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44 results on '"Fondation pour la Recherche sur la Biodiversite"'

1. Multi‐species hotspots detection using self‐organizing maps: Simulation and application to purse seine tuna fisheries management

Author: Stephan, Pauline, Gaertner, Daniel, Perez, Ilan, Guéry, Loreleï, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Fondation pour la Recherche sur la Biodiversite, Grant/Award Number: Gratification stages de master 2
Subjects: tropical tunas, FAD, ecosystem-based approach, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, time-area closures, self-organizing maps, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, bycatch, multispecies fisheries management
Abstract: International audience; To fulfil fisheries management objectives that often include implementing the precautionary and ecosystem-based approaches, multispecies fisheries data need to be analysed. Amongst the different methods dealing with these multidimensional data, self-organizing maps (SOMs) remain rarely used, although they are highly flexible in data input and offer visualization possibilities particularly suited to summarize complex datasets. Here, we propose to combine SOMs with a clustering approach to break down data complexity and produce simple geographic maps showing catch hotspots, which can indicate sensitive zones in terms of fishery management. To promote this approach, we tested it first on simulated datasets and then on the open-access ICCAT commercial catch database of the tropical tuna fisheries of the Atlantic Ocean. We aimed to detect drifting fish aggregating devices (dFADs) catch hotspots of juveniles of two tuna species, bigeye and yellowfin tunas and of the silky shark, a commonly bycaught vulnerable shark species, in tropical tuna purse seine fisheries. Simulations on datasets increasing in complexity (in number, geographic and duration extent of the hotspots and number of species in the analysis) informed us about the method's sensitivity and limits. Our findings showed that, in the context of multi-specific fisheries, the detection of the hotspot is dependent on a certain level of catch within the hotspot and that adding species to the analysis tended to mask small and short-duration hotspots. Applied to tropical tuna fisheries' data, the method confirmed the empirical knowledge on which first time-area closures were based and provided scientifical support. All in all, the visual support provided by the method, its interpretability and its potential transferability to other fisheries' systems constitute its main strengths and imply a possible implementation in management decisions; specifically, as a tool to reach agreement between stakeholders in the definition of regulated areas for protecting juveniles of tunas and vulnerable associated species to dFAD practices.
Published: 2022
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2. Differential effects of root-level exposure to triazine xenobiotics on root development plasticity in Arabidopsis thaliana

Author: Diana Alberto, Fanny Ramel, Cécile Sulmon, Gwenola Gouesbet, Ivan Couée, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), interdisciplinary program 'Ingenierie ecologique' [Centre National de la Recherche Scientifique (CNRS), France], Fondation pour la Recherche sur la Biodiversite (France), and Ministere de l'Enseignement superieur, de la Recherche et de l'Innovation (France)
Subjects: Herbicides, Physiology, Root growth, Soil pollution, Persistent organic pollutants, Atrazine, Root hair development, Plant Science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science
Abstract: International audience; Herbicides and their degradation products contribute to soil pollution and to its impact on soil biodiversity and functioning. Soil herbicide pollution presents characteristics of global planetary threats, with harmful consequences for soil ecology, for ecosystem functions and services mediated by natural plant communities and for crop production sustainability. However, the range and the mechanisms of soil herbicide pollution effects on plants are not fully understood. Effects on roots, as a first line of pollutant exposure, and on root plasticity, as a driver of below-ground ecological processes, must be further characterized. Because of worldwide intensive use of atrazine, of persistence in the environment and of toxicological effects, atrazine and its derived metabolites are typical persistent organic pollutants of soils. The coherent chemical series consisting of atrazine, desethylatrazine and hydroxyatrazine was used to analyse potential effects of triazine xenobiotics on root plasticity processes. Responses to atrazine, desethylatrazine and hydroxyatrazine applied at root level were comparatively analyzed in the model plant Arabidopsis thaliana, which is highly responsive to triazine xenobiotics. We report that triazine xenobiotics, whether as herbicidally active compounds or as degradation products, affect root plasticity in terms of primary root growth, lateral root development and root hair development, and that these effects differentially interact with the light, carbon and cytokinin status of the plant. The adaptive significance of these effects and of their interactions is discussed in terms of toxicity of, or resistance to, residual soil contaminants and in terms of potential cascading impact on plant and ecosystem functioning.
Published: 2022
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3. Association between temporal patterns in helminth assemblages and successful range expansion of exotic Mus musculus domesticus in Senegal

Author: Christophe Diagne, Carine Brouat, Arame Ndiaye, Youssoupha Niang, Mamadou Kane, Caroline Tatard, Laurent Granjon, M. S. Gueye, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), CERISE project (Fonds Francais pour l'Environnement Mondial via the Fondation pour la Recherche sur la Biodiversite) : AAP-SCEN-20B III, French Research Institute for Development (IRD), ANR-11-JSV7-0006,ENEMI,Conséquences évolutives des ennemis naturels dans des invasions biologiques majeures : le rôle des parasites dans le succès de l'invasion de deux rongeurs commensaux(2011), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Mus musculus domesticus, Ecology, biology, Rodent, Host (biology), Range (biology), Enemy release, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, 010604 marine biology & hydrobiology, Parasitism, Zoology, biology.organism_classification, Gastrointestinal helminths, 010603 evolutionary biology, 01 natural sciences, House mouse, biology.animal, Parasite hosting, Helminths, Mastomys erythroleucus, Spill-back, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Relationships between parasitism and invasion success are increasingly evidenced in the literature. However, the dynamic nature of the major parasite-related processes has been rarely taken into account until now, while the residence time of invaders in colonized regions was shown to be associated to crucial changes in parasite communities. Here, we strive to bridge this gap using a temporal survey of rodent populations along one invasion route of the exotic house mouseMus musculus domesticusthat currently invades North Senegal. In this study, we investigated whether gastrointestinal helminth (GIH) assemblages changed over time in native (Mastomys erythroleucus) and/or invasive (M. m. domesticus) rodent populations sampled at an invasion front, and whether these potential changes may be associated to the invasion success of the exotic mouse. Four years separated two rodent sampling campaigns (2013 and 2016/17) in six localities. Despite being relatively short, the timeframe considered here allowed to evidence significant patterns in rodent communities and their GIH assemblages. At the host community level, we showed that the exotic mouse was now established at all sites, becoming the dominant species in sites where it was not recorded before. At the GIH community level, increased infection of the single shared cestode (Mathevotaenia symmetrica) in both rodent species brought support to the "spill-back" hypothesis. Infection levels of GIH that remained low at the invasion front in invading mice over time also supported the "enemy release" hypothesis. Both hypotheses should deserve further experimental work to demonstrate their role in the invasion success of the house mouse in Senegal.
Published: 2020
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4. Come Rain, Come Shine: Peatland Carbon Dynamics Shift Under Extreme Precipitation

