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1. Flightless scaly-tailed squirrels never learned how to fly: A reappraisal of Anomaluridae phylogeny

Author: Philippe Gaubert, Christiane Denys, Violaine Nicolas, Laurent Marivaux, Pierre-Henri Fabre, Marie-Ka Tilak, Emmanuel J. P. Douzery, Institut des Sciences de l'Evolution de Montpellier ( ISEM ), Université de Montpellier ( UM ) -Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique ( CNRS ), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Biologie des Organismes et Ecosystèmes Aquatiques ( BOREA ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Muséum National d'Histoire Naturelle ( MNHN ) -Institut de Recherche pour le Développement ( IRD ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université des Antilles ( UA ), Mammifères et Oiseaux - MNHN ( UMR5202 ), Muséum National d'Histoire Naturelle ( MNHN ), 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, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0301 basic medicine, Arboreal locomotion, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Zenkerellinae, Flying mouse, Zenkerella, biology.organism_classification, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 03 medical and health sciences, 030104 developmental biology, [ SDV.BID.EVO ] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Sister group, Anomalurus, Phylogenetics, Evolutionary biology, Genetics, Animal Science and Zoology, Anomalurus beecrofti, Molecular Biology, Ecology, Evolution, Behavior and Systematics, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: International audience; Anomaluroidea, commonly known as the “scaly-tailed squirrels,” are an emblematic group of tropical African mammals that includes gliding forms. The family Anomaluridae was until recently represented by three genera: the flying scaly-tailed squirrels (Anomalurus), the flying mouse (Idiurus) and the flightless scaly-tailed squirrels (Zenkerella). Idiurus and Zenkerella have long been grouped into the Zenkerellinae subfamily, and Zenkerella was interpreted as a rare case of evolutionary reversal to non-gliding lifestyle. Recent studies have demonstrated that Zenkerella is sister to all other modern anomalurids, and represents in fact the monogeneric family Zenkerellidae. The Anomalurus genus was split into Anomalurus and Anomalurops, but no study has ever considered all Anomalurus species together in a phylogeny to test the status of Anomalurops. Here, we used mitogenomic next-generation sequencing to infer the phylogenetic relationships among all extant anomalurids and to estimate their divergence ages. We found that the arboreal Zenkerella is the sister group of all extant gliding anomalurids (Idiurus and Anomalurus). We confirmed that Anomaluroidea only evolved the gliding adaptation once. A comparison based on morphological traits indicates that Zenkerella harbours several unique morphological features. We propose new morphological characters for the novel classification of modern Anomaluroidea, which includes the families Zenkerellidae and Anomaluridae. Using different calibration schemes, we demonstrated that classical dating methods relying only on mitogenomes provide rather young Miocene estimates between Zenkerellidae and the Anomaluridae. The use of published nuclear genes, internal calibrations and tip dating converged towards an Eocene split between gliding and non-gliding scaly-tailed squirrels, which is in agreement with the African fossil record. Finally, we provide the first exhaustive species-level molecular phylogenetic inference for the genus Anomalurus. We found that Anomalurus beecrofti is the sister group of all other species of Anomalurus and branched off during the Miocene.
Published: 2018

2. Beyond ectomycorrhizal bipartite networks: projected networks demonstrate contrasted patterns between early- and late-successional plants in Corsica

Author: Taudiere, Adrien, Munoz, Francois, Lesne, Annick, Monnet, Anne-Christine, Bellanger, Jean-Michel, Selosse, Marc-Andre, Moreau, Pierre-Arthur, Richard, Franck, 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), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut Français de Pondichéry (IFP), Centre National de la Recherche Scientifique (CNRS)-Ministère de l'Europe et des Affaires étrangères (MEAE), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Droit et Santé, 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), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-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), 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]), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre d’Ecologie Fonctionnelle et Evolutive ( CEFE ), Université Paul-Valéry - Montpellier 3 ( UM3 ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -École pratique des hautes études ( EPHE ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -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 ), Botanique et Modélisation de l'Architecture des Plantes et des Végétations ( UMR AMAP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), French Institute of Pondicherry, Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Physique Théorique de la Matière Condensée ( LPTMC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier ( IGMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), and Département de botanique, Faculté des sciences pharmaceutiques et biologiques, Université de Lille
Subjects: [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [ SDV.BV.BOT ] Life Sciences [q-bio]/Vegetal Biology/Botanics, ecological mycorrhizal network, fungi, food and beverages, Plant Science, bipartite networks, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, ecological strategies, ectomycorrhiza, projected networks, Mediterranean forests, host-specificity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The ectomycorrhizal (ECM) symbiosis connects mutualistic plants and fungal species into bipartite networks. While links between one focal ECM plant and its fungal symbionts have been widely documented, systemic views of ECM networks are lacking, in particular, concerning the ability of fungal species to mediate indirect ecological interactions between ECM plant species (projected-ECM networks). We assembled a large dataset of plant–fungi associations at the species level and at the scale of Corsica using molecular data and unambiguously host-assigned records to: (i) examine the correlation between the number of fungal symbionts of a plant species and the average specialization of these fungal species, (ii) explore the structure of the plant–plant projected network and (iii) compare plant association patterns in regard to their position along the ecological succession. Our analysis reveals no trade-off between specialization of plants and specialization of their partners and a saturation of the plant projected network. Moreover, there is a significantly lower-than-expected sharing of partners between early- and late-successional plant species, with fewer fungal partners for early-successional ones and similar average specialization of symbionts of early- and late-successional plants. Our work paves the way for ecological readings of Mediterranean landscapes that include the astonishing diversity of below-ground interactions.
Published: 2015

3. Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies

Author: Huber , B., Whibley , A., Le Poul , Y., Navarro , Nicolas, Martin , A., Baxter , S., Shah , A., Gilles , B., Wirth , T., McMillan , W.O., Joron , M., Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Smithsonian Tropical Research Institute, Laboratoire Paléobiodiversité et Evolution (PALEVO), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Department of Molecular and Cell Biology, School of Molecular and Biomedical Science, University of Adelaide, Department of Zoology, University of Cambridge [UK] (CAM), Department of Animal Behaviour, Universität Bielefeld, Work funded by a Smithsonian Tropical Research Institute short-term fellowship, by a CNRS ATIP grant, an ERC grant (MimEvol) andan ANR grant (HybEvol)., ANR-12-JSV7-0005,HybEvol,Origines des innovations évolutives et hybridation(2012), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie intégrative des populations, École pratique des hautes études ( EPHE ), The Smithsonian Tropical Research Institute, Laboratoire PALEVO, Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), University of California [Berkeley], The University of Adelaide, University of Cambridge [UK] ( CAM ), ANR-12-JSV7-0005,HybEvol,Origines des innovations évolutives et hybridation ( 2012 ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Biogéosciences [UMR 6282] (BGS), and Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genotype, Quantitative Trait Loci, Chromosome Mapping, Color, [ SDV.GEN.GA ] Life Sciences [q-bio]/Genetics/Animal genetics, Adaptation, Physiological, Biological Evolution, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Phenotype, Animals, Wings, Animal, Original Article, Butterflies, Crosses, Genetic
Abstract: Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have undergone an adaptive radiation for wing-pattern mimicry and are influenced by distinct selection regimes. Using crosses between natural wing-pattern variants, we used genome-wide restriction site-associated DNA (RAD) genotyping, traditional linkage mapping and multivariate image analysis to study the evolution of the architecture of adaptive variation in two closely related species: Heliconius hecale and H. ismenius. We implemented a new morphometric procedure for the analysis of whole-wing pattern variation, which allows visualising spatial heatmaps of genotype-to-phenotype association for each quantitative trait locus separately. We used the H. melpomene reference genome to fine-map variation for each major wing-patterning region uncovered, evaluated the role of candidate genes and compared genetic architectures across the genus. Our results show that, although the loci responding to mimicry selection are highly conserved between species, their effect size and phenotypic action vary throughout the clade. Multilocus architecture is ancestral and maintained across species under directional selection, whereas the single-locus (supergene) inheritance controlling polymorphism in H. numata appears to have evolved only once. Nevertheless, the conservatism in the wing-patterning toolkit found throughout the genus does not appear to constrain phenotypic evolution towards local adaptive optima.Heredity advance online publication, 25 March 2015; doi:10.1038/hdy.2015.22.
Published: 2015

4. A new local score based method applied to behavior-divergent quail lines sequenced in pools precisely detects selection signatures on genes related to autism

Author: Fariello Rico, Maria Inès, Boitard, Simon, Mercier, Sabine, Robelin, David, Faraut, Thomas, Arnould, Cécile, Recoquillay, Julien, Bouchez, Olivier, Salin, Gérald, Dehais, Patrice, Gourichon, David, Leroux, Sophie, Pitel, Frederique, Leterrier, Christine, San Cristobal, Magali, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées, Bioinformatics / Bioinformática [Montevideo], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Facultad de Ingeniera, Universidad de la República [Montevideo] (UCUR), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), UFR SES, Département Mathématique-Informatique, Université Toulouse - Jean Jaurès (UT2J), Institut de Mathématiques de Toulouse UMR5219 (IMT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SINEGAE, Pôle d'Expérimentation Avicole de Tours (UE PEAT), Département Génie Mathématique, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Unidad de Bioinformatica - Bioinformatics unit, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), GeT PlaGe, Genotoul, Pôle d'Expérimentation Avicole de Tours (PEAT), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Université de Toulouse, Réseau International des Instituts Pasteur ( RIIP ) -Institut Pasteur de Montevideo, Universidad de la República, Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Université Toulouse - Jean Jaurès ( UT2J ), UMR5219, Institut de Mathématiques, Physiologie de la reproduction et des comportements [Nouzilly] ( PRC ), Institut National de la Recherche Agronomique ( INRA ) -Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Recherches Avicoles ( SRA ), Institut National de la Recherche Agronomique ( INRA ), Pôle d'Expérimentation Avicole de Tours ( PEAT ), Département de Génie Mathématiques, Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA ), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT), Universidad de la República [Montevideo] (UDELAR), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)
Subjects: Genomics (q-bio.GN), genomic, population and evolution, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], FOS: Biological sciences, Populations and Evolution (q-bio.PE), Quantitative Biology - Genomics, quantitative biology, [ SDV.OT ] Life Sciences [q-bio]/Other [q-bio.OT], Quantitative Biology - Populations and Evolution
Abstract: Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans allows increasing the detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium, accumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal, avoiding windowing methods. This method provided results similar to haplotype-based methods on two benchmark data sets with individual genotypes. Results obtained for a divergent selection experiment on behavior in quail, where two lines were sequenced in pools, are precise and biologically coherent, while competing methods failed: our approach led to the detection of signals involving genes known to act on social responsiveness or autistic traits. This local score approach is general and can be applied to other genome-wide analyzes such as GWAS or genome scans for selection., Comment: 32 pages, 4 figures
Published: 2015

5. Exploring phylogeography and species limits in the Altai vole (Rodentia: Cricetidae)

Author: Tougard, Christelle, Montuire, Sophie, Volobouev, Vitaly, Markova, Evgenia, Contet, Julien, Aniskin, Vladimir, Quéré, Jean-Pierre, 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), Laboratoire Paléobiodiversité et Evolution (PALEVO), École pratique des hautes études (EPHE), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Origine, structure et évolution de la biodiversité (OSEB), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), 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), Work financially supported by our laboratories (ISEM, Biogéosciences, CBGP and MNHN), the Department of Biology, Evolution and Environment of University Montpellier II, and the Russian Foundation for Basic Research (for EM, research grant 10-04-96102)., Institut des Sciences de l'Evolution de Montpellier ( ISEM ), Université de Montpellier ( UM ) -Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Paléobiodiversité et Evolution ( PALEVO ), École pratique des hautes études ( EPHE ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Ural Branch of Russian Academy of Sciences ( UB RAS ), Russian Academy of Sciences [Moscow] ( RAS ), Centre de Biologie pour la Gestion des Populations ( CBGP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), 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 Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), A.N. Severtsov Institute of Ecology and Evolution, 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)
Subjects: [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, Microtus obscurus, speciation, morphometrics, evolution, [SDV.BID]Life Sciences [q-bio]/Biodiversity, hybridization, cytogenetics
Abstract: 19 pages; International audience; Natural hybridization between species is not a rare event. In arvicoline rodents, hybridization is known to occur in the wild and/or in captivity. In the Microtus arvalis group, cytogenetic studies revealed that there were two distinct chromosomal forms (2n = 46 but a different fundamental number of autosomes). These forms have been attributed to two cryptic species: the common (arvalis) and Altai (obscurus) voles. Recently, individuals with intermediate karyotypes (F1 and backcrosses) were discovered in central European Russia, and, for this reason, other studies have regarded obscurus and arvalis as conspecific. In the present study, to address the question of the species limits in the Altai vole and to infer its evolutionary history, a phylogeographical analysis combined with multivariate morphometric methods and original chromosome data was performed. Two obscurus lineages were identified: the Sino-Russian and South Caucasian lineages. Both lineages are characterized by low genetic diversity, resulting, in the former, from a past bottleneck event caused by encroaching periglacial areas and, in the latter, from recent rapid population divergence. Introgressive hybridization between the Altai and common voles appears to be the result of a secondary contact following the Last Glacial Maximum in central European Russia. Despite the fact that speciation is an ongoing process in most arvicoline species, the common and Altai voles are genetically divergent, morphologically and karyologically distinct, and exhibit contrasting evolutionary histories. For all these reasons, they should be ranked as species: M. arvalis and M. obscurus.
Published: 2013

6. (1949) Proposal to conserve Tieghemella Pierre (Sapotaceae) against Tieghemella Berl. & De Toni (Absidiaceae)

Author: Mouly , Arnaud, Gautier , Laurent, Dupont , Joëlle, Chevillotte , Hervé, Guillaumet , Jean-Louis, Florence , Jacques, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Conservatoire et jardin botaniques de la ville de Genève, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), and Mouly, Arnaud
Subjects: [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: International audience; Tieghemella Pierre, Not. Bot. 1: 18. 30 Dec 1890 [Sapot.], nom. cons. prop. Typus: T. africana Pierre. Tieghemella Berl. & De Toni in Saccardo, Syll. Fungorum 7: 215. 1888 [Fungi], nom. rej. prop. Typus: T. repens (Tiegh.) Berl. & De Toni (Absidia repens Tiegh.).
Published: 2010

7. Species diversity of larval parasitoids of the European grapevine moth (Lobesia botrana, Lepidoptera: Tortricidae): the influence of region and cultivar

