arthropod defensins but is characterized by the presence of an additional disulfide bond, as previously observed in the mussel defensin (MGD-1). Nevertheless, despite a similar global fold, the Cg-Def and MGD-1 structures mainly differ by the size of their loops and by the presence of two aspartic residues in Cg-Def. Distribution of Cg-def mRNA in various oyster tissues revealed that Cg-def is mainly expressed in mantle edge where it was detected by mass spectrometry analyses. Furthermore, we observed that the Cg-def messenger concentration was unchanged after bacterial challenge. Our results suggest that Cg-def gene is continuously expressed in the mantle and would play a key role in oyster by providing a first line of defense against pathogen colonization.
Published: 2006

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