Author: Anna Sytiuk, Vincent Moulia, Janna M. Barel, Samuel Hamard, Vincent E. J. Jassey, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), 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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Fondation pour la Recherche sur la Biodiversite which acted in cooperation with the French Agency for Biodiversity (AFB), and its partners (FRB-www.fondationbiodiversite.fr), ANR-17-CE01-0007,MIXOPEAT,Repenser le cycle du carbone des tourbières : identifier le rôle des protistes mixotrophes dans la pompe à carbone biologique(2017), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0106 biological sciences, Peat, 010504 meteorology & atmospheric sciences, Water table, Growing season, Atmospheric sciences, 010603 evolutionary biology, 01 natural sciences, Mesocosm, resistance, chemistry.chemical_compound, Dissolved organic carbon, GE1-350, Ecosystem, Precipitation, resilience, 0105 earth and related environmental sciences, General Environmental Science, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, decomposition, rewetting, methane, water table fluctuation, carbon dioxide, 15. Life on land, dissolved organic carbon, Environmental sciences, chemistry, 13. Climate action, Carbon dioxide, Environmental science
Abstract: Precipitation patterns are becoming increasingly extreme, particularly at northern latitudes. Current climate models predict that this trend will continue in the future. While droughts have been repeatedly studied in many ecosystems over the last decades, the consequences of increasingly intense, but less frequent rainfall events, on carbon (C) cycling are not well understood. At northern latitudes, peatlands store one third of the terrestrial carbon and their functioning is highly dependent on water. Shifts in rainfall regimes could disrupt peatland C dynamics and speed-up the rates of C loss. How will these immense stocks of C be able to withstand and recover from extreme rainfall? We tested the resistance and resilience effects of extreme precipitation regimes on peatland carbon dioxide (CO2) and methane (CH4) fluxes, pore water dissolved organic carbon (DOC) and litter decomposition rates by exposing intact peat cores to extreme, spring-time rainfall patterns in a controlled mesocosm experiment. We find that more intense but less frequent rainfall destabilized water table dynamics, with cascading effects on peatland C fluxes. Decomposition and respiration rates increased with a deeper mean water table depth (WTD) and larger WTD fluctuations. We observed similar patterns for CO2 uptake, which were likely mediated by improved vascular plant performance. After a three-week recovery period, CO2 fluxes still displayed responses to the earlier WTD dynamics, suggesting lagged effects of precipitation regime shifts. Furthermore, we found that CH4 emissions decreased with deeper mean WTD, but this showed a high resilience once WTD dynamics stabilised. Not only do our results illustrate that shifting rainfall patterns translate in altered WTD dynamics and, consequentially, influence C fluxes, they also demonstrate that exposure to altered rainfall early in the growing season can have lasting effects on CO2 exchange. Even though the increased CO2 assimilation under extreme precipitation patterns signals peatland resistance under changing climatic conditions, it may instead mark the onset of vascular plant encroachment and the associated C loss.
Published: 2021
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5. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Author: Couvreur, Thomas, Dauby, Gilles, Blach-Overgaard, Anne, Deblauwe, Vincent, Dessein, Steven, Droissart, Vincent, Hardy, Oliver, Harris, David, Janssens, Steven, Ley, Alexandra, Mackinder, Barbara, Sonké, Bonaventure, Sosef, Marc, Stévart, Tariq, Svenning, Jens-Christian, Wieringa, Jan, Faye, Adama, Missoup, Alain, Tolley, Krystal, Nicolas, Violaine, Ntie, Stéphan, Fluteau, Frédéric, Robin, Cécile, Guillocheau, Francois, Barboni, Doris, Sepulchre, Pierre, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aarhus University [Aarhus], University of California [Los Angeles] (UCLA), University of California (UC), Meise Botanic Garden [Belgium] (Plantentuin), Université libre de Bruxelles (ULB), Université de Yaoundé I, Missouri Botanical Garden, Royal Botanic Garden [Edinburgh], Martin-Luther-University Halle-Wittenberg, Naturalis Biodiversity Center [Leiden], LNRPV Laboratoire National de Recherches et de Productions Végétales, Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), LPF, University of Douala, South African National Biodiversity Institute, University of the Witwatersrand [Johannesburg] (WITS), 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), Université des Sciences et Techniques de Masuku (USTM), Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - 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), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation du climat (CLIM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-15- CE02-0002-01, Agence Nationale de la Recherche, RAINBIO, Fondation pour la Recherche sur la Biodiversite, ANR-15-CE02-0002,AFRODYN,Forêts tropicales humides d'Afrique Centrale : dynamiques passées et résiliences futures(2015), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of California, Botanic Garden Meise, Royal Botanic Garden Edinburgh, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)
Subjects: [SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics, tropical Africa, Cenozoic, dated molecular phylogenies, palaeoclimate models, African geology, speciation models, Original Articles, Biodiversity, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Plants, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Animals, Original Article, fossils, Biologie, Ecosystem, Phylogeny, ComputingMilieux_MISCELLANEOUS
Abstract: Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2021
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6. Same Invasion, Different Routes: Helminth Assemblages May Favor the Invasion Success of the House Mouse in Senegal