Author: Claire Villemant, Denis Thiéry, Jérôme Moreau, Betty Benrey, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Zoologie, Université de Neuchâtel (UNINE), Santé Végétale (SV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB), Project funded by the National Centre of Competence in Research (NCCR) Plant Survival, a research program of the Swiss National Science Foundation., Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Neuchâtel, Santé Végétale ( SV ), and Institut National de la Recherche Agronomique ( INRA ) -École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux ( ENITAB )
Subjects: 0106 biological sciences, Tortricidae, [ SDV.MP.PAR ] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Tachinidae, Lobesia botrana, 010603 evolutionary biology, 01 natural sciences, Parasitoid, Bethylidae, Botany, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Host size, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, Species diversity, 15. Life on land, biology.organism_classification, 010602 entomology, Ichneumonidae, Insect Science, Biological control, Grape cultivars, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science, Braconidae, Geographical variation, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 7 pages; International audience; The European grapevine moth, Lobesia botrana (Denis & Schiffermüller, 1775) (Lepidoptera: Tortricidae) is a major pest of grapevines responsible for great economic losses and frequent insecticide applications. Nevertheless, the use of parasitoids as potential biological control agents has received very little attention. In this study, we present results from a survey on parasitoid species collected from French and Swiss vineyards over a period of 2 years. Over 2000 larvae of L. botrana were collected from six grape cultivars out of which a total of 118 parasitoids emerged. Ten species were identified. Exochus notatus (Holmgren, 1858) (Hymenoptera: Ichneumonidae) was the most abundant species and has a wide geographical distribution. Another parasitoid species, Agrypon anxium (Wesmael, 1849) (Hymenoptera: Ichneumonidae), had never been described on L. botrana before and two others remain unidentified Goniozus sp. (Förster, 1851) (Hymenoptera: Bethylidae) and Apanteles sp. (Hymenoptera: Braconidae). Other species include Phytomyptera nigrina (Meigen, 1824) (Diptera: Tachinidae) as well as Campoplex capitator (Aubert, 1960), Diadegma fenestralis (Holmgren, 1860), Dicaelotus inflexus (Thomson, 1891) Itoplectis maculator (Fabricius, 1775) and Triclistus meridiator Aubert, 1984 (all Hymenoptera: Ichneumonidae). We observed substantial regional variation in species richness and also found that abundance and diversity of several parasitoid species varied as a function of geographical location and grape cultivar. The parasitism rate by E. notatus was for example affected by grape cultivar suggesting that biological control may be affected by the cultivar of the host plant. These results are discussed in the context of tritrophic interactions and focus especially on the role of grape cultivar on parasitoid richness. We also suggest potential development of native parasitoid species in the implementation of biological control programs against L. botrana.
Published: 2010

8. Control of grape berry moth larvae using parasitoids: should it be developed?

Author: Denis Thiéry, Delbac, L., Claire Villemant, Jérôme Moreau, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) ( UMR SAVE ), Institut National de la Recherche Agronomique ( INRA ) -École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux ( ENITAB ) -Institut des Sciences de la Vigne et du Vin (ISVV), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), A. Calonnec, C. Duso, C. Gessler, H.H. Kassemeyer, M. Maixner, D. Thiéry & T. Zahavi, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, A. Calonnec, C. Duso, C. Gessler, H.H. Kassemeyer, M. Maixner, D. Thiéry & T. Zahavi, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), and Laffont, Rémi
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [ SDV.MP.PAR ] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 8 pages; International audience; Besides mating disruption techniques and progress in monitoring techniques (e.g. theuse of food traps against females), biological control may reveal itself very efficient at controllinggrape moth populations. Parasitoids active to control grape moths are known for long invineyards; few of them were already described in the middle of the 19th century in Frenchvineyards and their efficiency was already recognized especially against the diapausing and thefirst spring generations of the moths. Rather numerous attempts to release egg parasitoids havebeen done in different European countries using different species of trichogrammas. The resultsobtained varied a lot and could not yet clearly promote the use of this technique in vineyards. Webelieve that a biological control based on larval parasitoids could efficiently be developed as avaluable alternative to chemical control. In the present paper, we focus on larval parasitoidsamong which ichneumonids and chalcidoids (Hymenoptera) dominate, and present resultsobtained in different French vineyards (Bordeaux vineyard, Perpignan and Montpellier area,Côtes du Rhône and Alsace). We discuss factors that may favour or reduce their efficiency asbiocontrol agents.
Published: 2009

9. Groundwater biodiversity in Europe. In: Freshwater Biology Special Issue, Assessing and Conserving Groundwater Biodiversity (Eds. J. Gibert & D.C. Culver)

Author: Deharveng, L., Stoch, F., Gibert, J., Bedos, A., Galassi, D., Zagmajster, M., Brancelj, A., Camacho, A., Fiers, F., Martin, P., Giani, N., Magniez, G., Marmonier, Pierre, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Ambientali, Università degli Studi dell'Aquila (UNIVAQ), Hydrobiologie et Ecologie Souterraines, Laboratoire d'Ecologie des Hydrosystèmes Fluviaux (EHF), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Oddelek za biologijo, Univerza v Ljubljani, National Institute of Biology [Ljubljana] (NIB), Departamento de Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales (MNCN), Royal Belgian Institute of Natural Sciences (RBINS), Laboratoire d'écologie des hydrosystèmes (LEH), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, UFR Sciences de la Vie, de la Terre et de l'Environnement (Université de Bourgogne) (UFR SVTE), Université de Bourgogne (UB), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Università degli Studi dell'Aquila [L'Aquila] ( UNIVAQ.IT ), Laboratoire d'Ecologie des Hydrosystèmes Fluviaux ( EHF ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), National Institute of Biology, Vecna pot, Royal Belgian Institute of Natural Sciences ( RBINS ), Laboratoire d'écologie des hydrosystèmes ( LEH ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), UFR Sciences de la Vie, de la Terre et de l'Environnement (Université de Bourgogne) ( UFR SVTE ), Université de Bourgogne ( UB ), and Lyvet, Nathalie
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, endemism, hotspots, rarity, stygobionts, species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2009

10. Revision of Permo-Carboniferous griffenflies (Insecta: Odonatoptera: Meganisoptera) based upon new species and redescription of selected poorly known taxa from Eurasia

Author: Günther Fleck, Romain Garrouste, Georges Gand, Jakub Prokop, Seth M. Bybee, Jean Lapeyrie, André Nel, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Museu Integrado Roraima, Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Steinmetz Hall - Entomology and Nematology Department [Gainesville] (UF|IFAS), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Department of Zoology, Charles University [Prague] (CU), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Entomology and Nematology, University of Florida [Gainesville], Charles University [Prague], and Laffont, Rémi
Subjects: 0106 biological sciences, 010506 paleontology, biology, Permian, Stratigraphy, Odonatoptera, Paleontology, 15. Life on land, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Taxon, Phylogenetics, Carboniferous, Taxonomy (biology), [SDU.STU.PG] Sciences of the Universe [physics]/Earth Sciences/Paleontology, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Meganisoptera, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, [ SDU.STU.PG ] Sciences of the Universe [physics]/Earth Sciences/Paleontology
Abstract: 33 pages; International audience
Published: 2009

11. Phylogenetic Placement of Rhopalobrachium fragrans (Rubiaceae): Evidence from Molecular (rps16 and trnT-F) and Morphological Data

Author: Mouly , Arnaud, Razafimandimbison , Sylvain, Achille , Frédéric, Haevermans , Thomas, Bremer , Birgitta, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Bergius Foundation, The Royal Swedish Academy of Sciences, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Origine, structure et évolution de la biodiversité ( OSEB ), and Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: Chloroplast DNA, Rhopalobrachium, morphology, Vanguerieae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Cyclophyllum, palynology, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, molecular phylogeny
Abstract: International audience; Rhopalobrachium is an endemic New Caledonian genus of Rubiaceae with controversial tribal position, because its protologue was apparently based on two distantly related species, Rhopalobrachium fragrans and Rhopalobrachium congestum. Despite its new circumscription as a monotypic genus (Rhopalobrachium fragrans) the tribal placement of Rhopalobrachium remained unknown. We investigated, for Rhopalobrachium fragrans, all morphological characters currently used for circumscribing tribes in the subfamily Ixoroideae sensu lato. The species has axillary inflorescences, with valvate flower aestivation, drupaceous fruits with a single pendulous ovule per locule, and 3-pororate pollen grains. We also performed Bayesian and parsimony analyses based on two chloroplast markers, rps16 intron and trnT-F region, to assess the phylogenetic position of Rhopalobrachium within Ixoroideae sensu lato. These analyses produced well-resolved and strongly supported topologies. The results of both the morphological survey and phylogenetic analyses indicated a position of Rhopalobrachium fragrans in the tribe Vanguerieae and a close relationship with the Pacific genus Cyclophyllum.
Published: 2007

12. Revision of Ixora (Rubiaceae) in the Marquesas Islands (French Polynesia)

Author: Lorence, David, Wagner, Warren, Mouly, Arnaud, Florence, Jacques, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Bergius Foundation, The Royal Swedish Academy of Sciences, Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Origine, structure et évolution de la biodiversité (OSEB), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: endemism, conservation, myrmecophily, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Ixoreae, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: International audience; During the preparation of the Vascular Flora of the Marquesas Islands and Flore de la Polynésie française, four new species of Ixora L. (Rubiaceae) have come to light and are described and illustrated herein: Ixora jourdanii Mouly & J.Florence, Ixora tahuataensis Mouly & J.Florence, Ixora uahukaensis Lorence & W.L.Wagner, and Ixora uapouensis Lorence & W.L.Wagner. In addition to these new taxa, the following three species of Ixora previously described from the Marquesas are recognized: Ixora marquesensis F.Br., Ixora ooumuensis J.Florence, and Ixora spathoidea F.Br. As the Marquesan environment is under serious threat from human impact, feral animals and weeds, the conservation status was estimated for each Ixora species. It is concluded that all Marquesan taxa are in need of inclusion in the IUCN Red List, their status ranging from endangered to critically endangered.
Published: 2007

13. A diagnostic real-time PCR assay for the rapid identification of the tomato-potato psyllid, Bactericera cockerelli (Šulc, 1909) and development of a psyllid barcoding database

Author: David Ouvrard, Roland Sigvald, J. C. Sumner-Kalkun, James R. Bell, F. Highet, David Kenyon, M. J. Sjolund, A. F. C. Greenslade, Mairi Carnegie, Yvonne M. Arnsdorf, Department of Animal Health and Antimicrobial Strategy, National Veterinary Institute, Origine, structure et évolution de la biodiversité (OSEB), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Time Factors, Molecular biology, DNA cloning, Pest, Artificial Gene Amplification and Extension, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Polymerase Chain Reaction, DNA annealing, Biochemistry, 01 natural sciences, law.invention, Solanum lycopersicum, law, Databases, Genetic, Vegetables, Bactericera, Genetic annealing, DNA extraction, Polymerase chain reaction, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, Bacterial Genomics, Physics, Microbial Genetics, Eukaryota, food and beverages, Genomics, Plants, Insects, Nucleic acids, Chemistry, Biosecurity, Physical Sciences, Nucleic acid thermodynamics, Medicine, Potato, Research Article, Bactericera cockerelli, Arthropoda, Science, Magnesium Chloride, Biophysics, Microbial Genomics, Biology, Real-Time Polymerase Chain Reaction, Solanum, Microbiology, Phytosanitary, Hemiptera, Extraction techniques, Chlorides, Genetics, TaqMan, Animals, DNA Barcoding, Taxonomic, Bacterial Genetics, Diagnostic, Agricultural Science, 15 ‘Candidatus Liberibacter solanacearum’, fungi, Organisms, Chemical Compounds, Computational Biology, Biology and Life Sciences, Bacteriology, Sequence Analysis, DNA, biology.organism_classification, Invertebrates, Virology, Research and analysis methods, 010602 entomology, genomic DNA, Molecular biology techniques, Vector, PEST analysis, Cloning, Real-time PCR, 010606 plant biology & botany, Specific identification
Abstract: The accurate and rapid identification of insect pests is an important step in the prevention and control of outbreaks in areas that are otherwise pest free. The potato-tomato psyllid Bactericera cockerelli (Sulc, 1909) is the main vector of 'Candidatus Liberibacter solanacearum' on potato and tomato crops in North America and New Zealand; and is considered a threat for introduction in Europe and other pest-free regions. This study describes the design and validation of the first species-specific TaqMan probe-based real-time PCR assay, targeting the ITS2 gene region of B. cockerelli. The assay detected B. cockerelli genomic DNA from adults, immatures, and eggs, with 100% accuracy. This assay also detected DNA from cloned plasmids containing the ITS2 region of B. cockerelli with 100% accuracy. The assay showed 0% false positives when tested on genomic and cloned DNA from 73 other psyllid species collected from across Europe, New Zealand, Mexico and the USA. This included 8 other species in the Bactericera genus and the main vectors of 'Candidatus Liberibacter solanacearum' worldwide. The limit of detection for this assay at optimum conditions was 0.000001ng DNA (similar to 200 copies) of ITS2 DNA which equates to around a 1:10000 dilution of DNA from one single adult specimen. This assay is the first real-time PCR based method for accurate, robust, sensitive and specific identification of B. cockerelli from all life stages. It can be used as a surveillance and monitoring tool to further study this important crop pest and to aid the prevention of outbreaks, or to prevent their spread after establishment in new areas.
Published: 2020

14. First occurrence of the pest Drosophila suzukii (Diptera: Drosophilidae) in the Comoros Archipelago (Western Indian Ocean)

Author: A. Suwalski, Amir Yassin, I.M. Hassani, Jean R. David, Emily L. Behrman, L.H. Raveloson Ravaomanarivo, Stéphane R. Prigent, Vincent Debat, Nelly Gidaszewski, Institut National de la Recherche pour l'Agriculture, la Pêche et l'Environnement (INRAPE), Janelia Research Campus [Ashburn] (HHMI Janelia), Howard Hughes Medical Institute (HHMI), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Université d’Antananarivo, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)
Subjects: 0106 biological sciences, spotted-wing Drosophila, Insular biogeography, [SDV]Life Sciences [q-bio], 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, taxonomy, Drosophilidae, Drosophila suzukii, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, geography, geography.geographical_feature_category, biology, island biogeography, Ecology, biology.organism_classification, Indian ocean, Habitat, Insect Science, Archipelago, Taxonomy (biology), PEST analysis, ecology, Agronomy and Crop Science, Biological invasion
Abstract: International audience; Drosophila suzukii (Matsumura, 1931) is an Asian pest of grapes and other soft fruits that has invaded North America and Europe during the last decade. Here we report its recent occurrence in two islands of the Comoros archipelago in the Mozambique Channel, namely Mayotte and Ngazidja (Grande Comore), in April 2017 and November 2018, respectively. We also document its absence from other African islands of the Mozambique Channel and the Western Indian Ocean including Mayotte until 2013. Drosophila ashburneri Tsacas, 1984 is the only member of the suzukii species subgroup known from the Comoros, but it is morphologically distinct and likely distantly related to D. suzukii. Drosophila suzukii has likely been recently introduced to the Comoros archipelago, perhaps from La Réunion island where it first appeared in November 2013. In all these tropical islands, D. suzukii was found in high-altitude habitats in agreement with its adaptation to cold environments. These results suggest the high susceptibility of highlands in Eastern and Southern Africa to be infested by this pest in a near future.
Published: 2020

15. First case of parthenogenesis in ladybirds (Coleoptera: Coccinellidae) suggests new mechanisms for the evolution of asexual reproduction

Author: Jean-Louis Hemptinne, Helmut Fürsch, Alexandra Magro, António O. Soares, Emilie Lecompte, Jérôme Murienne, Anne-Marie Dutrillaux, Bernard Dutrillaux, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institute for Systems and Computer Engineering, Technology and Science [Braga] (INESC TEC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), and Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, Nephus, [SDV]Life Sciences [q-bio], Zoology, Asexual reproduction, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Robertsonian translocations, Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Parthenogenesis, biology.organism_classification, Insularity, the “mate scarcity hypothesis”, Robertsonian Translocations, Coccinellidae, Animal Science and Zoology, Wolbachia, insularity
Abstract: Parthenogenesis, the development of unfertilized eggs resulting in the exclusive production of female offspring, is rare in animals relative to sexual reproduction and is mainly reported in invertebrates. It has been hypothesized that polyploidy, hybridization and endosymbiont infections are its major causal events but the mechanisms triggering asexual reproduction remain unclear. Here, we study the proximate causes at the origin of parthenogenesis in the first reported case of asexuality in the Coccinellidae (Coleoptera). The asexual populations were found in the Azores and the Mascarene archipelagos, and were identified as Nephus voeltzkowi Weise, a bisexual species widespread in sub-Saharan Africa. The specimens from both populations are diploid but present different karyotypes and heterozygosities that evoke hybrid origins, commonly associated with parthenogenesis in Coleoptera. However, the close proximity of their genomes (99.8% homology for the complete mitochondrial genome and 99.9% for the complete nuclear ribosomal cluster) together with the congruence between the mtDNA tree and the nuclear tree, and the low heterozygosity levels, suggests that the two populations are not hybrid. We propose that they belong to a single chromosomally polymorphic species undergoing Robertsonian fusions. Furthermore, specimens from both populations are infected with Wolbachia (supergroup B strain), contrary to sympatric bisexual species of the same genus. Although Wolbachia has been shown to induce parthenogenesis in haplodiploid organisms, it has been recently suggested that it could also induce parthenogenesis in hosts with other sex determination systems. Whether chromosome rearrangements and/or Wolbachia infections are post-parthenogenetic events or are at the origin of parthenogenesis still needs to be determined. “Laboratoire d'Excellence” LabEx TULIP; Grant/Award Number: ANR‐10‐LABX‐41; "Laboratoire d'Excellence" LabEx CEBA, Grant/Award Number: ANR‐10‐LABX‐25‐01. info:eu-repo/semantics/publishedVersion
Published: 2020