Author: Diagne, Christophe, Granjon, Laurent, Tatard, Caroline, Ribas, Alexis, Ndiaye, Arame, Kane, Mamadou, Niang, Youssoupha, Brouat, Carine, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain] (IRBio UB), Universitat de Barcelona (UB), BIOPASS, ISRA-UCAD, Institut de Recherche pour le Développement (IRD [France-Ouest]), This work was supported by the CERISE project (funded by the Fond Francais pour l’Environnement Mondial via the Fondation pour la Recherche sur la Biodiversite’: AAP-SCEN-20B III) and the Labex DRIIHM, French programme Investissements d’Avenir (ANR-11-LABX-0010) managed by the Agence Nationale pour la Recherche (ANR). The French Research Institute for Development (IRD) provided the funding for a postdoctoral position., and ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011)
Subjects: Mus musculus domesticus, enemy release, Paràsits, Parasitologia, biological invasions, spill-back, Senegal, spatial survey, Helminths, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, gastrointestinal helminths, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Veterinary Science, Mastomys erythroleucus, Parasites, Parasitology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Helmints, Original Research
Abstract: Samples are preserved in the CBGP—Small mammal collection (https://doi.org/10.15454/WWNUPO) and referenced in the associated Small Mammal Database. Molecular data necessary for helminth identification were generated at the molecular biology platform of the CBGP.; International audience; Previous field-based studies have evidenced patterns in gastrointestinal helminth (GIH) assemblages of rodent communities that are consistent with “enemy release” and “spill-back” hypotheses, suggesting a role of parasites in the ongoing invasion success of the exotic house mouse (Mus musculus domesticus) in Senegal (West Africa). However, these findings came from a single invasion route, thus preventing to ascertain that they did not result from stochastic and/or selective processes that could differ across invasion pathways. In the present study, we investigated the distribution of rodent communities and their GIH assemblages in three distinct zones of Northern Senegal, which corresponded to independent house mouse invasion fronts. Our findings first showed an unexpectedly rapid spread of the house mouse, which reached even remote areas where native species would have been expected to dominate the rodent communities. They also strengthened previous insights suggesting a role of helminths in the invasion success of the house mouse, such as: (i) low infestation rates of invading mice by the exotic nematode Aspiculuris tetraptera at invasion fronts—except in a single zone where the establishment of the house mouse could be older than initially thought, which was consistent with the “enemy release” hypothesis; and (ii) higher infection rates by the local cestode Mathevotaenia symmetrica in native rodents with long co-existence history with invasive mice, bringing support to the “spill-back” hypothesis. Therefore, “enemy release” and “spill-back” mechanisms should be seriously considered when explaining the invasion success of the house mouse—provided further experimental works demonstrate that involved GIHs affect rodent fitness or exert selective pressures. Next steps should also include evolutionary, immunological, and behavioral perspectives to fully capture the complexity, causes and consequences of GIH variations along these invasion routes.
Published: 2021
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7. Grasping darkness: the dark ecological network as a social-ecological framework to limit the impacts of light pollution on biodiversity

Author: Isabelle Le Viol, Magalie Franchomme, Clélia Sirami, Alexis Laforge, Johan Milian, Samuel Challéat, Dany Lapostolle, Kévin Barré, Christian Kerbiriou, Géographie de l'environnement (GEODE), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Théoriser et modéliser pour aménager (UMR 6049) (ThéMA), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Territoires, Villes, Environnement & Société - ULR 4477 (TVES), Université du Littoral Côte d'Opale (ULCO)-Université de Lille, Laboratoire Dynamiques Sociales et Recomposition des Espaces (LADYSS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), ITTECOP (Land transport infrastructure, ecosystems, and landscapes) CHIROLUM programme, 'TRAME NOIRE' project (Conseil Regional Nord-Pas-de-Calais), 'TRAME NOIRE' project (Fondation pour la Recherche sur la Biodiversite), ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011), Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Université de Franche-Comté (UFC), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB), and Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Université de Paris (UP)
Subjects: 0106 biological sciences, QH301-705.5, media_common.quotation_subject, Biodiversity, Wildlife, Light pollution, 010603 evolutionary biology, 01 natural sciences, artificial light at night (ALAN), darkness, 0103 physical sciences, 11. Sustainability, participatory processes, Quality (business), Biology (General), ecological network, 010303 astronomy & astrophysics, QH540-549.5, media_common, Ecology, Scale (chemistry), light pollution, Land-use planning, [SHS.GEO]Humanities and Social Sciences/Geography, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Ecological network, Geography, multilevel approach, social-ecological systems, 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, land-use planning, Global biodiversity
Abstract: International audience; Artificial light at night (ALAN) is nowadays recognized as a major anthropogenic pressure on the environment on a global scale and as such is called light pollution. Through its attractive or deterrent effects, and its disruption of the biological clock for many animal and plant taxa, ALAN is increasingly recognized as a major threat to global biodiversity, which ultimately alters the amount, the quality, and the connectivity of available habitats for taxa. Biodiversity conservation tools should, therefore, include ALAN spatial and temporal effects. The ecological network, i.e., the physical and functional combination of natural elements that promote habitat connectivity, provides a valuable framework for that purpose. Understood as a social-ecological framework, it offers the opportunity to take into account the multiple uses of nocturnal spaces and times, by humans and nonhumans alike. Here we present the concept of "dark ecological network." We show this concept is able to grasp the effects of ALAN in terms of habitat disturbances and integrates temporal dimensions of ecological processes into biodiversity conservation planning. Moreover, it is also intended to trivialize the practices of darkness protection by turning them into the ordinary practices of land use planning. From an operational point of view, the challenge is to translate the levers for reducing ALAN-induced effects into a political method for its "territorialization." To achieve this objective, we propose a course of action that consists of building an interdisciplinary repertoire of contextualized knowledge (e.g., impacts on wildlife, human/lightscape relationship, existing legal tools, etc.), in order to deduce from it a number of practical supports for the governance of the dark ecological network in response to societal and ecological issues.
Published: 2021
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8. Local-scale dynamics of plant-pesticide interactions in a northern Brittany agricultural landscape

Author: Ivan Couée, Anne-Antonella Serra, Cendrine Mony, Cécile Sulmon, Fredérique Pallois, Kahina Slimani, Anne-Kristel Bittebiere, David Renault, Gwenola Gouesbet, 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), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique, Fondation pour la Recherche sur la Biodiversite, Université de Rennes 1, Conseil Régional de Bretagne, 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), and 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)
Subjects: Vegetative filter strips, Environmental Engineering, 010504 meteorology & atmospheric sciences, Agrostis stolonifera, Soil pollution, 010501 environmental sciences, 01 natural sciences, Lolium perenne, Soil, Environmental Chemistry, Ecotoxicity, Pesticides, Waste Management and Disposal, Ecosystem, 0105 earth and related environmental sciences, Riparian zone, 2. Zero hunger, geography, geography.geographical_feature_category, biology, Persistent organic pollutants, food and beverages, Plant community, Agriculture, Plant community dynamics, 15. Life on land, Pesticide, biology.organism_classification, Pollution, Soil contamination, Agronomy, 13. Climate action, Environmental science, France, Centaurea cyanus, Festuca rubra, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Soil pollution by anthropogenic chemicals is a major concern for sustainability of crop production and of ecosys- tem functions mediated by natural plant biodiversity. Understanding the complex effects of soil pollution re- quires multi-level and multi-scale approaches. Non-target and agri-environmental plant communities of field margins and vegetative filter strips are confronted with agricultural xenobiotics through soil contamination, drift, run-off and leaching events that result from chemical applications. Plant-pesticide dynamics in vegetative filter strips was studied at field scale in the agricultural landscape of a long-term ecological research network in northern Brittany (France). Vegetative filter strips effected significant pesticide abatement between the field and riparian compartments. However, comparison of pesticide usage modalities and soil chemical analysis re- vealed the extent and complexity of pesticide persistence in fields and vegetative filter strips, and suggested the contribution of multiple sources (yearly carry-over, interannual persistence, landscape-scale contamination). In order to determine the impact of such persistence, plant dynamics was followed in experimentally-designed vegetative filter strips of identical initial composition (Agrostis stolonifera, Anthemis tinctoria/Cota tinctoria, Cen- taurea cyanus, Fagopyrum esculentum, Festuca rubra, Lolium perenne, Lotus corniculatus, Phleum pratense, Trifolium pratense). After homogeneous vegetation establishment, experimental vegetative filter strips underwent rapid changes within the following two years, with Agrostis stolonifera, Festuca rubra, Lolium perenne and Phleum pratense becoming dominant and with the establishment of spontaneous vegetation. Co-inertia analysis showed that plant dynamics and soil residual pesticides could be significantly correlated, with the triazole fungicide epoxiconazole, the imidazole fungicide prochloraz and the neonicotinoid insecticide thiamethoxam as strong drivers of the correlation. However, the correlation was vegetative-filter-strip-specific, thus showing that corre- lation between plant dynamics and soil pesticides likely involved additional factors, such as threshold levels of residual pesticides. This situation of complex interactions between plants and soil contamination is further discussed in terms of agronomical, environmental and health issues.
Published: 2020
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9. Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)

Author: Laso‐jadart, Romuald, Sugier, Kevin, Petit, Emmanuelle, Labadie, Karine, Peterlongo, Pierre, Ambroise, Christophe, Wincker, Patrick, Jamet, Jean-Louis, Madoui, Mohammed‐amin, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS) European Molecular Biology Laboratory Genoscope/Commissariat a l'Energie AtomiqueVeolia Environment Foundation Region Bretagne World CourierIllumina Cap L'Orient Electricite de France (EDF) Foundation EDF Diversiterre Fondation pour la Recherche sur la Biodiversite Prince Albert II de Monaco Foundation Etienne Bourgois Tara schooner, ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Tara Oceans-GOSEE (FR2022), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)
Subjects: metagenomics, metatranscriptomics, copepod, lcsh:QH540-549.5, allelic expression, selection, lcsh:Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Arctic seas, ComputingMilieux_MISCELLANEOUS
Abstract: Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population‐scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009–2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR
Published: 2020
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10. Beyond trees: Biogeographical regionalization of tropical Africa

Author: Tariq Stévart, Anne Blach-Overgaard, Jens-Christian Svenning, Olivier J. Hardy, Thomas L. P. Couvreur, Steven Janssens, Bonaventure Sonké, Barbara A. Mackinder, Vincent Droissart, David Harris, Vincent Deblauwe, Gilles Dauby, Marc S.M. Sosef, Jan J. Wieringa, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), 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]), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Evolutionary Biology and Ecology, Department of Organism Biology, Université libre de Bruxelles (ULB), Department of Ecology and Evolutionary Biology, Center for Tropical Research, Institute of the Environment and Sustainability, University of California [Los Angeles] (UCLA), University of California-University of California, Royal Botanical Garden Edinburgh, Royal Botanical Garden, Botanic Garden Meise, Royal Botanic Garden Edinburgh, Aarhus University [Aarhus], University of Yaoundé [Cameroun], Herbarieum et Bibliothèque de Botanique africaine, Section for Ecoinformatics & Biodiversity, Department of Bioscience, Naturalis Biodiversity Center [Leiden], Fondation pour la Recherche sur la Biodiversite Fonds de la Recherche Scientifique - FNRS Villum Fonden 16549 French Foundation for Research on Biodiversity (FRB) Region Provence-Alpes-Cote d'Azur Belgian Fund for Scientific Research, 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]), Université Libre de Bruxelles [Bruxelles] (ULB), Aarhus University, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, 0301 basic medicine, RAINBIO database, nestedness, CONSERVATION, African bioregions, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Phytogeography, 010603 evolutionary biology, 01 natural sciences, diversity, 03 medical and health sciences, network clustering, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, growth forms, SPECIES COMPOSITION, Growth form, SUB-SAHARAN AFRICA, Endemism, Ecology, Evolution, Behavior and Systematics, PLANT DIVERSITY, 2. Zero hunger, Diversity, FLORA, Ecology, phytogeography, Species diversity, RAIN-FOREST, ENDEMISM, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 15. Life on land, REGIONS, 030104 developmental biology, Geography, Liana, Network clustering, PATTERNS, Nestedness, BIODIVERSITY, Ordination, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Woody plant
Abstract: Aim: To delineate bioregions in tropical Africa and determine whether different plant growth forms (trees, terrestrial herbs, lianas and shrubs) display the same pattern of regionalization, diversity and endemism as the whole flora.Location: Tropical Africa (excl. Madagascar), from 20 degrees N to 25 degrees S.Taxon: Vascular plants.Methods: Analyses were based on occurrences of 24,719 vascular plant species distributed across tropical Africa extracted from the RAINBIO database. The majority of species (93%) were classified into four growth forms: terrestrial herbs, trees, shrubs and lianas. Biogeographical regions (bioregions) were delimited using a bipartite network clustering approach on the whole dataset and then separately for each growth form. Relationships among bioregions were investigated using non-metric multidimensional scaling ordination, flora nestedness and endemism patterns.Results: Analyses of the whole dataset identified 16 bioregions and 11 transition zones. These were congruent with most of the currently recognized phytogeographical classifications, and also highlighted previously under-recognized bioregions. Bioregion endemism rates were lower and species richness higher when compared to estimates from the White/Association pour l'Etude Taxonomique de la Flore d'Afrique Tropicale (AETFAT) classification. Analysed separately, plant growth forms showed contrasting geographical patterns. Bioregionalization was better resolved for closed forest types using trees and lianas and for open vegetation types using terrestrial herbs, while shrubs showed good discriminative power in all vegetation types.Main conclusions: We show that distribution patterns based on solely trees are not sufficient to define floristic bioregions in tropical Africa. Analyses of spatial patterns using different growth forms are complementary, likely reflecting different evolutionary processes and ecological relationships. The contribution of growth forms to delimit geographical floristic patterns across tropical Africa is of critical importance for land use planning and management, and for selecting priority conservation areas.
Published: 2018
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11. Plant–Pesticide Interactions and the Global Chloromethane Budget