16. Les variations des composés chimiques au sein d'Heliconiini sauvages révèlent l'implication de facteurs écologiques dans l'évolution des défenses chimiques des papillons mimétiques

Author: Sculfort, Ombeline, de Castro, Erika, Kozak, Krzysztof, Bak, Søren, Elias, Marianne, Nay, Bastien, Llaurens, Violaine, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Department of Zoology, University of Cambridge, Cambridge, United Kingdom, Smithonian Environmental Research Center, Research Center, University of Copenhagen = Københavns Universitet (KU), Laboratoire de synthèse organique (DCSO), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), and Sculfort, Ombeline
Subjects: [CHIM.ANAL] Chemical Sciences/Analytical chemistry, [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, cyanogenic glucosides, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Aposematism, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [CHIM] Chemical Sciences, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [CHIM]Chemical Sciences, LC-MS/MS, ComputingMilieux_MISCELLANEOUS, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.TOX.ECO] Life Sciences [q-bio]/Toxicology/Ecotoxicology, Müllerian mimicry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BA]Life Sciences [q-bio]/Animal biology, Heliconius, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [CHIM.ORGA] Chemical Sciences/Organic chemistry, [STAT] Statistics [stat], [STAT]Statistics [stat], [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, [SDV.BA.ZI] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, [SDV.BID] Life Sciences [q-bio]/Biodiversity, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience
Published: 2020

17. The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity

Author: Erik Verheyen, Terrence C. Demos, Marc Colyn, Akaibe Dudu, Christiane Denys, Ayodeji Olayemi, Pierre-Henri Fabre, Josef Bryja, Pionus Katuala, Julian C. Kerbis Peterhans, Violaine Nicolas, Alain Didier Missoup, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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, Masaryk University [Brno] (MUNI), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Royal Belgian Institute of Natural Sciences (RBINS), Université de Douala, Obafemi Awolowo University (OAU), Université de Kisangani, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes 1 (UR1), Field Museum of Natural History [Chicago, USA], Roosevelt University [Chicago], This work was supported by the ‘Action Transversale du Muséum: Génomique et collections’ (MNHN), EU-DGVIII BIOFAC and ECOFAC programs, WHO-Ebola Research Project in Côte d’Ivoire, WWF Gabon, PGRR-GFA Terra Systems Project in Guinea, INCO-DEV Threat Control in Guinea and Côte d’Ivoire, PAMF project in Benin, ANR Biodiversité (grant number IFORA ANR-06-BDIV-0014), Czech Science Foundation (grant numbers P506/10/0983, 15-20229S), Grant Agency of the University of South Bohemia (grant number 018/2017/P), the Belgian Directorate for Development Cooperation (DGD), the Flemish Inter-University Council –University Development Cooperation (VLIR-UOS)., ANR-06-BDIV-0014,IFORA,Les îles forestières africaines : modèles d'une nouvelle approche de la dynamique de structuration de la biodiversité(2006), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), 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 de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Université de Rennes (UR)
Subjects: 0106 biological sciences, 0301 basic medicine, Nuclear gene, Biogeography, Speciation, Late Miocene, Biology, Forests, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, Rodents, 03 medical and health sciences, Monophyly, Mice, Phylogenetics, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genetics, Animals, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Ecosystem, Phylogeny, Taxonomy, Cell Nucleus, Mammals, Tropical Climate, Hylomyscus, Genetic Variation, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, Tropical Africa, Biological Evolution, 030104 developmental biology, Taxon, Evolutionary biology, Africa, Genome, Mitochondrial, Taxonomy (biology), Murinae
Abstract: International audience; Wood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used complete mitochondrial genomes and five nuclear genes to infer the number of candidate species within this genus and depict its evolutionary history. In terms of gene sampling and geographical and taxonomic coverage, this is the most comprehensive review of the genus Hylomyscus to date. The six species groups (aeta, alleni, anselli, baeri, denniae and parvus) defined on morphological grounds are monophyletic. Species delimitation analyses highlight undescribed diversity within this genus: perhaps up to 10 taxa need description or elevation from synonymy, pending review of type specimens. Our divergence dating and biogeographical analyses show that diversification of the genus occurred after the end of the Miocene and is closely linked to the history of the African forest. The formation of the Rift Valley combined with the declining global temperatures during the Late Miocene caused the fragmentation of the forests and explains the first split between the denniae group and remaining lineages. Subsequently, periods of increased climatic instability during Plio-Pleistocene probably resulted in elevated diversification in both lowland and montane forest taxa.
Published: 2020

18. Chemical defences of native European coccinellid eggs against intraguild predation by the invasive Asian coccinellid, Harmonia axyridis (Pallas)

Author: Dirk Babendreier, Felipe Ramon-Portugal, Angelos Katsanis, Alexandra Magro, Marc Kenis, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Origine, structure et évolution de la biodiversité (OSEB), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Larva, media_common.quotation_subject, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Competition (biology), Harmonia axyridis, Predation, 010602 entomology, Animal ecology, Insect Science, Botany, Instar, Coccinellidae, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science, ComputingMilieux_MISCELLANEOUS, Intraguild predation, media_common
Abstract: Harmonia axyridis (Pallas) is a coccinellid of Asian origin that has recently invaded substantial parts of Europe and is suspected to affect native coccinellid populations through intraguild predation and competition for food. Previous work has shown that two species from the Calvia genus appeared to be well protected against H. axyridis predation. To deepen our understanding on chemical protection of Calvia spp. and the predation risk by H. axyridis, we tested for susceptibility and palatability of Calvia spp. and H. axyridis eggs against predation by H. axyridis neonate larvae. Results show that eggs of C. quatuordecimguttata were mostly not eaten by H. axyridis, while eggs of the congeneric C. decemguttata were found to be largely unprotected against predation by the invasive coccinellid. We also observed that H. axyridis first instars successfully cannibalized on conspecific eggs. Removing the surface chemicals from C. quatuordecimguttata eggs resulted in significantly reduced protection from being preyed upon by H. axyridis, while applying these extracts onto C. decemguttata and H. axyridis eggs resulted in increased protection against H. axyridis larvae. The importance of surface chemicals in the interactions between H. axyridis and native coccinellids was confirmed by GC–MS analysis, showing a high diversity of hydrocarbons located on the surface of C. quatuordecimguttata eggs, i.e. more than twice as many when compared to C. decemguttata. Survival of H. axyridis larvae feeding on eggs of C. quatuordecimguttata, C. decemguttata or conspecific eggs, from which surface chemicals were removed by washing them with hexane, was not different from survival on unwashed eggs.
Published: 2017

19. Ecomorphological diversification of the Late Palaeozoic Palaeodictyopterida reveals different larval strategies and amphibious lifestyle in adults

Author: Wiesław Krzemiński, Martina Pecharová, Jakub Prokop, André Nel, Ewa Krzemińska, Kateřina Rosová, Michael S. Engel, Charles University [Prague] (CU), Polish Academy of Sciences (PAN), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics (University of Kansas), and University of Kansas [Lawrence] (KU)
Subjects: 0106 biological sciences, Gill, ecomorphology, animal structures, Insecta, Ecomorphology, media_common.quotation_subject, Palaeodictyoptera, Zoology, Insect, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, tracheal respiratory system, Water environment, Respiratory function, lcsh:Science, 030304 developmental biology, media_common, Ecological niche, Appendage, 0303 health sciences, Multidisciplinary, biology, nymph, fungi, Biology (Whole Organism), Megasecoptera, biology.organism_classification, lcsh:Q, Research Article
Abstract: International audience; The Late Palaeozoic insect superorder Palaeodictyopterida exhibits a remarkable disparity of larval ecomorphotypes, enabling these animals to occupy diverse ecological niches. The widely accepted hypothesis presumed that their immature stages only occupied terrestrial habitats, although authors more than a century ago hypothesized they had specializations for amphibious or even aquatic life histories. Here, we show that different species had a disparity of semiaquatic or aquatic specializations in larvae and even the supposed retention of abdominal tracheal gills by some adults. While a majority of mature larvae in Palaeodictyoptera lack unambiguous lateral tracheal gills, some recently discovered early instars had terminal appendages with prominent lateral lamellae like in living damselflies, allowing support in locomotion along with respiratory function. These results demonstrate that some species of Palaeodictyopterida had aquatic or semiaquatic larvae during at least a brief period of their post-embryonic development. The retention of functional gills or gill sockets by adults indicates their amphibious lifestyle and habitats tightly connected with a water environment as is analogously known for some modern Ephemeroptera or Plecoptera. Our study refutes an entirely terrestrial lifestyle for all representatives of the early diverging pterygote group of Palaeodictyopterida, a greatly varied and diverse lineage which probably encompassed many different biologies and life histories.
Published: 2019

20. Comparison between anion and cation emission from CH 4 molecules colliding with 10.5-keV C + ions: fragment-energy aspects

Author: Jean-Yves Chesnel, J. A. Tanis, Jimmy Rangama, J. C. Poully, S. T. S. Kovács, Béla Sulik, Zoltán Juhász, E. Lattouf, Violaine Vizcaino, P. Herczku, A. Méry, Bernd A. Huber, E. Bene, Hahn-Meitner-Institut Berlin, Institute for Nuclear Research [Budapest] (ATOMKI), Hungarian Academy of Sciences (MTA), Centre de recherche sur les Ions, les MAtériaux et la Photonique (CIMAP - UMR 6252), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), 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)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), and Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: History, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Kinetic energy, 01 natural sciences, Endothermic process, Methane, 010305 fluids & plasmas, Education, Ion, chemistry.chemical_compound, Physics::Plasma Physics, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, 0103 physical sciences, Molecule, Physics::Chemical Physics, Nuclear Experiment, 010306 general physics, ComputingMilieux_MISCELLANEOUS, Projectile, Chemistry, [PHYS.PHYS.PHYS-ATM-PH]Physics [physics]/Physics [physics]/Atomic and Molecular Clusters [physics.atm-clus], Computer Science Applications, Physical chemistry, Astrophysics::Earth and Planetary Astrophysics, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], [CHIM.RADIO]Chemical Sciences/Radiochemistry
Abstract: It is shown that both positive and negative ions can be ejected from gas-phase methane molecules when bombarded with positive ions at keV energies. The kinetic energy distribution of the negatively charged fragments shows strong similarities with that of the ejected cations. However, in a hard binary collision between the C+ projectile and an H atom, the formation of H− ions is more endothermic than the formation of H+ ions.
Published: 2019

21. Adaptive evolution of butterfly wing shape: from morphology to behaviour

Author: Vincent Debat, Camille Le Roy, Violaine Llaurens, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, diversification, Ecology (disciplines), Morphology (biology), Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, wing morphology, Animals, Wings, Animal, Ecosystem diversity, Coevolution, 030304 developmental biology, flight behaviour, 0303 health sciences, Natural selection, Wing, aerodynamic performance, Adaptation, Physiological, Biological Evolution, fitness, Lepidoptera, Evolutionary biology, Sexual selection, Flight, Animal, Butterfly, coevolution, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Butterflies
Abstract: International audience; Butterflies display extreme variation in wing shape associated with tremendous ecological diversity. Disentangling the role of neutral versus adaptive processes in wing shape diversification remains a challenge for evolutionary biologists. Ascertaining how natural selection influences wing shape evolution requires both functional studies linking morphology to flight performance, and ecological investigations linking performance in the wild with fitness. However, direct links between morphological variation and fitness have rarely been established. The functional morphology of butterfly flight has been investigated but selective forces acting on flight behaviour and associated wing shape have received less attention. Here, we attempt to estimate the ecological relevance of morpho-functional links established through biomechanical studies in order to understand the evolution of butterfly wing morphology. We survey the evidence for natural and sexual selection driving wing shape evolution in butterflies, and discuss how our functional knowledge may allow identification of the selective forces involved, at both the macro-and micro-evolutionary scales. Our review shows that although correlations between wing shape variation and ecological factors have been established at the macro-evolutionary level, the underlying selective pressures often remain unclear. We identify the need to investigate flight behaviour in relevant ecological contexts to detect variation in fitness-related traits. Identifying the selective regime then should guide experimental studies towards the relevant estimates of flight performance. Habitat, predators and sex-specific behaviours are likely to be major selective forces acting on wing shape evolution in butterflies. Some striking cases of morphological divergence driven by contrasting ecology involve both wing and body morphology, indicating that their interactions should be included in future studies investigating co-evolution between morphology and flight behaviour.
Published: 2019

22. A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

Author: Mónica Medina, Arite Bigalke, Ezequiel M. Marzinelli, Eve Toulza, Elena Kazamia, Tilmann Harder, Ulisse Cardini, Soizic Prado, Johan Decelle, François H. Lallier, Fabrice Not, Claire M. M. Gachon, Sarah Griffiths, Enora Briand, Paco Cárdenas, Ehsan Kayal, Marc-André Selosse, José Pintado Valverde, Willem Stock, Derek J. Skillings, Damien Eveillard, Mahasweta Saha, Simon M. Dittami, Enrique Arboleda, Teresa Maria Morganti, Catherine Leblanc, Shinichi Sunagawa, Laura Núñez Pons, Ashwin Engelen, Alexey Vorobev, Jean-Christophe Auguet, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), 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)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), 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), Institute for Inorganic and Analytical Chemistry, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of Medicinal Chemistry, Uppsala University, Sweden, Uppsala University, Stazione Zoologica Anton Dohrn (SZN), Laboratoire de physiologie cellulaire végétale, Institut National de la Recherche Agronomique (INRA), Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Scottish Association for Marine Science, Scottish Marine Institute, School of Science and the Environment, Manchester Metropolitan University (MMU), University of Bremen, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), 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), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), 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)-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), Pennsylvania State University (Penn State), Penn State System, Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), IIM CSIC, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Department of Biological Sciences, University of Essex, Origine, structure et évolution de la biodiversité (OSEB), University of Gdansk, University of Pennsylvania, Laboratory of Protistology & Aquatic Ecology, Institute of Microbiology and Swiss Institute of Bioinformatics, 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Stazione Zoologica Anton Dohrn, Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-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), Singapore Centre for Environmental Life Sciences Engineering [Singapore, Singapore] (SCELSE), Nanyang Technological University [Singapour]-Interdisciplinary Graduate School [Singapore, Singapore], Helmholtz Center for Ocean Research, University of Pennsylvania [Philadelphia], Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Adaptation and Diversity in the Marine Environment, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), 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), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), 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), 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), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0303 health sciences, 010604 marine biology & hydrobiology, media_common.quotation_subject, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Populations and Evolution (q-bio.PE), Complex system, Community perspective, 01 natural sciences, Data science, Holobiont, 03 medical and health sciences, State (polity), 13. Climate action, FOS: Biological sciences, Marine ecosystem, Evolutionary ecology, 14. Life underwater, Sociology, Quantitative Biology - Populations and Evolution, 030304 developmental biology, media_common
Abstract: Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help describe and understand these complex systems. It posits that a host and its associated microbiota, living together in a long-lasting relationship, form the holobiont, and have to be studied together, as a coherent biological and functional unit, in order to understand the biology, ecology and evolution of the organisms. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences with comparisons to terrestrial science whenever appropriate. A deeper understanding of such complex systems, however, will require further technological and conceptual advances. The most significant challenge will be to bridge functional research on simple and tractable model systems and global approaches. This will require scientists to work together as an (inter)active community in order to address, for instance, ecological and evolutionary questions and the roles of holobionts in biogeochemical cycles., PeerJ Preprints, Computer Science Preprints., 2019
Published: 2019
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23. Out of Africa: demographic and colonization history of the Algerian mouse (Mus spretus Lataste)