Author: Françoise Bringel, Ivan Couée, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), 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), Centre National de la Recherche Scientifique (CNRS), France, Fondation pour la Recherche sur la Biodiversite (FRB), France, National Research Agency (ANR), France (CHLOROFILTER) [ANR-14-CE35-0005-01], ANR-14-CE35-0005,CHLOROFILTER,Impact of microorganisms as sinks of atmospheric chloromethane(2014), 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), and 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)
Subjects: 0106 biological sciences, Plant Science, Environment, 010501 environmental sciences, Biology, 01 natural sciences, stratospheric ozone, chemistry.chemical_compound, Ozone layer, Hydrocarbons, Chlorinated, methyl chloride, Pesticides, 0105 earth and related environmental sciences, chlorinated pesticides, Chloromethane, fungi, food and beverages, Plants, Pesticide, Hydrocarbons.chlorinated, Biodegradation, Environmental, chemistry, 13. Climate action, Environmental chemistry, halocarbons, planetary boundary threat, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Atmospheric ozone, 010606 plant biology & botany
Abstract: International audience; Ecological, signaling, metabolic, and chemical processes in plant-microorganism systems and in plant-derived material may link the use of chlorinated pesticides in the environment with plant chloromethane emission. This neglected factor should be taken into account to assess global planetary budgets of chloromethane and impacts on atmospheric ozone depletion.
Published: 2018
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12. Donskoy cats as a new model of oculocutaneous albinism with the identification of a splice-site variant in Hermansky-Pudlak Syndrome 5 gene

Author: Marie Abitbol, Marina Mériot, Vincent Gache, Caroline Dufaure de Citres, Christophe Hitte, Maud Rimbault, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Antagene, Institut NeuroMyoGène (INMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Fondation pour la Recherche sur la Biodiversite, 71VAL0419, Genespoir, VetAgro Sup, Fondation pour la Recherche sur la Biodiversité, Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Jonchère, Laurent
Subjects: 0301 basic medicine, Candidate gene, RNA Splicing, [SDV]Life Sciences [q-bio], Hermansky-Pudlak Syndrome 5, HPS5, [SDV.CAN]Life Sciences [q-bio]/Cancer, Dermatology, albinism, Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Mice, 03 medical and health sciences, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, ruby-eye 2, medicine, Animals, Humans, Genetic Predisposition to Disease, Felis catus, Gene, Alleles, Genetics, Base Sequence, Homozygote, Intron, Exons, medicine.disease, Disease gene identification, Chromosomes, Mammalian, Oculocutaneous albinism, [SDV] Life Sciences [q-bio], Disease Models, Animal, Phenotype, 030104 developmental biology, Oncology, Albinism, Oculocutaneous, Genetic Loci, 030220 oncology & carcinogenesis, Cats, Albinism, RNA Splice Sites, Hermansky–Pudlak syndrome, Carrier Proteins, BLOC2S2, Genome-Wide Association Study
Abstract: International audience; In the feline Donskoy breed, a phenotype that breeders call "pink‐eye," with associated light‐brown skin, yellow irises and red‐eye effect, has been described. Genealogical data indicated an autosomal recessive inheritance pattern. A single candidate region was identified by genome‐wide association study and SNP‐based homozygosity mapping. Within that region, we further identified HPS5 (HPS5 Biogenesis Of Lysosomal Organelles Complex 2 Subunit 2 ) as a strong candidate gene, since HPS5 variants have been identified in humans and animals with Hermansky–Pudlak syndrome 5 or oculocutaneous albinism. A homozygous c.2571‐1G>A acceptor splice‐site variant located in intron 16 of HPS5 was identified in pink‐eye cats. Segregation of the variant was 100% consistent with the inheritance pattern. Genotyping of 170 cats from 19 breeds failed to identify a single carrier in non‐Donskoy cats. The c.2571‐1G>A variant leads to HPS5 exon‐16 splicing that is predicted to produce a 52 amino acids in‐frame deletion in the protein. These results support an association of the pink‐eye phenotype with the c.2571‐1G>A variant. The pink‐eye Donskoy cat extends the panel of reported HPS5 variants and offers an opportunity for in‐depth exploration of the phenotypic consequences of a new HPS5 variant.
Published: 2020
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13. Species- and organ-specific responses of agri-environmental plants to residual agricultural pollutants

Author: Anne-Antonella Serra, Fanny Ramel, Cécile Sulmon, Amélie Miqueau, Gwenola Gouesbet, Ivan Couée, 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), Fondation pour la Recherche sur la Biodiversite, FRBFondation pour la Recherche sur la Biodiversite, FRBCentre 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), and 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)
Subjects: Environmental Engineering, 010504 meteorology & atmospheric sciences, Soil pollution, Biodiversity, 010501 environmental sciences, 01 natural sciences, chemistry.chemical_compound, Environmental Chemistry, Ecosystem, Ecotoxicity, Pesticides, Waste Management and Disposal, 0105 earth and related environmental sciences, 2. Zero hunger, Pollutant, Persistent organic pollutants, food and beverages, Plant community, Agriculture, 15. Life on land, Pesticide, Pollution, Soil contamination, Heavy metals, chemistry, Field margin plants, 13. Climate action, Environmental chemistry, Environmental science, Environmental Pollutants, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Xenobiotic, Agrochemicals, Environmental Monitoring
Abstract: International audience; Soil pollution by anthropogenic chemicals is a major concern for sustainability of crop production and of ecosystem functions mediated by natural plant biodiversity. The complex effects on plants are however difficult to apprehend. Plant communities of field margins, vegetative filter strips or rotational fallows are confronted with agricultural pollutants through residual soil contamination and/or through drift, run-off and leaching events that result from chemical applications. Exposure to xenobiotics and heavy metals causes biochemical, physiological and developmental effects. However, the range of doses, modalities of exposure, metabolization of contaminants into derived xenobiotics, and combinations of contaminants result in variable and multi-level effects. Understanding these complex plant-pollutant interactions cannot directly rely on toxicological or agronomical approaches that focus on the effects of field-rate pesticide applications. It must take into account exposure at root level, sublethal concentrations of bioactive compounds and functional biodiversity of the plant species that are affected. The present study deals with agri-environmental plant species of field margins, vegetative filter strips or rotational fallows in European agricultural landscapes. Root and shoot physiological and growth responses were compared under controlled conditions that were optimally adjusted for each plant species. Contrasted responses of growth inhibition, no adverse effect or growth enhancement depended on species, organ and nature of contaminant. However, all of the agricultural contaminants under study (pesticides, pesticide metabolites, heavy metals, polycyclic aromatic hydrocarbons) had significant effects under conditions of sublethal exposure on at least some of the plant species. The fungicide tebuconazole and polycyclic aromatic hydrocarbon fluoranthene, which gave highest levels of responses, induced both activation or inhibition effects, in different plant species or in different organs of the same plant species. These complex effects are discussed in terms of dynamics of agri-environmental plants and of ecological consequences of differential root-shoot growth under conditions of soil contamination. © 2019 Elsevier B.V.
Published: 2019
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14. A functional diversity approach of crop sequences reveals that weed diversity and abundance show different responses to environmental variability

Author: Guillaume Fried, Lucie Mahaut, Sabrina Gaba, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), INRA-CEBC, Institut National de la Recherche Agronomique (INRA), Anses, Laboratoire de la Santé des Végétaux [France], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Etudes Biologiques de Chizé [France] (USC 1339 INRA), Fondation pour la Recherche sur la Biodiversite, and Agence Nationale de la Recherche [ANR-13-AGRO-0001]
Subjects: 0106 biological sciences, agroecology, Biology, 010603 evolutionary biology, 01 natural sciences, resource availability, Crop, crop rotation, Abundance (ecology), parasitic diseases, crop sequences, 2. Zero hunger, disturbance, Ecology, 010604 marine biology & hydrobiology, fungi, food and beverages, Sowing, respiratory system, 15. Life on land, Crop rotation, Weed control, functional diversity, Agronomy, Hill's number, [SDE]Environmental Sciences, Species richness, Monoculture, Weed, human activities, weed management
Abstract: International audience; Combining several crop species and associated agricultural practices in a crop sequencehas the potential to control weed abundance while promoting weed diversityin arable fields. However, how the variability in environmental conditions thatarise from crop sequences affects weed diversity and abundance remains poorlyunderstood, with most studies to‐date simply opposing weed communities inmonoculture and in crop rotation. Here, we describe crop sequences along gradientsof disturbance and resource variability using a crop functional trait and associatedagricultural practices. We tested the hypothesis that in disturbancesreduces weed abundance, whereas variability in resources promotes weeddiversity.2. We used functional Hill's numbers to compute crop sequence functional diversitybased on sowing date, herbicide spectrum and crop height—these are the respectiveproxies of disturbance timings, disturbance types and light availability. Usinga large‐scale weed monitoring database, we assessed crop sequence diversity for1,045 crop sequences of five consecutive cropping seasons. We computed weedrichness and abundance at pluri‐annual (pool of weeds observed across five croppingseasons) and annual (pool of weeds observed during a winter cereal croppingseason preceded by five cropping seasons) scales. We also accounted for herbicideand tillage intensities to test whether management intensity affects the responseof weed diversity and abundance to crop sequence diversity.3. At the pluri‐annual scale, weed richness increased with the diversity of crop heightand sowing date, whereas weed abundance decreased with sowing date diversity.Annual weed richness decreased with sowing date diversity, whereas annual weedabundance poorly relied on crop sequence diversity.4. Synthesis and applications. This study establishes a scientific basis for designingcrop sequences according to specific weed management goals. We show thatfarmers may enhance arable weed diversity on a pluri‐annual scale by sequentiallysowing crop species that differ in their competitive ability and sowing date. Theymay also achieve a better control of weed abundance by increasing the diversityof crop sowing dates across the crop sequence.
Published: 2019
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15. Herbicide-related signaling in plants reveals novel insights for herbicide use strategies, environmental risk assessment and global change assessment challenges

Author: Anne-Antonella Serra, Gwenola Gouesbet, Diana Alberto, Cécile Sulmon, Ivan Couée, 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), Ecosphere continentale et cotiere interdisciplinary program from the Centre National de la Recherche Scientifique (CNRS, France), 'Ingenierie ecologique' interdisciplinary program from the Centre National de la Recherche Scientifique (CNRS, France), Fondation pour la recherche sur la biodiversite (FRB, France), Ministere de l'Education nationale, de l'Enseignement superieur et de la Recherche (France), regional council of Brittany (France), 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), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Environmental Engineering, Circadian clock, activated protein-kinase, sugar-induced tolerance, planetary boundary threats, arabidopsis-thaliana, Biology, Risk Assessment, 01 natural sciences, stress responses, 03 medical and health sciences, Stress, Physiological, circadian clock, site-based resistance, Environmental Chemistry, Environmental impact assessment, Mode of action, Hormone signaling, lolium-rigidum, Waste Management and Disposal, Plant Physiological Phenomena, Environmental risk assessment, 2. Zero hunger, Herbicides, business.industry, Abiotic stress, gene-expression, Pollution, Biotechnology, amino-acid-metabolism, Crosstalk (biology), 030104 developmental biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Risk assessment, Signal Transduction, 010606 plant biology & botany
Abstract: International audience; Herbicide impact is usually assessed as the result of a unilinear mode of action on a specific biochemical target with a typical dose-response dynamics. Recent developments in plant molecular signaling and crosstalk between nutritional, hormonal and environmental stress cues are however revealing a more complex picture of inclusive toxicity. Herbicides induce large-scale metabolic and gene-expression effects that go far beyond the expected consequences of unilinear herbicide-target-damage mechanisms. Moreover, groundbreaking studies have revealed that herbicide action and responses strongly interact with hormone signaling pathways, with numerous regulatory protein-kinases and -phosphatases, with metabolic and circadian clock regulators and with oxidative stress signaling pathways. These interactions are likely to result in mechanisms of adjustment that can determine the level of sensitivity or tolerance to a given herbicide or to a mixture of herbicides depending on the environmental and developmental status of the plant. Such regulations can be described as rheostatic and their importance is discussed in relation with herbicide use strategies, environmental risk assessment and global change assessment challenges. (C) 2016 Elsevier B.V. All rights reserved.
Published: 2016
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16. Does pollution influence small mammal diet in the field? A metabarcoding approach in a generalist consumer

Author: Frédéric Mora, Thierry Cornier, Benoît Valot, Clémentine Fritsch, Shinji Ozaki, Renaud Scheifler, Francis Raoul, 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), XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Ingénierie des milieux aquatiques et des corridors fluviaux (IMACOF), Université de Tours (UT), Agence De l'Environnement et de la Maitrise de l'Energie [1172C0030], Conseil Regional du Nord-Pas de Calais [12000921, 14001044], Fondation pour la Recherche sur la Biodiversite, Conseil Regional de Franche-Comte [2015C-06107], and Université de Tours
Subjects: 0301 basic medicine, Pollution, Apodemus sylvaticus, media_common.quotation_subject, Biodiversity, trace metals, 010501 environmental sciences, Generalist and specialist species, 01 natural sciences, food selection, 03 medical and health sciences, diet diversity, Genetics, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, media_common, Trophic level, biodiversity, 2. Zero hunger, biology, Ecology, Contamination, biology.organism_classification, Soil contamination, [SDE.ES]Environmental Sciences/Environmental and Society, Wood mouse, 030104 developmental biology, 13. Climate action, Species richness
Abstract: International audience; Mammals are mainly exposed to trace metals (TMs) via consuming contaminated food. Several studies have demonstrated relationships between metal concentrations in food and in animal tissues. However, potential effects of TMs on feeding behaviour of wildlife have been poorly documented under field conditions, despite experimental evidence showing that food selection is impacted by resource contamination. Here, we test the hypothesis that the diet of a generalist rodent, the wood mouse (Apodemus sylvaticus), is altered by soil TM contamination in the field. Wood mice were sampled in spring and in autumn along a gradient of soil contamination in the surroundings of a former smelter located in northern France. Available resources in the field were inventoried, and the diet of the animals was analysed using DNA metabarcoding. We demonstrated that (a) relationship between the resource richness in the diet and their richness in the field was altered by soil metal contamination. Wood mice specialized their dietalong the gradient of soil metal contamination for both plant and invertebrate resources in spring. We also showed that (b) preference for Salicaceae, a plant family accumulating metals, decreased when soil contamination increased. These results suggest that environmental TM pollution could act as a force modulating trophic interactions in terrestrial food webs, thereby affecting wildlife exposure to contaminants by trophic route.
Published: 2018
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17. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races