Author: Ali Ouarour, Stefano Mona, Karim Souttou, François Bonhomme, Stéphane Aulagnier, Christiane Denys, Emmanuelle Stoetzel, Violaine Nicolas, Aude Lalis, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Muséum national d'Histoire naturelle (MNHN), Histoire naturelle de l'Homme préhistorique (HNHP), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), Génome, Population, Interactions, Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), 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 de Djelfa, Université de Tétouan, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Projet CMEP TASSILI MDU 09MDU755, Projet ATM MNHN: Taxonomie moléculaire, DNA Barcode & Gestion Durable des Collections, Service de Systématique Moléculaire du MNHN (UMS 2700, Paris, France), network Bibliothèque du Vivant (CNRS, MNHN, INRA, CEA), ANR-09-PEXT-0004,Mohmie,Influence de l'installation des hommes modernes au Maroc sur l'évolution de la biodiversité des petits vertébrés terrestres(2009), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), and Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, 0301 basic medicine, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Mus spretus, Climate, [SDV]Life Sciences [q-bio], Biology, DNA, Mitochondrial, 010603 evolutionary biology, 01 natural sciences, Mediterranean Basin, Article, Mice, 03 medical and health sciences, Africa, Northern, Peninsula, Genetics, Animals, Colonization, Endemism, Phylogeny, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Local adaptation, geography, geography.geographical_feature_category, Ecology, 15. Life on land, biology.organism_classification, humanities, Environmental niche modelling, Europe, 030104 developmental biology, Spain, Biological dispersal, Animal Migration, Microsatellite Repeats
Abstract: International audience; North Africa is now recognized as a major area for the emergence and dispersal of anatomically modern humans from at least 315 kya. The Mediterranean Basin is thus particularly suited to study the role of climate versus human-mediated changes on the evolutionary history of species. The Algerian mouse (Mus spretus Lataste) is an endemic species from this basin, with its distribution restricted to North Africa (from Libya to Morocco), Iberian Peninsula and South of France. A rich paleontological record of M. spretus exists in North Africa, suggesting hypotheses concerning colonization pathways, and the demographic and morphologic history of this species. Here we combined genetic (3 mitochondrial DNA loci and 18 microsatellites) and climatic niche modeling data to infer the evolutionary history of the Algerian mouse. We collected 646 new individuals in 51 localities. Our results are consistent with an anthropogenic translocation of the Algerian mouse from North Africa to the Iberian Peninsula via Neolithic navigators, probably from the Tingitane Peninsula. Once arrived in Spain, suitable climatic conditions would then have favored the dispersion of the Algerian mice to France. The morphological differentiation observed between Spanish, French and North African populations could be explained by a founder effect and possibly local adaptation. This article helps to better understand the role of climate versus human-mediated changes on the evolutionary history of mammal species in the Mediterranean Basin.
Published: 2019

24. Effects of natural wing damage on flight performance in Morpho butterflies: what can it tell us about wing shape evolution?

Author: Violaine Llaurens, Camille Le Roy, Raphaël Cornette, Vincent Debat, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Leading edge, diversification, animal structures, Physiology, 030310 physiology, Aquatic Science, Natural variation, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Gliding flight, wing morphology, geometric morphometrics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, flight behaviour, 0303 health sciences, aerodynamic performance, Wing, biology, Lepidoptera 34 35, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Flight speed, Morpho, Flight behaviour, biology.organism_classification, behaviour, fitness, Lepidoptera, Evolutionary biology, Insect Science, coevolution, Butterfly, Animal Science and Zoology, aerodynamics
Abstract: International audience; Flying insects frequently experience wing damage during their life. Such irreversible alterations of wing shape affect flight performance and ultimately fitness. Insects have been shown to compensate for wing damage through various behavioural adjustments, but the importance of damage location over the wings has scarcely been studied. Using natural variation in wing damage, we tested how the loss of different wing parts affects flight performance. We quantified flight performance in two species of large butterflies, Morpho helenor and Morpho achilles, caught in the wild and displaying large variation in the extent and location of wing damage. We artificially generated more severe wing damage in our sample to contrast natural versus higher magnitude wing loss. Wing shape alteration across our sample was quantified using geometric morphometrics to test the effect of different damage distributions on flight performance. Our results show that impaired flight performance clearly depends on damage location over the wings, pointing to a relative importance of different wing parts for flight. A deteriorated forewing leading edge most critically affected flight performance, specifically decreasing flight speed and the proportion of gliding flight. In contrast, the most frequent natural damage, deteriorated wing margin, had no detectable effect on flight behaviour. Damage located on the hindwings – although having a limited effect on flight – was associated with reduced flight height, suggesting that the forewings and hindwings play different roles in butterfly flight. By contrasting harmless and deleterious consequences of various types of wing damage, our study highlights different selective regimes acting on morphological variations of butterfly wings.
Published: 2019

25. Evolutionary history of the Persian Jird,Meriones persicus,based on genetics, species distribution modelling and morphometric data

Author: Mansour Aliabadian, Violaine Nicolas, Malahatosadat Dianat, Jamshid Darvish, Raphaël Cornette, University of Mashad, Iran, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Origine, structure et évolution de la biodiversité (OSEB), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Ecological niche, [SDV]Life Sciences [q-bio], Biogeography, Zoology, 15. Life on land, Biology, Subspecies, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Environmental niche modelling, Gene flow, 03 medical and health sciences, 030104 developmental biology, Genetic structure, Meriones persicus, Genetics, Animal Science and Zoology, Taxonomy (biology), Molecular Biology, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics
Abstract: The Persian Jird, Meriones persicus, is distributed from Eastern Anatolia to Afghanistan and western Pakistan. Six subspecies were described based on skull features and coat colours, but the validity of these subspecies is uncertain, and no molecular work has ever been conducted on this species. Iran appears to be a key geographical region in which to revise the systematic and evolutionary history of this species, because five of the six subspecies are present in this country. To evaluate the phylogeographical history and taxonomy of this species in Iran, we used a combination of genetic (cytochrome b gene sequences of 70 specimens) and geometric morphometric (2D landmarks on the ventral side of skull of 258 specimens) analyses. We also used ecological niche modelling to make inferences about the evolutionary history of these lineages. Our molecular data highlight the existence of four genetic lineages, but they only partly correspond to the previously described subspecies. Our molecular and morphometric data confirm the validity of M. p. rossicus and show that it has a wider geographical range than previously thought. M. p. gurganensis and M. p. baptistae are genetically very close. The skull of M. p. gurganensis is morphologically distinguishable from other subspecies. The subspecies M. p. persicus and M. p. baptistae are genetically distinct, but morphologically close. Meriones p. ambrosius is genetically close to M. p. persicus, and additional analyses with more specimens are needed to validate its subspecific status. The genetic structure observed in Iran seems to fit the topography and biogeography of the country and emphasize the role of the Abarkooh, Central and Lut deserts as barriers to gene flow. All intraspecific divergent events within the Persian Jird occurred during the last 1.4 My, suggesting that climatic changes probably trigger diversification within this species. Our genetic and species niche modelling results suggest that potential refugial areas persisted during glacial periods for this species in north-western Zagros Mountains, north-eastern Alborz Mountains and Kohrud Mountains.
Published: 2016

26. A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa

Author: E. A. Bennett, Julien Daligault, Nathalie M. L. Côté, Aude Lalis, Violaine Nicolas, Emmanuelle Stoetzel, Thierry Grange, Eva-Maria Geigl, Christiane Denys, Mélanie Pruvost, Silvia Guimaraes, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD), PhD fellowship from the Franche-Comte region, Grant from the University Paris Diderot, Grant from the Fondation pour la Recherche Médicale (DGE20111123014), Grant from Région Ile-de-France, ANR-09-PEXT-0004,Mohmie,Influence de l'installation des hommes modernes au Maroc sur l'évolution de la biodiversité des petits vertébrés terrestres(2009), ANR-11-LABX-0071,WHO AM I,Determinants de l'Identité : de la molécule à l'individu(2011), ONERA - The French Aerospace Lab [Lille], ONERA, Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), Origine, structure et évolution de la biodiversité, Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Université de Brest (UBO), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale 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), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Nanophysique et Semiconducteurs (NEEL - NPSC), Institut Néel (NEEL), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0106 biological sciences, 0301 basic medicine, Genotype, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV]Life Sciences [q-bio], Ecology (disciplines), Rodentia, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Computational biology, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, DNA sequencing, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Phylogenetics, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genetics, Animals, DNA Barcoding, Taxonomic, Genotyping, Phylogeny, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, [SDV.GEN]Life Sciences [q-bio]/Genetics, Phylogenetic tree, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], High-Throughput Nucleotide Sequencing, Ecological genetics, Morocco, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Ancient DNA, Archaeology, Biotechnology
Abstract: International audience; We present a cost-effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next-generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human- and/or climate-induced environmental changes. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive highthroughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour-intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology.
Published: 2016

27. Genetic diversity and structuring across the range of a widely distributed ladybird: focus on rear‐edge populations phenotypically divergent

Author: Mohand-Ameziane Bouanani, Emilie Lecompte, Brigitte Crouau-Roy, Alexandra Magro, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, 0301 basic medicine, Range (biology), Population, rear‐edge populations, Population genetics, Biology, 010603 evolutionary biology, 01 natural sciences, Bottleneck, Gene flow, 03 medical and health sciences, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Coccinella, Nature and Landscape Conservation, Local adaptation, Original Research, Genetic diversity, education.field_of_study, Ecology, population genetics, Palearctic region, Genetic divergence, 030104 developmental biology, Genetic distance, Evolutionary biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, local adaptation
Abstract: Population genetics and phenotypic structures are often predicted to vary along the geographic range of a species. This phenomenon would be accentuated for species with large range areas, with discontinuities and marginal populations. We herein compare the genetic patterns of central populations of Coccinella septempunctata L. with those of two phenotypically differentiated populations considered as rear‐edge populations and subspecies based on phenotype (Algeria and Japan). According to the central‐marginal model and expected characteristics of rear‐edge populations, we hypothesize that these rear‐edge populations have (1) a reduced genetic diversity, resulting from their relative isolation over long periods of time, (2) a higher population genetic differentiation, explained by low contemporary gene flow levels, and (3) a relationship between genetic diversity characteristics and phenotypes, due to historical isolation and/or local adaptation. Based on genotyping of 28 populations for 18 microsatellite markers, several levels of regional genetic diversity and differentiation are observed between and within populations, according to their localization: low within‐population genetic diversity and higher genetic differentiation of rear‐edge populations. The genetic structuring clearly dissociates the Algerian and Eastern Asia populations from the others. Geographical patterns of genetic diversity and differentiation support the hypothesis of the central‐marginal model. The pattern observed is in agreement with the phenotypic structure across species range. A clear genetic break between populations of Algeria, the Eastern Asia, and the remaining populations is a dominant feature of the data. Differential local adaptations, absence of gene flow between marginal and central populations, and/or incapacity to mate after colonization, have contributed to their distinct genotypic and phenotypic characteristics.
Published: 2016

28. Agricultural research, or a new bioweapon system?

Author: R. G. Reeves, Felix Beck, Christophe Boëte, D. Caetano-Anollés, Silja Voeneky (Vöneky), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-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, 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: 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Insecta, Gene Transfer, Horizontal, Ecology (disciplines), [SDV]Life Sciences [q-bio], Gene transfer, Zea mays, [SHS]Humanities and Social Sciences, 03 medical and health sciences, [SHS.DROIT]Humanities and Social Sciences/Law, Genome editing, Solanum lycopersicum, Biological Warfare, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Gene Editing, Multidisciplinary, business.industry, fungi, Agriculture, 030112 virology, Biotechnology, [SDV.ETH]Life Sciences [q-bio]/Ethics, Social Control, Formal, 030104 developmental biology, Biological warfare, [SDE]Environmental Sciences, Viruses, business
Abstract: Insect-delivered horizontal genetic alteration is concerning
Published: 2018

29. Prevalence of Yersinia Species in the Ileum of Crohn's Disease Patients and Controls

Author: Guillaume Le Baut, Claire O'Brien, Paul Pavli, Maryline Roy, Philippe Seksik, Xavier Tréton, Stéphane Nancey, Nicolas Barnich, Madeleine Bezault, Claire Auzolle, Dominique Cazals-Hatem, Jérome Viala, Matthieu Allez, The REMIND GROUP, Jean-Pierre Hugot, Anne Dumay, Cibles et médicaments de l'infection, de l'immunité et du cancer (IICiMed), Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Australian National University (ANU), CRI UMR 1149, Lab Excellence Inflamex, Université Paris Diderot - Paris 7 (UPD7), Service de Gastroentérologie et nutrition [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Saint-Antoine [APHP], Centre de recherche biomédicale Bichat-Beaujon (CRB3), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service d'hépato-gastroentérologie, Hospices Civils de Lyon (HCL), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), INSERM, U1160, Département de Gastroentérologie, Hôpital Saint-Louis, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Diderot - Paris 7 (UPD7), Origine, structure et évolution de la biodiversité, Centre National de la Recherche Scientifique (CNRS), Centre de recherche sur l'Inflammation (CRI (UMR_S_1149 / ERL_8252 / U1149)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Cibles et Médicaments des Infections et de l'Immunité (IICiMed), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Investissements d'Avenir programme, Sorbonne Paris Cite, Laboratoire d'excellence INFLAMEX ANR-11-IDEX-0005-02, Université Paris Diderot - Paris 7 (UPD7)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Microbiology (medical), système immunitaire, Immunology, lcsh:QR1-502, Ileum, Biology, Gut flora, Yersinia, Microbiology, Inflammatory bowel disease, lcsh:Microbiology, yersinia, 03 medical and health sciences, 0302 clinical medicine, NOD2, Immunologie, medicine, mucosal immune system, ATG16L1, innate immunity, Crohn's disease, gut microbiota, ileal mucosa, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, maladie de crohn, medicine.disease, biology.organism_classification, molecular test, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, ileon, 030104 developmental biology, Infectious Diseases, medicine.anatomical_structure, microflore digestive, IRGM, 030211 gastroenterology & hepatology
Abstract: International audience; Yersinia are common contaminants of food products, but their prevalence in the human gut is poorly documented. Yersinia have been implicated in Crohn's Disease (CD, an inflammatory bowel disease) however their role in CD is controversial. We performed highly sensitive PCR assays of specific sequences for the gyrB gene of Y. aldovae, Y. bercovieri, Y. enterocolitica, Y. intermedia, Y. mollaretii and the inv gene of Y. pseudotuberculosis. We analyzed a total of 470 ileal samples taken from 338 participants (262 CD patients and 76 controls) belonging to three independent cohorts. All patients and controls were phenotyped and genotyped for the main CD susceptibility variants: NOD2, ATG16L1, and IRGM. Yersinia were found in 7.7% of ileal samples (respectively 7.9 and 7.6% in controls and CD patients) corresponding to 10% of participants (respectively 11.8 and 9.5% in controls and CD patients). Y. enterocolitica, Y. pseudotuberculosis and Y. intermedia were the most frequently identified species. The bacteria were more frequent in resected specimens, lymph nodes and Peyer's patches. Yersinia were no more likely to be detected in CD tissues than tissues from inflammatory and non-inflammatory controls. CD patients treated with immunosuppressants were less likely to be Yersinia carriers. In conclusion, this work shows that Yersinia species are frequently found at low levels in the human ileum in health and disease. The role of Yersinia species in this ecosystem should now be explored.
Published: 2018