Author: Renaud Vitalis, Jean Peccoud, Julie Jaquiéry, Carole M. Smadja, Anaïs Gouin, Lucie Mieuzet, Pierre Nouhaud, Fabrice Legeai, Jean-Christophe Simon, Claire Lemaitre, Mathieu Gautier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Ecologie, Evolution, Symbiose (EES), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique, PA00P3-139720, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, AAP-IN-2009-020, Fondation pour la Recherche sur la Biodiversite, ANR-09-GENM-017-001, Agence Nationale de la Recherche, INRA-AIP BioRessources, ANR-09-GENM-0017,GW-Aphid,Génomique et transcriptomique des populations pour l'identification de gènes contrôlant la variation du mode reproducteur chez le puceron du pois(2009), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers, École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: 2. Zero hunger, 0301 basic medicine, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Candidate gene, Natural selection, [SDV]Life Sciences [q-bio], food and beverages, Biology, biology.organism_classification, Phenotype, Genome, Acyrthosiphon pisum, Gene flow, 03 medical and health sciences, 030104 developmental biology, Evolutionary biology, Genetics, Gene, Genome size, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Identifying the genomic bases of adaptation to novel environments is a long‐term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant‐specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model‐based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population‐specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host–plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host–plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
Published: 2018
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18. Vegetation ecology meets ecosystem science: Permanent grasslands as a functional biogeography case study

Author: Eric Garnier, Nicolas Viovy, Servane Lemauviel-Lavenant, Guilhem Debarros, Cyrille Violle, Sandra Lavorel, Alexis Mikolajczak, François Munoz, Jessy Loranger, Jens Kattge, Claudy Jolivet, Sophie Gachet, Bernard Amiaud, Benjamin Borgy, Sylvain Diquélou, Jean Olivier, Philippe Choler, 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), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Unité INFOSOL (ORLEANS INFOSOL), Institut National de la Recherche Agronomique (INRA), Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, Institut Français de Pondichéry (IFP), Centre National de la Recherche Scientifique (CNRS)-Ministère de l'Europe et des Affaires étrangères (MEAE), 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]), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Fondation pour la Recherche sur la Biodiversite, National Eye Research Centre, 221060, Marie Curie International Outgoing Fellowship, DIVERSITAS, IGBP, Global Land Project, GIS 'Climat, Environnement et Société' France, 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), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), InfoSol (InfoSol), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation des Surfaces et Interfaces Continentales (MOSAIC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-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]), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), 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]), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3)
Subjects: Environmental Engineering, Biogeography, Big data, Biodiversity, Functional diversity, Biology, Nutrient cycling, Plant databases, Ecoinformatics, Environmental Chemistry, Ecosystem, Plant traits, Waste Management and Disposal, Ecosystem science, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, Ecology, Land use, Community weighed mean (CWM), business.industry, Environmental resource management, 15. Life on land, Grassland, Pollution, 13. Climate action, Land Surface Models, Plant functional trait, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, C3 grasslands, business
Abstract: International audience; The effect of biodiversity on ecosystem functioning has been widely acknowledged, and the importance of the functional roles of species, as well as their diversity, in the control of ecosystem processes has been emphasised recently. However, bridging biodiversity and ecosystem science to address issues at a biogeographic scale is still in its infancy. Bridging this gap is the primary goal of the emerging field of functional biogeography. While the rise of Big Data has catalysed functional biogeography studies in recent years, comprehensive evidence remains scarce. Here, we present the rationale and the first results of a country-wide initiative focused on the C-3 permanent grasslands. We aimed to collate, integrate and process large databases of vegetation releves, plant traits and environmental layers to provide a country-wide assessment of ecosystem properties and services which can be used to improve regional models of climate and land use changes. We outline the theoretical background, data availability, and ecoinformatics challenges associated with the approach and its feasibility. We provide a case study of upscaling of leaf drymatter content averaged at ecosystemlevel and country-wide predictions of forage digestibility. Our framework sets milestones for further hypothesis testing in functional biogeography and earth system modelling. (C) 2015 Elsevier B.V. All rights reserved.
Published: 2015
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19. Neobodonids are dominant kinetoplastids in the global ocean

Author: Flegontova, Olga, Flegontov, Pavel, Malviya, Shruti, Poulain, Julie, de Vargas, Colomban, Bowler, Chris, Lukes, Julius, Horak, Ales, Czech Academy of Sciences [Prague] (CAS), University of South Bohemia, Technical University of Ostrava [Ostrava] (VSB), 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), Tata Institute for Fundamental Research (TIFR), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ERC [CZ LL1601], Czech Grant Agency [15-17643S, 14-23986S], ERC, Foundation Prince Albert II de Monaco, Tara Foundation, Louis D Foundation, PSL* Research University [ANR-1253 11-IDEX-0001-02], Radcliffe Institute of Advanced Study at Harvard University, CNRS [GDR3280], European Molecular Biology Laboratory (EMBL), Agence Nationale de la Recherche, Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, Electricit e de France (EDF) Foundation, Fondation pour la recherche sur la biodiversite (FRB), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), 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: Oceans and Seas, [SDV]Life Sciences [q-bio], parasitic diseases, fungi, RNA, Ribosomal, 18S, Biodiversity, Kinetoplastida, Plankton, DNA, Ribosomal, Phylogeny
Abstract: International audience; Kinetoplastid flagellates comprise basal mostly free-living bodonids and derived obligatory parasitic trypanosomatids, which belong to the best-studied protists. Due to their omnipresence in aquatic environments and soil, the bodonids are of ecological significance. Here, we present the first global survey of marine kinetoplastids and compare it with the strikingly different patterns of abundance and diversity in their sister clade, the diplonemids. Based on analysis of 18S rDNA V9 ribotypes obtained from 124 sites sampled during the Tara Oceans expedition, our results show generally low to moderate abundance and diversity of planktonic kinetoplastids. Although we have identified all major kinetoplastid lineages, 98% of kinetoplastid reads are represented by neobodonids, namely specimens of the Neobodo and Rhynchomonas genera, which make up 59% and 18% of all reads, respectively. Most kinetoplastids have small cell size (0.8-5 mu m) and tend to be more abundant in the mesopelagic as compared to the euphotic zone. Some of the most abundant operational taxonomic units have distinct geographical distributions, and three novel putatively parasitic neobodonids were identified, along with their potential hosts.
Published: 2018
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20. Representing taxonomic, phylogenetic and functional diversity: new challenges for Mediterranean marine-protected areas