30. Swimmers, Diggers, Climbers and More, a Study of Integration Across the Mustelids’ Locomotor Apparatus (Carnivora: Mustelidae)

Author: Raphaël Cornette, Alexandra Houssaye, Anthony Herrel, Anne-Claire Fabre, Léo Botton-Divet, Biogéochimie et écologie des milieux continentaux (Bioemco), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Département Adaptations du vivant (AVIV), Muséum national d'Histoire naturelle (MNHN), Evolutionary Morphology of Vertebrates, Ghent University [Belgium] (UGENT), Duke University, 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)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Origine, structure et évolution de la biodiversité, Centre National de la Recherche Scientifique (CNRS), Paléobiodiversité et paléoenvironnements, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, 0301 basic medicine, Phylogenetic tree, biology, Functional specialization, Mustelidae, Terrestrial locomotion, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Evolutionary biology, Mustela putorius, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, [SDE]Environmental Sciences, Carnivora, Allometry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Clade, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Phenotypic integration, defined as the coordinated co-variation of parts of an organism can be an important constraint on phenotypic diversification. Functional factors, by having an heterogeneous impact across the animal body, may reinforce the integration of some parts while causing a perturbation of the integration among other parts. The integration across the locomotor apparatus should thus reflect to a certain extent the locomotor ecology of the animal. Using the mustelids as study group, we track changes in the patterns of co-variation in species belonging to four different locomotor ecologies (terrestrial, semi-arboreal, semi-fossorial, and semi-aquatic). Our results highlight the strong overall integration in mustelid long bones. The main shape changes associated with co-variations between skeletal elements are the bone robustness and proportions of the epiphyses. The pattern of co-variation is, however, only slightly impacted by allometry. Changes in co-variation between species mostly scale with phylogenetic divergence time, except for the (Mustela putorius, M. eversmanni, M. lutreola) clade which, despite a short divergence time, presents strong differences in co-variation. Co-variation patterns differ between locomotor ecologies, but few of these variations match the hypothesis of a reduction of integration due to functional specialization. This may reflect our lack of knowledge on the functional modules in species with locomotor ecologies that differ from terrestrial locomotion rather than invalidate our a priori hypotheses.
Published: 2018

31. The impact of artificial selection on morphological integration in the appendicular skeleton of domestic horses

Author: Pauline Hanot, Claude Guintard, Raphaël Cornette, Anthony Herrel, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Evolutionary Morphology of Vertebrates, Universiteit Gent = Ghent University [Belgium] (UGENT), Service d’Anatomie Comparée Animale, Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), and Origine, structure et évolution de la biodiversité (OSEB)
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Histology, Appendicular skeleton, Diversification (marketing strategy), Biology, Breeding, Muscle Development, 010603 evolutionary biology, 01 natural sciences, Bone and Bones, 03 medical and health sciences, medicine, Animals, Body Size, Horses, Bone shape, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, Morphometrics, Ligaments, Extremities, Cell Biology, Biodiversity, Original Articles, 030104 developmental biology, medicine.anatomical_structure, Phenotype, Morphological integration, Limb bones, Evolutionary biology, [SDE]Environmental Sciences, Female, Anatomy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Function (biology), Locomotion, Developmental Biology
Abstract: The relationships between the different component parts of organisms, such as the sharing of common development or function, produce a coordinated variation between the different traits. This morphological integration contributes to drive or constrain morphological variation and thus impacts phenotypic diversification. Artificial selection is known to contribute significantly to phenotypic diversification of domestic species. However, little attention has been paid to its potential impact on integration patterns. This study explores the patterns of integration in the limb bones of different horse breeds, using 3D geometric morphometrics. The domestic horse is known to have been strongly impacted by artificial selection, and was often selected for functional traits. Our results confirm that morphological integration among bones within the same limb is strong and apparently partly produced by functional factors. Most importantly, they reveal that artificial selection, which led to the diversification of domestic horses, impacts covariation patterns. The influence of selection on the patterns of covariation varies along the limbs and modulates bone shape, likely due to a differential ligament or muscle development. These results highlight that, in addition to not being constrained by a strong morphological integration, artificial selection has modulated the covariation patterns according to the locomotor specificities of the breeds. More broadly, it illustrates the interest in studying how micro-evolutionary processes impact covariation patterns and consequently contribute to morphological diversification of domestic species.
Published: 2018

32. Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis, Diarrhea, Impaired Hearing, and Bone Fragility

Author: Ludmila Francescatto, Catherine Guettier-Bouttier, Jean-Baptiste Rivière, Evelyne Marinier, Olivier Goulet, Philippe Gauchez, Alexandre Fabre, Yves Rimet, Jean-Pierre Hugot, Aurélie Bourchany, Laurence Faivre, Catherine Badens, Arnauld Delarue, Emmanuel Gonzales, Frédéric Huet, Raphaelle Maudinas, Arnaud Blanchard, Nicholas Katsanis, Céline Brochier-Armanet, Christel Thauvin-Robinet, Sabine Sigaudy, Julien Thevenon, Caroline Lacoste, Karin Mazodier, Ange-Line Bruel, Emmanuelle Ecochard-Dugelay, Nicolas Lévy, Cécile de Leusse, Mina Komuta, Géraldine Hery, Yannis Duffourd, Jacques Sarles, Bertrand Roquelaure, Xavier Stéphenne, Patrice Bourgeois, Perciliz L. Tan, Clothilde Esteve, Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Pediatric Gastroenterology, Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité-Assistance Publique-Hopitaux de Paris-AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Neuro-Oncologie [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), 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), Génétique des Anomalies du Développement (GAD), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Hôpital de la Timone [CHU - APHM] (TIMONE), Service de pédiatrie multidisciplinaire [Hôpital de la Timone Enfants - APHM], Centre Européen de Recherche en Imagerie médicale (CERIMED), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-École Centrale de Marseille (ECM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Centre National de la Recherche Scientifique (CNRS), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Signalisation calcique et interactions cellulaires dans le foie, Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Génétique Moléculaire [Hôpital de la Timone - APHM], Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de pédiatrie multidiciplinaire, Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Pédiatrie Multidisciplinaire, Centre de référence maladie rare Thalassémie, Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Center for Human Disease Modeling, Duke University [Durham], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille medical genetics - Centre de génétique médicale de Marseille ( MMG ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Lipides - Nutrition - Cancer [Dijon - U1231] ( LNC ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Paris Diderot - Paris 7 ( UPD7 ) -PRES Sorbonne Paris Cité-Robert Debré Hospital-Assistance Publique-Hopitaux de Paris-Centre National de la Recherche Scientifique ( CNRS ), Aix Marseille Université ( AMU ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Génétique des Anomalies du Développement ( GAD ), IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne ( UB ), Hôpital de la Timone [CHU - APHM] ( TIMONE ), Centre Européen de Recherche en Imagerie médicale ( CERIMED ), Aix Marseille Université ( AMU ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Ecole Centrale de Marseille ( ECM ) -Institut Paoli-Calmettes-Centre National de la Recherche Scientifique ( CNRS ), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Aix Marseille Université ( AMU ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Aix Marseille Université ( AMU ), Assistance Publique - Hôpitaux de Marseille ( APHM ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ), Origine, structure et évolution de la biodiversité, Centre National de la Recherche Scientifique ( CNRS ), Duke university [Durham], UCL - SSS/IREC/PEDI - Pôle de Pédiatrie, UCL - SSS/IREC/GAEN - Pôle d'Hépato-gastro-entérologie, UCL - (SLuc) Service d'anatomie pathologique, UCL - (SLuc) Service de gastro-entérologie et hépatologie pédiatrique, Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité-AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance Publique-Hopitaux de Paris-Centre National de la Recherche Scientifique (CNRS), IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne (UB), Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU), and Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)
Subjects: 0301 basic medicine, Diarrhea, Male, Candidate gene, Adolescent, Bone fragility, Article, Bone and Bones, 03 medical and health sciences, Young Adult, Cholestasis, Loss of Function Mutation, GCUNC-45, Myosin, Genetics, Medicine, Animals, Humans, Family, Lymphocytes, [ SDV.GEN.GH ] Life Sciences [q-bio]/Genetics/Human genetics, Hearing Loss, Gene, Genetics (clinical), Loss function, Zebrafish, business.industry, Infant, Newborn, Intracellular Signaling Peptides and Proteins, Syndrome, Fibroblasts, medicine.disease, 3. Good health, Pedigree, 030104 developmental biology, Phenotype, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Concomitant, Child, Preschool, Immunology, Female, medicine.symptom, business, Gastrointestinal Motility
Abstract: International audience; Despite the rapid discovery of genes for rare genetic disorders, we continue to encounter individuals presenting with syndromic manifestations. Here, we have studied four affected people in three families presenting with cholestasis, congenital diarrhea, impaired hearing, and bone fragility. Whole-exome sequencing of all affected individuals and their parents identified biallelic mutations in Unc-45 Myosin Chaperone A (UNC45A) as a likely driver for this disorder. Subsequent in vitro and in vivo functional studies of the candidate gene indicated a loss-of-function paradigm, wherein mutations attenuated or abolished protein activity with concomitant defects in gut development and function.
Published: 2018

33. Differential influences of allometry, phylogeny and environment on the rostral shape diversity of extinct South American notoungulates

Author: Bhart-Anjan S. Bhullar, Raphaël Cornette, Julien Clavel, Marcos Fernández-Monescillo, Karen Moreno, Guillaume Billet, Anthony Herrel, Helder Gomes Rodrigues, Guillermo Hernán Cassini, Centre de Recherche en Paléontologie - Paris (CR2P), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional de Luján [Buenos Aires], Glaciología y Ciencias Ambientales (IANIGLA), Instituto de Geociencias [Valdivia], Universidad Austral de Chile, Evolutionary Morphology of Vertebrates, Universiteit Gent = Ghent University [Belgium] (UGENT), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), and Mécanismes Adaptatifs et Evolution (MECADEV)
Subjects: convergences, 0106 biological sciences, 010506 paleontology, GEOMETRIC MORPHOMETRICS, masticatory apparatus, evolutionary rates, media_common.quotation_subject, adaptation, Biology, 010603 evolutionary biology, 01 natural sciences, Paleontología, Ciencias de la Tierra y relacionadas con el Medio Ambiente, purl.org/becyt/ford/1 [https], purl.org/becyt/ford/1.5 [https], Phylogenetics, mammals, geometric morphometrics, lcsh:Science, Clade, ADAPTATION, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, media_common, CONVERGENCES, Multidisciplinary, Dentition, Phylogenetic tree, EVOLUTIONARY RATES, Biology (Whole Organism), Evolutionary biology, South american, MAMMALS, MASTICATORY APPARATUS, [SDE]Environmental Sciences, lcsh:Q, Allometry, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, CIENCIAS NATURALES Y EXACTAS, Research Article, Diversity (politics)
Abstract: Understanding the mechanisms responsible for phenotypic diversification, and the associated underlying constraints and ecological factors represents a central issue in evolutionary biology. Mammals present a wide variety of sizes and shapes, and are characterized by a high number of morphological convergences that are hypothesized to reflect similar environmental pressures. Extinct South American notoungulates evolved in isolation from northern mammalian faunas in highly disparate environments. They present a wide array of skeletal phenotypes and convergences, such as ever-growing dentition. Here, we focused on the origins of the rostral diversity of notoungulates by quantifying the shape of 26 genera using three-dimensional geometric morphometric analysis. We tested the influence of allometry and phylogeny on rostral shape and evaluated rates of evolutionary change in the different clades. We found strong allometric and phylogenetic signals concerning the rostral shape of notoungulates. Despite convergent forms, we observed a diffuse diversification of rostral shape, with no significant evidence of influence by large-scaled environmental variation. This contrasts with the increase in dental crown height that occurred in four late-diverging families in response to similar environmental pressures. These results illustrate the importance of considering both biological components and evolutionary rates to better understand some aspects of phenotypic diversity. Fil: Gomes Rodrigues, Helder. Muséum National d'Histoire Naturelle; Francia. Centre National de la Recherche Scientifique; Francia Fil: Cornette, Raphaël. Centre National de la Recherche Scientifique; Francia. Muséum National d'Histoire Naturelle; Francia Fil: Clavel, Julien. Ecole Normale Supérieure; Francia. Centre National de la Recherche Scientifique; Francia Fil: Cassini, Guillermo Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Argentina. Universidad Nacional de Luján. Departamento de Ciencias Básicas; Argentina Fil: Bhullar, Bhart-Anjan S. . University of Yale; Estados Unidos Fil: Fernández-Monescillo, Marcos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; Argentina Fil: Moreno, Karen. Universidad Austral de Chile. Instituto de Ciencias de la Tierra; Chile Fil: Herrel, Anthony. Centre National de la Recherche Scientifique; Francia. Muséum National d'Histoire Naturelle; Francia Fil: Billet, Guillaume. Muséum National d'Histoire Naturelle; Francia. Centre National de la Recherche Scientifique; Francia
Published: 2018

34. How the environment shapes animal signals: a test of the acoustic adaptation hypothesis in frogs

Author: Alain Dubois, Rafael Márquez, J.M. Dehling, S.D. Howard, Frédéric Legendre, Jodi J. L. Rowley, Philippe Grandcolas, R.C. Xiong, Sandra Goutte, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), National University of Singapore (NUS), Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Australian Museum Research Institute (AMRI), Australian Museum [Sydney], Universität Koblenz-Landau [Koblenz], and Ministerio de Ciencia e Innovación (España)
Subjects: 0106 biological sciences, 0301 basic medicine, Microhylidae, Bioacoustics, [SDV]Life Sciences [q-bio], Environment, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Animals, Animal communication, Signal evolution, Rhacophoridae, Phylogeny, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Dicroglossidae, biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Anuran, Noisy environments, Phylogenetic comparative methods, biology.organism_classification, Adaptation, Physiological, 030104 developmental biology, Habitat, Anura, Vocalization, Animal, Adaptation
Abstract: Long-distance acoustic signals are widely used in animal communication systems and, in many cases, are essential for reproduction. The acoustic adaptation hypothesis (AAH) implies that acoustic signals should be selected for further transmission and better content integrity under the acoustic constraints of the habitat in which they are produced. In this study, we test predictions derived from the AAH in frogs. Specifically, we focus on the difference between torrent frogs and frogs calling in less noisy habitats. Torrents produce sounds that can mask frog vocalizations and constitute a major acoustic constraint on call evolution. We combine data collected in the field, material from scientific collections and the literature for a total of 79 primarily Asian species, of the families Ranidae, Rhacophoridae, Dicroglossidae and Microhylidae. Using phylogenetic comparative methods and including morphological and environmental potential confounding factors, we investigate putatively adaptive call features in torrent frogs. We use broad habitat categories as well as fine-scale habitat measurements and test their correlation with six call characteristics. We find mixed support for the AAH. Spectral features of torrent frog calls are different from those of frogs calling in other habitats and are related to ambient noise levels, as predicted by the AAH. However, temporal call features do not seem to be shaped by the frogs’ calling habitats. Our results underline both the complexity of call evolution and the need to consider multiple factors when investigating this issue., This project was supported by internal grants: the Ministerio de Ciencia e Innovacion, Spain (projects TATANKA CGL2011-25062, CGL2010-09700), and the Ministerio de Economia y Competitividad, Spain (project CGL2011-16159-E; PI. R. Marquez).
Published: 2018

35. Diagnostic Yield of Next-Generation Sequencing in Very Early-Onset Inflammatory Bowel Diseases: A Multicenter Study

Author: Charbit-Henrion, Fabienne, Parlato, Marianna, Hanein, Sylvain, Duclaux-Loras, Rémi, Nowak, Jan, Begue, Bernadette, Rakotobe, Sabine, Bruneau, Julie, Fourrage, Cécile, Alibeu, Olivier, Rieux-Laucat, Frédéric, Lévy, Eva, Stolzenberg, Marie-Claude, Mazerolles, Fabienne, Latour, Sylvain, Lenoir, Christelle, Fischer, Alain, Picard, Capucine, Aloi, Marina, Amil Dias, Jorge, Ben Hariz, Mongi, Bourrier, Anne, Breuer, Christian, Breton, Anne, Bronski, Jiri, Buderus, Stephan, Cananzi, Mara, Coopman, Stéphanie, Crémilleux, Clara, Dabadie, Alain, Dumant-Forest, Clémentine, Egritas Gurkan, Odul, Fabre, Alexandre, Fischer, Aude, German Diaz, Marta, Gonzalez-Lama, Yago, Goulet, Olivier, Guariso, Graziella, Gurcan, Neslihan, Homan, Matjaz, Hugot, Jean-Pierre, Jeziorski, Eric, Karanika, Evi, Lachaux, Alain, Lewindon, Peter, Lima, Rosa, Magro, Fernando, Major, Janos, Malamut, Georgia, Mas, Emmanuel, Mattyus, Istvan, Mearin, Luisa M., Melek, Jan, Navas-Lopez, Victor Manuel, Paerregaard, Anders, Pelatan, Cecile, Pigneur, Bénédicte, Pinto Pais, Isabel, Rebeuh, Julie, Romano, Claudio, Siala, Nadia, Strisciuglio, Caterina, Tempia-Caliera, Michela, Tounian, Patrick, Turner, Dan, Urbonas, Vaidotas, Willot, Stéphanie, Ruemmele, Frank M., Cerf-Bensussan, Nadine, Laboratory of Intestinal Immunity (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Gastroentérologie, d'hépatologie et nutrition pédiatrique [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), GENIUS Group, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Pathology, University of Alabama at Birmingham [ Birmingham] (UAB), Université Paris Descartes - Paris 5 (UPD5), Service de pathologie [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), The Clinical Bioinformatics laboratory (Equipe Inserm U1163), Immunogenetics of pediatric autoimmune diseases (Equipe Inserm U1163), Immunité et cancer (U932), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Service d'immuno-hématologie pédiatrique [CHU Necker], Université Sorbonne Paris Cité (USPC), Chaire Médecine expérimentale (A. Fischer), Collège de France (CdF (institution)), Service de Gastroentérologie et nutrition [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Gastro-entérologie, Hépatologie, Nutrition, Diabétologie, Hôpital des Enfants, CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], Unité Pédiatrique [Jeanne de Flandre], Hôpital Jeanne de Flandre [Lille], CHU Pontchaillou [Rennes], Service de pédiatrie médicale et médecine de l'adolescent [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Hospices Civils de Lyon (HCL), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National de la Recherche Agronomique (INRA), Hospital de São João [Porto], Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Unité de Gastroentérologie, Hépatologie, Nutrition, Diabétologie et Maladies Héréditaires du Métabolisme, Centre Hospitalier Universitaire de Toulouse, Institut de Recherche en Santé Digestive (IRSD ), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Le Mans (CH Le Mans), University of Messina, Department of Pediatrics, Centre Hospitalier Universitaire Mongi Slim [La Marsa], CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Sorbonne Université (SU), CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), This work was supported by ERC-2013-AdG-339407-IMMUNOBIOTA, Investissement d’Avenir ANR-10-IAHU-01, Fondation des Maladies Rares, and Association François Aupetit. FC-H was supported by a fellowship from INSERM. JN received a fellowship from the Polish National Science Centre [2015/16/T/NZ5/00168]., The authors acknowledge the use of the bioresources of the Necker Imagine DNA biobank [BB-033-00065]. They are grateful to the members of the Department of Clinical Research of the Imagine Institute, headed by Elisabeth Hullier-Ammar, for their guidance with ethical procedures, and to Pauline Touche for her help with the Immunobiota protocol., ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), European Project: 339407,EC:FP7:ERC,ERC-2013-ADG,IMMUNOBIOTA(2014), roussel, pascale, Instituts Hospitalo-Universitaires - Institut Hospitalo-Universitaire Imagine - - Imagine2010 - ANR-10-IAHU-0001 - IAHU - VALID, Host-microbiota interactions across the gut immune system:lessons from early onset inflammatory bowel diseases and from gnotobiotic mice - IMMUNOBIOTA - - EC:FP7:ERC2014-03-01 - 2019-02-28 - 339407 - VALID, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Collège de France - Chaire Médecine expérimentale (A. Fischer), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service Diabétologie [CHU Toulouse], Pôle Cardiovasculaire et Métabolique [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Gastroentérologie et pancréatologie [CHU Toulouse], Pôle Maladies de l'appareil digestif [CHU Toulouse], Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Necker - Enfants Malades [AP-HP], Université Paris Descartes - Paris 5 (UPD5)-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Collège de France (CDF), Collège de France (CdF), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Saint-Antoine [APHP], Institut de Recherche juridique sur l'Entreprise et les Relations Professionnelles (IRERP), Université Paris Nanterre (UPN), Origine, structure et évolution de la biodiversité, Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), CHU Le MAns, ANR-10-IAHU-0001/10-IAHU-0001,Imagine,Imagine(2010), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Institut Curie-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: [SDV] Life Sciences [q-bio], paediatrics, VEO-IBD, [SDV]Life Sciences [q-bio], TNGS, Genetics and molecular epidemiology, monogenic disorders
Abstract: International audience; Background and Aims: An expanding number of monogenic defects have been identified as causative of severe forms of very early-onset inflammatory bowel diseases (VEO-IBD). The present study aimed at defining how next-generation sequencing (NGS) methods can be used to improve identification of known molecular diagnosis and adapt treatment. Methods: 207 children were recruited in 45 Paediatric centres through an international collaborative network (ESPGHAN GENIUS working group) with a clinical presentation of severe VEO-IBD (n=185) or an anamnesis suggestive of a monogenic disorder (n=22). Patients were divided at inclusion into three phenotypic subsets: predominantly small bowel inflammation, colitis with perianal lesions, and colitis only. Methods to obtain molecular diagnosis included functional tests followed by specific Sanger sequencing, custom-made targeted NGS, and in selected cases whole exome sequencing (WES) of parents-child trios. Genetic findings were validated clinically and/or functionally. Results: Molecular diagnosis was achieved in 66/207 children (32%): 61% with small bowel inflammation, 39% with colitis and perianal lesions and 18% with colitis only. Targeted NGS pinpointed gene mutations causative of atypical presentations and identified large exonic copy number variations previously missed by WES. Conclusions: Our results lead us to propose an optimised diagnostic strategy to identify known monogenic causes of severe IBD.
Published: 2018

36. Preliminary study of the rodent assemblages of Goda Buticha : new insights on Late Quaternary environmental and cultural changes in southeastern Ethiopia

Author: Asfawossen Asrat, David Pleurdeau, Emmanuel Desclaux, Christiane Denys, Workalemahu Bekele Sime, Zelalem Assefa, Emmanuelle Stoetzel, Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), Addis Ababa University (AAU), National Museum of Natural History, Washington, DC 20008, USA., Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Muséum national d'Histoire naturelle (MNHN), Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Gratification de Master 2 LabEx BCDiv, ANR-14-CE31-0023,Big Dry,Ruptures et continuité dans le peuplement de l'Afrique à la fin du Pléistocène : paléoanthropologie, paléoenvironnement et archéologies comparées du Rift et du Nil dans leur cadre continental(2014), ANR-10-LABX-0003,BCDiv,Biological and Cultural Diversities : Origins, Evolution, Interactions, Future(2010), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD), Institut de Paléontologie Humaine (IPH), Fondation I.P.H-Centre National de la Recherche Scientifique (CNRS), Laboratoire Départemental de Préhistoire du Lazaret (LDPL), Département des Alpes-Maritimes, Origine, structure et évolution de la biodiversité (OSEB), and Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)
Subjects: 0106 biological sciences, 010506 paleontology, geography, Taphonomy, geography.geographical_feature_category, Environmental change, Later Stone Age, Pleistocene, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Archaeology, Cave, Period (geology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Quaternary, Holocene, Geology, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Earth-Surface Processes
Abstract: International audience; Given its proximity to the Strait of Bab el Mandeb and the Red Sea, the Horn of Africa is particularly important for understanding human and faunal migration events to and from Africa. Towards the end of the Pleistocene, the Middle/Later Stone Age (MSA/LSA) transition represents a critical step in human cultural evolution. However, in the Horn of Africa, the environmental conditions associated with this transition remain poorly understood. The Goda Buticha (Buticha cave) sequence, located in southeastern Ethiopia, and dated from ca. 63 ka cal BP to ca. 1 ka cal BP, provides a rare opportunity to examine the environmental contexts associated with major cultural sequences documented in the region during this time period. A preliminary analysis of the rich microvertebrate (and especially rodent) remains recovered from the levels dated between 43 and 4 ka BP identified fourteen different rodent genera, including two species that are locally extinct in southeastern Ethiopia today. While the taphonomic signature is similar throughout the sequence, indicating an in situ accumulation by an owl without major perturbation, the palaeoecological analysis showed environmental change through time, characterized by open-dry setting during the Late Pleistocene, shifting to wetter and more wooded conditions heading to the Holocene. These results are generally consistent with other diverse records which include the large mammals, speleothems and lake basins records, and allow a better understanding of the dynamics of environmental contexts associated with observed cultural change and continuity in eastern Africa from the Late Pleistocene to Late Holocene.
Published: 2018

37. Combined Immunodeficiency in Patients With Trichohepatoenteric Syndrome

Author: Vély, Frédéric, Barlogis, Vincent, Marinier, Evelyne, Coste, Marie-Edith, Dubern, Béatrice, Dugelay, Emmanuelle, Lemale, Julie, Martinez-Vinson, Christine, Peretti, Noël, Perry, Ariane, Bourgeois, Patrice, Badens, Catherine, Goulet, Olivier, Hugot, Jean-Pierre, Farnarier, Catherine, Fabre, Alexandre, Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service d'hématologie pédiatrique [AP-HM Hôpital de la Timone], Assistance Publique - Hôpitaux de Marseille (APHM)-Université de la Méditerranée - Aix-Marseille 2- Hôpital de la Timone [CHU - APHM] (TIMONE), Department of Pediatric Gastroenterology, Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité-Assistance Publique-Hopitaux de Paris-AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Service de pédiatrie multidisciplinaire [Hôpital de la Timone Enfants - APHM], Hôpital de la Timone [CHU - APHM] (TIMONE), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de gastroentérologie et nutrition pédiatrique, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de référence maladie rare Thalassémie, Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Descartes - Paris 5 (UPD5), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Hôpital de la Conception [CHU - APHM] (LA CONCEPTION), Institut National de la Sante et de la Recherche Medicale, Centre National de la Recherche Scientifique, Aix-Marseille Universite, French National Research Agency (ANR THE-RNA), ANR-15-CE17-0017,THE-RNA,Syndrome tricho-hépato-entérique des anomalies de la dégradation des ARN à un syndrome(2015), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité-Robert Debré Hospital-Assistance Publique-Hopitaux de Paris-Centre National de la Recherche Scientifique (CNRS), Gastroentérologie et Nutrition Pédiatrique, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institute of Cardiometabolism and Nutrition-CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Origine, structure et évolution de la biodiversité, Centre National de la Recherche Scientifique (CNRS), Hôpital de la Conception [CHU - APHM] (LA CONCEPTION ), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité-AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance Publique-Hopitaux de Paris-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: T-Lymphocytes, Immunology, diarrhée, Case Report, NK cells, Cohort Studies, Interferon-gamma, memory B cells, syndromic diarrhea/trichohepatoenteric syndrome, Humans, Lymphocyte Count, t cells, sKIV2L, SKIV2L, TTC37, immunodeficiency, T cells, B-Lymphocytes, Fetal Growth Retardation, immunodéficience, DNA Helicases, Immunologic Deficiency Syndromes, Infant, Newborn, Facies, Infant, Killer Cells, Natural, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Diarrhea, Infantile, Mutation, ttC37, Carrier Proteins, Hair Diseases, Immunologic Memory
Abstract: International audience; The syndromic diarrhea/trichohepatoenteric syndrome (SD/THE) is a rare and multi-system genetic disorder caused by mutation in SKIV2L or in TTC37, two genes encoding subunits of the putative human SKI complex involved in RNA degradation. The main features are intractable diarrhea of infancy, hair abnormalities, facial dysmorphism, and intrauterine growth restriction. Immunologically this syndrome is associated with a hypogammaglobulinemia leading to an immunoglobulin supplementation. Our immune evaluation of a large French cohort of SD/THE patient revealed several immunological defects. First, switched memory B lymphocytes count is very low. Second, IFN-gamma production by T and NK cells is impaired and associated with a reduced degranulation of NK cells. Third, T cell proliferation was abnormal in 3/6 TTC37-mutated patients. These three patients present with severe EBV infection and a transient hemophagocytosis which may be related to these immunological defects. Moreover, an immunological screening of patients with clinical features of SD/THE could facilitate both diagnosis and therapeutic management of these patients.
Published: 2018

38. Comparative morphology of snake (Squamata) endocasts: evidence of phylogenetic and ecological signals

Author: Rémi Allemand, Renaud Boistel, Peggy Vincent, Nathalie Bardet, Alexandra Houssaye, Gheylen Daghfous, Zoé Blanchet, Raphaël Cornette, Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut International de Paléoprimatologie, Paléontologie Humaine : Evolution et Paléoenvironnement (IPHEP), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), Agence Nationale de la Recherche under the LabEx ANR-10-LABX-0003-BCDiv, in the program ‘Investissements d’avenir’ ANR-11-IDEX-0004-02., ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011), ANR-10-LABX-0003,BCDiv,Biological and Cultural Diversities : Origins, Evolution, Interactions, Future(2010), Département Adaptations du vivant (AVIV), Muséum national d'Histoire naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers, Allemand, Rémi, Sorbonne Universités à Paris pour l'Enseignement et la Recherche - - SUPER2011 - ANR-11-IDEX-0004 - IDEX - VALID, and Biological and Cultural Diversities : Origins, Evolution, Interactions, Future - - BCDiv2010 - ANR-10-LABX-0003 - LABX - VALID
Subjects: 0106 biological sciences, 0301 basic medicine, Histology, Squamata, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Zoology, Morphology (biology), Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Phylogenetics, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, medicine, Animals, brain endocast, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, Phylogenetic tree, morphometrics, Ecology, Fossorial, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Brain, computed tomography, Cell Biology, Original Articles, biology.organism_classification, snakes, Anatomy, Comparative, 030104 developmental biology, medicine.anatomical_structure, squamates, Mammal, [SDV.BA.ZV] Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Anatomy, Tomography, X-Ray Computed, Endocast, sensory information, Developmental Biology, Neuroanatomy, ecological signal
Abstract: International audience; Brain endocasts obtained from computed tomography (CT) are now widely used in the field of comparative neuroanatomy. They provide an overview of the morphology of the brain and associated tissues located in the cranial cavity. Through anatomical comparisons between species, insights on the senses, the behavior, and the lifestyle can be gained. Although there are many studies dealing with mammal and bird endocasts, those performed on the brain endocasts of squamates are comparatively rare, thus limiting our understanding of their morphological variability and interpretations. Here, we provide the first comparative study of snake brain endocasts in order to bring new information about the morphology of these structures. Additionally, we test if the snake brain endocast encompasses a phylogenetic and/or an ecological signal. For this purpose, the digital endocasts of 45 snake specimens, including a wide diversity in terms of phylogeny and ecology, were digitized using CT, and compared both qualitatively and quantitatively. Snake endocasts exhibit a great variability. The different methods performed from descriptive characters, linear measurements and the outline curves provided complementary information. All these methods have shown that the shape of the snake brain endocast contains, as in mammals and birds, a phylogenetic signal but also an ecological one. Although phylogenetically related taxa share several similarities between each other, the brain endocast morphology reflects some notable ecological trends: e.g. (i) fossorial species possess both reduced optic tectum and pituitary gland; (ii) both fossorial and marine species have cerebral hemispheres poorly developed laterally; (iii) cerebral hemispheres and optic tectum are more developed in arboreal and terrestrial species.
Published: 2017

39. Influences on the stable oxygen and carbon isotopes in gerbillid rodent teeth in semi-arid and arid environments: Implications for past climate and environmental reconstruction

Author: Christiane Denys, Emmanuelle Stoetzel, Amy Jeffrey, Julia A. Lee-Thorp, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), University of Oxford [Oxford], RHOI (NSF) project, NERC training grant NE/K500811/1, Boise Trust Fund, St Cross College, ANR-09-PEXT-0004,Mohmie,Influence de l'installation des hommes modernes au Maroc sur l'évolution de la biodiversité des petits vertébrés terrestres(2009), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), and Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)
Subjects: [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Ecology, Stable isotope ratio, fungi, 15. Life on land, Gerbil, Arid, Isotopes of oxygen, stomatognathic diseases, Paleontology, Geophysics, stomatognathic system, 13. Climate action, Space and Planetary Science, Geochemistry and Petrology, Isotopes of carbon, parasitic diseases, Earth and Planetary Sciences (miscellaneous), Meteoric water, Precipitation, Quaternary, ComputingMilieux_MISCELLANEOUS, Geology
Abstract: The stable isotope composition of small mammal tissues has the potential to provide detailed information about terrestrial palaeoclimate and environments, because their remains are abundant in palaeontological and archaeological sites, and they have restricted home ranges. Applications to the Quaternary record, however, have been sparse and limited by an acute lack of understanding of small mammal isotope ecology, particularly in arid and semi-arid environments. Here we document the oxygen and carbon isotope composition of Gerbillinae (gerbil) tooth apatite across a rainfall gradient in northwestern Africa, in order to test the relative influences of the 18O/16O in precipitation or moisture availability on gerbil teeth values, the sensitivity of tooth apatite 13C/12C to plant responses to moisture availability, and the influence of developmental period on the isotopic composition of gerbil molars and incisors. The results show that the isotopic composition of molars and incisors from the same individuals differs consistent with the different temporal periods reflected by the teeth; molar teeth are permanently rooted and form around the time of birth, whereas incisors grow continuously. The results indicate that tooth choice is an important consideration for applications as proxy Quaternary records, but also highlights a new potential means to distinguish seasonal contexts. The oxygen isotope composition of gerbil tooth apatite is strongly correlated with mean annual precipitation (MAP) below 600 mm, but above 600 mm the teeth reflect the oxygen isotope composition of local meteoric water instead. Predictably, the carbon isotope composition of the gerbil teeth reflected C3 and C4 dietary inputs, however arid and mesic sites could not be distinguished because of the high variability displayed in the carbon isotope composition of the teeth due to the microhabitat and short temporal period reflected by the gerbil. We show that the oxygen isotope composition of small mammal teeth strongly reflects moisture availability in semi-arid and arid environments and would provide an excellent record of palaeo-aridity in a terrestrial setting. The results illustrate that an understanding of an animal's physiology is essential for interpreting the animal's isotopic responses to external contexts, especially in arid zones.
Published: 2015

40. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

Author: Sabine Rüsch-Gerdes, Hans P eter Beck, Vladyslav Nikolayevskyy, Irina Kontsevaya, Petras Stakenas, Kadri Toit, Shinji Maeda, Eman Aleksic, Marie Ballif, Stefano Mona, Troels Lillebaek, Maryline Bonnet, Caroline Allix-Béguec, Sophie Lecher, Robin M. Warren, Isdore Chola Shamputa, Francesca Barletta, Isolina Campos-Herrero, Wei wei Jiao, Thomas Kohl, Suzanne M. Crowe, Ewa Augustynowicz-Kopeć, Solomon Ghebremichael, Branislava Savic, Francis Varaine, Dragana Vuković, Camille Blin, Annick Antierens, Li Hwei Sng, Maryse Fauville-Dufaux, Céline Wahl, Thierry Wirth, Stefan Niemann, Eve Willery, Helen Cox, Valeriu Crudu, Emanuele Borroni, Sebastien Gagneux, Philip Supply, Sven Hoffner, Adong Shen, Stobdan Kalon, Michael Rasmussen, Francis Drobniewski, Igor Mokrousov, Michael G. B. Blum, Madeleine Hanekom, Sofía Samper, Matthias Merker, Clifton E. Barry, Nicolas Duforet-Frebourg, Roland Diel, Nalin Rastogi, Daniela Maria Cirillo, Elisabeth Sanchez-Padilla, Molecular Mycobacteriology, Research Center Borstel - Leibniz Lung Center [Germany], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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 Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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 d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), National Reference Center for Mycobacteria, Institut Pasteur de Saint-Pétersbourg, Réseau International des Instituts Pasteur (RIIP), Centre for Biomedical Research, Burnet Institute [Melbourne, Victoria], genoscreen, GenoScreen, Medical Department, Médecins sans Frontières [Genève] (MSF), Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Institute of Social and Preventive Medicine, Universität Bern [Bern] (UNIBE), Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit–Tuberculosis, Instituto de Medicina Tropical 'Alexander von Humboldt' (IMT AvH), Universidad Peruana Cayetano Heredia (UPCH)-Universidad Peruana Cayetano Heredia (UPCH), Medical Parasitology and Infection Biology [Basel, Suisse] (MPI), Swiss Tropical and Public Health Institute [Basel], Laboratoire de Recherche en Informatique d'Amiens (LaRIA), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Epicentre [Paris] [Médecins Sans Frontières], Emerging Bacterial Pathogen Unit, San Raffaele Scientific Institute, hospital Universitario de Gran Canaria Dr Negrin, Macfarlane Burnet Institute for Medical Research, Laboratoire Jean Alexandre Dieudonné (LJAD), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), PHE National Mycobacterial Reference Laboratory and Clinical TB and HIV Group, Queen Mary's School of Medicine and Dentistry, Division of Infectious Diseases, Imperial College London, Centre national de Référence et Laboratoire Tuberculose et Mycobactéries = National Reference Centre of Tuberculosis and Mycobacteria [Brussels] (CNR), Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), MRC National Institute for Medical Research, Department of Preparedness, Swedish Institute for Infectious Disease Control, Faculty of Medicine and Health Sciences, stellen, Key Laboratory of Major Diseases in Children, Beijing Children's Hospital affiliated to Capital Medical University-Beijing Pediatric Research Institute-Chine - Ministry of Education, Samara Oblast TB Service, Research institute of Tuberculosis, Anti-tuberculosis Association, Institut Pasteur de la Guadeloupe, LAboratoire de Recherche en Mécanique Appliquée (LARMAUR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Microbiology Unit, Tropical Diseases Research Centre [Zambia] (TDRC), Alcatel-Thalès III-V lab (III-V Lab), THALES [France]-ALCATEL, Central Tuberculosis Laboratory, Singapore General Hospital, Medecins Sans Frontieres (Medecins Sans Frontieres), Médecins Sans Frontières, DTU Fotonik - Department of Photonics Engineering, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), molecular biology and human genetics, Stell, Molecular Mycobacteriology Group, National Reference Center for Mycobacyeria, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), We acknowledge J. Peh for her assistance and support in the study andI. Comas for statistical advice. Parts of this work have been supported by grantsfrom the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement 278864 in the framework of the European UnionPathoNGenTrace project and grant agreement 223681 in the framework of theTB-PAN-NET project. We also thank Action Transversale du Muséum Nationald’Histoire Naturelle ‘Les Microorganismes, Acteurs Clés dans les Ecosystèmes’for financial support, European Project: 223681,EC:FP7:HEALTH,FP7-HEALTH-2007-B,TB PAN-NET(2009), European Project: 278864,FP7/2007- 2013, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Universität Bern [Bern], Laboratoire Jean Alexandre Dieudonné (JAD), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), THALES-ALCATEL, and Technical University of Denmark [Lyngby] (DTU)
Subjects: Tuberculosis, Lineage (genetic), MESH: Mutation, MESH: Mycobacterium tuberculosis, Genotype, MESH: Biological Evolution, MESH: Global Health, Biology, MESH: Genome, Bacterial, Global Health, Genetic analysis, Mycobacterium tuberculosis, MESH: Genotype, Evolution, Molecular, Phylogenetics, Tuberculosis, Multidrug-Resistant, Genetics, Global health, medicine, Humans, MESH: Phylogeny, MESH: Evolution, Molecular, MESH: Tuberculosis, Multidrug-Resistant, Phylogeny, MESH: Humans, Ecology, Population size, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Biological Evolution, 3. Good health, Mycobacterium tuberculosis/classification/genetics/isolation & purification, Evolutionary biology, Mutation, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Tuberculosis, Multidrug-Resistant/epidemiology/microbiology, Genome, Bacterial, purl.org/pe-repo/ocde/ford#1.06.07 [https]
Abstract: International audience; Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.
Published: 2015
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41. Nomenclatural puzzle in early Xenophrys nomina (Anura, Megophryidae) solved with description of two new species from India (Darjeeling hills and Sikkim)

Author: Deuti, Kaushik, Grosjean, Stéphane, Nicolas, Violaine, Vasudevan, Karthikeyan, Ohler, Annemarie, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2017

42. Systematics and evolution of the Meriones shawii/grandis complex (Rodentia, Gerbillinae) during the Late Quaternary in northwestern Africa: Exploring the role of environmental and anthropogenic changes

Author: Aude Lalis, Raphaël Cornette, Christiane Denys, Violaine Nicolas, Thomas Cucchi, Emmanuelle Stoetzel, Département Systématique et Évolution, Muséum National d'Histoire Naturelle ( MNHN ), Plate-forme de morphométrie, Mammifères et Oiseaux - MNHN ( UMR5202 ), Centre de recherche d'histoire quantitative ( CRHQ ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ), Archéozoologie et histoire des sociétés ( AHS ), Centre National de la Recherche Scientifique ( CNRS ), Origine, structure et évolution de la biodiversité ( OSEB ), Muséum National d'Histoire Naturelle ( MNHN ) -Centre National de la Recherche Scientifique ( CNRS ), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), SYNTHESYS - Synthesis of systematic resources (2013) - FP7 'Capacities' Program, Allocation Post-doctorale LabEx BCDiv, ANR-09-PEXT-0004,Mohmie,Influence de l'installation des hommes modernes au Maroc sur l'évolution de la biodiversité des petits vertébrés terrestres(2009), ANR-10-LABX-0003,BCDiv,Biological and Cultural Diversities : Origins, Evolution, Interactions, Future(2010), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Ecological niche, Systematics, 010506 paleontology, Archeology, Global and Planetary Change, Pleistocene, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Ecology, Geology, Anthropization, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, [ SHS.ARCHEO ] Humanities and Social Sciences/Archaeology and Prehistory, Interglacial, Biological dispersal, Quaternary, Ecology, Evolution, Behavior and Systematics, Holocene, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: Rodents of the Meriones shawii/grandis complex have been attested to in North Africa since the Middle Pleistocene and are abundant in archaeological sites. Today, they are widely spread and represent a major pest to local human populations. This complex, therefore, represents an accurate model for investigating the roles of climate change and human impact in shaping Quaternary faunal diversity and distribution. Many gray areas still exist regarding the systematics, ecology and geographical distribution of this complex, for both present and past populations. The purpose of this study is to compare modern genotyped and fossil Meriones specimens in order to 1) clarify the current systematics and distribution of the Meriones populations of the shawii/grandis complex, 2) document the taxonomic diversity in fossil Meriones from northwestern Africa, and 3) track their phenotypic and biogeographic evolution through time. To answer these questions we used geometric morphometrics on skulls (landmarks) and first upper molars (landmarks and sliding landmarks). We evidenced the existence of two morpho-groups within the M. shawii/grandis complex, with a clear geographic pattern ( M. grandis in Morocco vs. M. shawii in Algeria and Tunisia). Currently only one morpho-group, attributed to M. grandis , seems to exist in Morocco, with a small overlap with M. shawii in the most eastern part of the country. However, according to fossil data, M. shawii was also present in Atlantic Morocco during the Late Pleistocene. We have also highlighted the impact of Holocene climate change and habitat anthropization on this arid adapted group. During the Middle Holocene, a major climatic event (last interglacial optimum) seems to have induced a demographic collapse in Moroccan populations and the disappearance of the shawii clade from Morocco (except in the most eastern areas). Both species then re-expanded, benefitting from the increasing aridity and the new ecological niche driven by agriculture dispersal from the Neolithic onwards.
Published: 2017

43. Can species distribution models really predict the expansion of invasive species?

Author: Morgane Barbet-Massin, Claire Villemant, Quentin Rome, Franck Courchamp, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Office français de la biodiversité (OFB), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre de Recherches sur la Biologie des Populations d'Oiseaux (CRBPO ), Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, China, Atmospheric Science, Conservation Biology, Range (biology), Climate, Climate Change, Species distribution, Wasps, Biodiversity, lcsh:Medicine, Invasive Species, Introduced species, Biology, 010603 evolutionary biology, 01 natural sciences, Models, Biological, Invasive species, Geographical Locations, Species Colonization, Genetics, Animals, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Conservation Science, Ecological niche, Climatology, Multidisciplinary, Ecology, 010604 marine biology & hydrobiology, lcsh:R, Ecology and Environmental Sciences, Biology and Life Sciences, Europe, [SDE]Environmental Sciences, People and Places, Earth Sciences, Conservation Genetics, Climate model, lcsh:Q, Conservation biology, Ecological Niches, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Introduced Species, Research Article, Climate Modeling
Abstract: International audience; Predictive studies are of paramount importance for biological invasions, one of the biggest threats for biodiversity. To help and better prioritize management strategies, species distribution models (SDMs) are often used to predict the potential invasive range of introduced species. Yet, SDMs have been regularly criticized, due to several strong limitations, such as violating the equilibrium assumption during the invasion process. Unfortunately, validation studies–with independent data–are too scarce to assess the predictive accuracy of SDMs in invasion biology. Yet, biological invasions allow to test SDMs usefulness, by retrospectively assessing whether they would have accurately predicted the latest ranges of invasion. Here, we assess the predictive accuracy of SDMs in predicting the expansion of invasive species. We used temporal occurrence data for the Asian hornet Vespa velutina nigrithorax, a species native to China that is invading Europe with a very fast rate. Specifically, we compared occurrence data from the last stage of invasion (independent validation points) to the climate suitability distribution predicted from models calibrated with data from the early stage of invasion. Despite the invasive species not being at equilibrium yet, the predicted climate suitability of validation points was high. SDMs can thus adequately predict the spread of V. v. nigrithorax, which appears to be—at least partially–climatically driven. In the case of V. v. nigrithorax, SDMs predictive accuracy was slightly but significantly better when models were calibrated with invasive data only, excluding native data. Although more validation studies for other invasion cases are needed to generalize our results, our findings are an important step towards validating the use of SDMs in invasion biology.
Published: 2017

44. The ‘terril’ effect: coal mine spoil tips select for collembolan functional traits in post-mining landscapes of northern France

Author: Sandrine Salmon, Cédric Devigne, Jean-François Ponge, Benoit Vanhee, Alain Leprêtre, Louis Deharveng, Université catholique de Lille (UCL), Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génie Civil et Géo-Environnement (LGCgE) - ULR 4515 (LGCgE), Université d'Artois (UA)-Université de Lille-Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Lille Douai), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), and Origine, structure et évolution de la biodiversité (OSEB)
Subjects: 0106 biological sciences, Soil texture, ved/biology.organism_classification_rank.species, Microclimate, Soil Science, Ecological succession, Biology, Functional diversity, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 010603 evolutionary biology, 01 natural sciences, Shrub, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Coal mine spoil tips, Hauts de France, Ecosystem, Ecology, ved/biology, business.industry, Coal mining, 04 agricultural and veterinary sciences, 15. Life on land, Collembolan communities, Agricultural and Biological Sciences (miscellaneous), Vegetation succession, 040103 agronomy & agriculture, Trait, 0401 agriculture, forestry, and fisheries, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Functional traits
Abstract: International audience; We sampled collembolan communities in 11 coal mine spoil tips (locally called 'terrils') from the North of France, and their surroundings, in various stages of vegetation development (bare soil, herb, shrub and tree vegetation). We wondered whether species, functional trait (Community Weighted Mean trait or CWM) composition and trait diversity (Rao's quadratic entropy) responded to the particular environment of coal mine spoil tips (here called 'terril' effect) and to successional effects and which of these three sets was the best indicator of soil and vegetation effects, taking into account that spoil tips were spatially distant and idiosyncratic (e.g. varying in height, area, past history and surrounding environment). We showed that species, but not traits, were strongly influenced by site effects, while traits were influenced by both 'terril' and successional effects to a significant extent, making traits more robust than species when trying to discern patterns of community response to soil and vegetation changes. Functional diversity did not show any significant multi-trait response to either 'terril' or successional effects, but several functional traits showed an increase in diversity with succession. The overall response of trait diversity was intermediate between species and trait responses. The 'terril' effect was mainly mediated by a coarser soil texture (51% coarse sand compared to 14% in the surrounding environment) which, combined with harsher microclimate conditions, stems in a better representation of functional traits linked to subterranean life, such as shorter body length and increased representation of parthenogenesis. Successional effects (in particular the increase in diversity shown by several functional traits varying with vertical distribution) were mediated by the increasing development of organic horizons but other factors like microclimate were seemingly involved, too. More generally this study showed that shift to subterranean life was an adapted response of collembolan communities to harshness of the environment and that vertically stratified ecosystems allow a more complete expression of their functional diversity.
Published: 2017

45. Rapport d'exécution de marché : La faune des sols des jardins publics de Monaco. Rapport, 84 p

Author: Lemaire, Jean-Michel, Raffaldi, Jean, Deharveng, Louis, Geoffroy, Jean-Jacques, Iorio, Etienne, Judson, Mark, Noël, Franck, Ponel, Philippe, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Association Mayenne-Nature-Environnement, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), and IMBE Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale
Subjects: [SDE]Environmental Sciences
Published: 2017

46. Linking species, traits and habitat characteristics of Collembola at European scale

Author: Sandrine Salmon, Sophie Gachet, Florian Delabrosse, Louis Deharveng, Jean-François Ponge, Noella Lefebvre, Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), Mécanismes adaptatifs : des organismes aux communautés (MAOAC), Muséum national d'Histoire naturelle (MNHN)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Muséum national d'Histoire naturelle (MNHN), Poitou-Charentes Nature, Poitou-Charentes Nature (PCN), and Vienne Nature
Subjects: 0106 biological sciences, Gradient analysis, media_common.quotation_subject, Species distribution, Soil Science, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Biology, 010603 evolutionary biology, 01 natural sciences, Microbiology, Broad scale distribution, Competition (biology), Species assemblages, Canonical correspondence analysis, media_common, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Edaphic, 04 agricultural and veterinary sciences, 15. Life on land, Habitats, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Habitat, 040103 agronomy & agriculture, Trait, Collembola, 0401 agriculture, forestry, and fisheries, Species traits, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental filtering
Abstract: International audience; Although much work has been done on factors which influence the patterning of species and species trait assemblages in a variety of groups such as plants, vertebrates and invertebrates, few studies have been realized at a broad geographic scale. We analyzed patterns of relationships between species, species trait distribution/assembly, and environmental variables from the west of Europe to Slovakia, Poland and Sweden. We created a database by compiling traits and occurrence data of European collembolan species, using literature and personal field studies embracing a large range of environmental gradients (vertical stratification, habitat closure, humus form, soil acidity and moisture, temperature, rainfall, altitude) over which Collembola are supposed to be distributed. Occurrences of the 58 best-documented species, environmental variables and species traits allowed us to (i) show which environmental variables impact the distribution of the 58 species at broad scale and (ii) document to what extent environmental variables and species trait assemblages are related and which trends could be found in trait/environment relationships. The impact of vertical stratification, habitat closure, humus form, soil acidity, soil moisture, temperature, and to a lesser extent rainfall and altitude on species distribution, firstly revealed by indirect gradient analysis (correspondence analysis, CA), was further shown to be significant by direct gradient analysis (canonical correspondence analysis, CCA). RLQ analyses were performed to find linear combination of variables of table R (environmental variables) and linear combinations of the variables of table Q (species traits) of maximum covariance weighted by species occurrence data contained in table L. RLQ followed by permutation tests showed that all tested environmental variables apparently contributed significantly to the assemblages of the twelve species traits studied. A convergence was observed between traits related to vertical stratification and those related to habitat closure/aperture. Well-developed locomotory organs (furcula, legs), presence of sensorial organs sensitive to air movements and light (e.g. trichobothria and eye spots), spherical body, large body size, pigmentation (UV protection and signaling) and sexual reproduction largely occur in epigeic and open habitats, while most of woodland and edaphic habitats are characterized by short locomotory appendages, small body size, high number of defense organs (pseudocelli), presence of post-antennal organs and parthenogenesis. Climate and especially temperature exert an effect on the assemblage of traits that are mostly present above-ground and in open habitats. The contribution of combinations of some environmental variables to the occurrence of each species trait was tested by linear, logistic or multinomial regression (Generalized Linear Models). Vertical stratification, followed by temperature, played a dominant role in the variation of the twelve studied traits. Relationships between traits and environment tested here shows that it is possible to use some traits as proxies to identify potential ecological preferences or tolerances of invertebrate species. However, a significant part of species distribution remained unexplained, probably partly because some traits, like ecophysiological ones, or traits involved in biotic interactions (e.g. competition) were unavailable. The present work is thus a first step towards the creation of models predicting changes in collembolan communities. Further studies are required to inform ecophysiological traits, in order to complete such models. Moreover the niche width of species will have to be determined.
Published: 2014

47. Crickets of New Caledonia (Insecta, Orthoptera, Grylloidea): a key to genera, with diagnoses of extant genera and descriptions of new taxa

Author: Jeremy Anso, Hervé Jourdan, Laure Desutter-Grandcolas, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU)
Subjects: 0106 biological sciences, Insecta, Arthropoda, Orthoptera, Fauna, [SDV]Life Sciences [q-bio], 010607 zoology, Biodiversity, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010603 evolutionary biology, 01 natural sciences, Phalangopsidae, Gryllidae, Genus, Cricket, Animalia, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Taxonomy, Trigonidiidae, biology, Ecology, Haglotettigoniidae, 15. Life on land, biology.organism_classification, Taxon, [SDE]Environmental Sciences, Key (lock), Animal Science and Zoology, Grylloidea, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Crickets (Insecta, Orthoptera, Gryllidea) are amongst the most abundant and diverse insects in New Caledonia: 40 genera are recorded today from the Archipelago and 180 cricket species have been reported; 19 genera and more than 90% of the species are endemic. Owing to this diversity, crickets prove an interesting model to test evolutionary hypotheses about New Caledonia and its fauna. They also reveal useful ecological indicators to survey and manage New Caledonian biodiversity. Both research and conservation developments need however that crickets are properly identified. In the present paper, an illustrated key to the identification of New Caledonian cricket genera is proposed, based on specimen examination; an emended diagnosis is given for each genus, using general morphology, coloration and the main traits of male genitalia, together with available data on habitat and biology. The genus Paora Gorochov, 1986 n. stat. is restored from its synonymy with Apteronemobius Chopard, 1929, Trigonidomo...
Published: 2016

48. Does shape co-variation between the skull and the mandible have functional consequences? A 3D approach for a 3D problem

Author: Chazeau, C., Marchal, J., Hackert, R., Perret, M., Cornette, Raphaël, Baylac, Michel, Souter, Thibaud, Herrel, Anthony, Institut Jean Le Rond d'Alembert (DALEMBERT), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Plateforme de morphométrie, Muséum national d'Histoire naturelle (MNHN), Mécanismes adaptatifs : des organismes aux communautés, and Outils et Méthodes de la Systématique Intégrative (OMSI)
Subjects: Models, Anatomic, 0106 biological sciences, Histology, [SDV]Life Sciences [q-bio], Context (language use), Mandible, Biology, Models, Biological, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Imaging, Three-Dimensional, medicine, Animals, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Shrews, [SDV.BA]Life Sciences [q-bio]/Animal biology, Skull, Original Articles, Cell Biology, Anatomy, Co variation, Surface shape, Biomechanical Phenomena, medicine.anatomical_structure, Biting, Mastication, Biomechanical model, Adductor muscles, Developmental Biology
Abstract: Morpho-functional patterns are important drivers of phenotypic diversity given their importance in a fitness-related context. Although modularity of the mandible and skull has been studied extensively in mammals, few studies have explored shape co-variation between these two structures. Despite being developmentally independent, the skull and mandible form a functionally integrated unit. In the present paper we use 3D surface geometric morphometric methods allowing us to explore the form of both skull and mandible in its 3D complexity using the greater white-toothed shrew as a model. This approach allows an accurate 3D description of zones devoid of anatomical landmarks that are functionally important. Two-block partial least-squares approaches were used to describe the co-variation of form between skull and mandible. Moreover, a 3D biomechanical model was used to explore the functional consequences of the observed patterns of co-variation. Our results show the efficiency of the method in investigations of complex morpho-functional patterns. Indeed, the description of shape co-variation between the skull and the mandible highlighted the location and the intensity of their functional relationships through the jaw adductor muscles linking these two structures. Our results also demonstrated that shape co-variation in form between the skull and mandible has direct functional consequences on the recruitment of muscles during biting.
Published: 2013

49. Asthenopodichnium in fossil wood: Different trace makers as indicators of different terrestrial palaeoenvironments

Author: Jorge F. Genise, Pierre Maurizot, Raphaël Cornette, Patricia Nel, André Nel, Dominique Cluzel, Philippe Grandcolas, Anne-Claire Fabre, Romain Garrouste, Museo Paleontológico Egidio Feruglio [Chubut] (MEF), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), AgroParisTech, Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Pôle Pluridisciplinaire de la Matière et de l'Environnement (PPME), and Université de la Nouvelle-Calédonie (UNC)
Subjects: 010506 paleontology, A. lignorum isp n, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010502 geochemistry & geophysics, Oceanography, 01 natural sciences, Paleontología, Ciencias de la Tierra y relacionadas con el Medio Ambiente, Paleontology, Mayfly, New Caledonia, Ephemeroptera, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Earth-Surface Processes, biology, Ecology, Asthenopodichnium lignorum, Fungi, Palaeoecology, 15. Life on land, biology.organism_classification, Wide area, Asthenopodichnium xylobiontum, Paleoecology, Fossil wood, CIENCIAS NATURALES Y EXACTAS, Geology
Abstract: The ichnospecies Asthenopodichnium xylobiontum comprises U-shaped traces in wood, usually attributed to the activity of mayfly nymphs (Insecta, Ephemeroptera), which indicate the presence of freshwater palaeoenvironments. The record of a new ichnospecies in wood, Asthenopodichnium lignorum, in the Miocene of New Caledonia, strongly indicates that it may correspond to other trace makers because the potential producing Ephemeroptera are absent around these Miocene oceanic islands and in a wide area comprising New Zealand and Australia. We present herein the evidence for wood rotting fungi as potential trace maker of the new ichnospecies that has been previously recorded from Argentina, Egypt, Czech Republic, USA, and Lithuania. The new ichnospecies A. lignorum, in contrast with A. xylobiontum, is an indicator of terrestrial, humid to subhumid, palaeonvironments. Fil: Genise, Jorge Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Argentina Fil: Garrouste, Romain. Centre National de la Recherche Scientifique; Francia. Muséum National d'Histoire Naturelle; Francia Fil: Nel, Patricia. Centre National de la Recherche Scientifique; Francia. Muséum National d'Histoire Naturelle; Francia Fil: Grandcolas, Philippe. Muséum National d'Histoire Naturelle; Francia. Centre National de la Recherche Scientifique; Francia Fil: Maurizot, Pierre. Bureau de Recherches Géologiques et Minières; Francia Fil: Cluzel, Dominique. Universidad de Nueva Caledonia; Francia Fil: Cornette, Raphaël. Muséum National d'Histoire Naturelle; Francia Fil: Fabre, Anne-Claire. Muséum National d'Histoire Naturelle; Francia. Colegio Universitario de Londres; Reino Unido. Université Paris Diderot - Paris 7; Francia Fil: Nel, André. Centre National de la Recherche Scientifique; Francia. Muséum National d'Histoire Naturelle; Francia
Published: 2012

50. A new 3D imaging method for micropaleontology in ambers and entomology using basic light source: the Optical Coherence Tomography (FF-OCT)

Author: Chassot, J.-M., Garrouste, Romain, Boistel, R, Nel, Patricia, Nel, André, Azar, Dany, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut International de Paléoprimatologie, Paléontologie Humaine : Evolution et Paléoenvironnement (IPHEP), Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), AgroParisTech, Lebanese University [Beirut] (LU), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and Picardi, Luca
Subjects: [SDV] Life Sciences [q-bio], Micropaleontology, Full-Field Optical Coherence Tomography, [SDV]Life Sciences [q-bio], Amber fossils, Entomology
Abstract: National Museum of Scotland; International audience; 3D methods are gaining importance in the reconstruction of palaeontological objects for illustration in both scientific and popular realms. The availability of various methods, mainly techniques using X-rays, has enabled a very rapid development of powerful tools in the study of fossils. These include synchrotron facilities and CT scanners of different size and power.However, some tomographic methods using basic light (optical tomographies), developed for biological samples and in vivo studies, may also be used for some paleontological samples, such as inclusions in amber or small arthropod specimens. Here we present several case studies on the use of Full-Field Optical Coherence Tomography (FF-OCT), as applied to fossils preserved in amber. The method is based on low coherence interferometry using basic light. The OCT microscope used was developed in a physics institute specialising in medical imaging, and demonstrates the possibility of using such devices to image certain inclusions in amber, complementary to X-ray tomography methods or as an alternative in some specific cases. This method is also suitable for small biological objects, such as small to very small insects.
Published: 2016

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