Author: Emmanuel J. P. Douzery, Marc Troussellier, Christine N. Meynard, Camille Albouy, Joachim Claudet, Nicolas Mouquet, Miguel B. Araújo, David Mouillot, Laure Velez, François Guilhaumon, Frida Ben Rais Lasram, Jean-Antoine Tomasini, 'Rui Nabeiro' Biodiversity Chair, Centro de Investigaçao em Biodiversidade e Recursos Genéticos, Ecologie des systèmes marins côtiers (Ecosym), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), 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 d'Excellence CORAIL (LabEX CORAIL), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Laboratoire Ecosystèmes et Ressourcs Aquatiques, Institut National Agronomique de Tunisie, 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, 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), 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), Laboratório de Oceanografia Física Estuarina e Costeira, Depto. Oceanografia, 'Range Shift' project from Fundacao para a Ciencia e a Tecnologia (Portugal) [PTDC/AAC-AMB/098163/2008], European Social Fund, Delta Cafes, MELS-FQRNT post-doctoral fellowship, biodivERsA BUFFER project, Integrated Program of ICDT [1/SAESCTN/ALENT-07-0224-FEDER-001755], Spanish Research Council (CSIC), Danish NSF, Marie Curie International Outgoing Fellowship (FISHECO) [IOF-GA-2009-236316], Total Foundation, the 'Fondation pour la Recherche sur la Biodiversite' (project BIODIVMED), European Project: 287844,EC:FP7:KBBE,FP7-OCEAN-2011,COCONET(2012), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA)
Subjects: Range (biology), Ecology, Null model, education, fungi, Species distribution, Biodiversity, Gap analysis (conservation), respiratory system, Functional diversity, Biology, reserves, taxonomic diversity, Phylogenetic diversity, Mediterranean sea, marine-protected area, parasitic diseases, phylogenetic diversity, Mediterranean fishes, Marine protected area, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, gap analysis, human activities, Ecology, Evolution, Behavior and Systematics
Abstract: François Guilhaumon [et al.], Aim: To assess gaps in the representation of taxonomic, phylogenetic and functional diversity among coastal fishes in Mediterranean marine-protected areas (MPAs)., Location: Mediterranean Sea, Methods: We first assessed gaps in the taxonomic representation of the 340 coastal fish species in Mediterranean MPAs, with representation targets (the species range proportion to be covered by MPAs) set to be inversely proportional to species’ range sizes. We then asked whether MPAs favoured representation of phylogenetically and functionally more distinct species or whether there was a tendency to favour less distinctive ones. We finally evaluated the overall conservation effectiveness of the MPAs using a metric that integrates species’ phylogenetic and functional relationships and targets achievement. The effectiveness of the MPA system at protecting biodiversity was assessed by comparison of its achievements against a null model obtained by siting current MPAs at random over the study area., Results: Among the coastal fish species analysed, 16 species were not covered by any MPA. All the remaining species only partially achieved the pre-defined representation target. The current MPA system missed fewer species than expected from siting MPAs at random. However, c. 70% of the species did not achieve better protection in the current MPAs than expected from siting MPAs at random. Functional and evolutionary distinctiveness were weakly correlated with target achievement. The observed coverage of taxonomic, phylogenetic and functional diversity was not different or lower than expected from siting MPAs at random., Main conclusions: The Mediterranean MPA system falls short in meeting conservation targets for coastal fish taxonomic diversity, phylogenetic diversity and functional diversity. Mediterranean MPAs do not encompass more biodiversity than expected by chance. This study reveals multiple ongoing challenges and calls for regional collaboration for the extension of the Mediterranean system of MPAs to meet international commitments and reduce the ongoing loss of marine biodiversity., M.B.A. also acknowledges the Integrated Program of IC&DT Call No. 1/SAESCTN/ALENT-07-0224-FEDER-001755, the Spanish Research Council (CSIC) and the Danish NSF for support of his research.
Published: 2014
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21. Relative impact of mateversuspollinator availability on pollen limitation and outcrossing rates in a mass-flowering species

Author: Peter Winterton, André Pornon, Chloé E. L. Delmas, Olivia Charrier, S. Ruzafa, P-O. Cheptou, Nathalie Escaravage, Santé et agroécologie du vignoble (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), 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, Université de Montpellier (UM), Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, and La Fondation Pour la Recherche sur la Biodiversite (COMBIO project) [AAP-IN-2009-013]
Subjects: Insecta, Rhododendron, Pollination, [SDV]Life Sciences [q-bio], Floral display, Outcrossing, Flowers, Plant Science, Biology, medicine.disease_cause, self-incompatibility, mass flowering, Geitonogamy, Rhododendron ferrugineum, Herkogamy, Pollinator, outcrossing rate, Pollen, medicine, Animals, Crosses, Genetic, reproductive traits, Ecology, Evolution, Behavior and Systematics, Ecology, Reproduction, fungi, food and beverages, Selfing, General Medicine, 15. Life on land, Mating system, insect visits, pollen limitation, Phenotype, Multivariate Analysis, Seeds
Abstract: International audience; Plant mating systems are driven by several pre-pollination factors, including pollinator availability, mate availability and reproductive traits. We investigated the relative contributions of these factors to pollination and to realized outcrossing rates in the patchily distributed mass-flowering shrub Rhododendron ferrugineum. We jointly monitored pollen limitation (comparing seed set from intact and pollen-supplemented flowers), reproductive traits (herkogamy, flower size and autofertility) and mating patterns (progeny array analysis) in 28 natural patches varying in the level of pollinator availability (flower visitation rates) and of mate availability (patch floral display estimated as the total number of inflorescences per patch). Our results showed that patch floral display was the strongest determinant of pollination and of the realized outcrossing rates in this mass-flowering species. We found an increase in pollen limitation and in outcrossing rates with increasing patch floral display. Reproductive traits were not significantly related to patch floral display, while autofertility was negatively correlated to outcrossing rates. These findings suggest that mate limitation, arising from high flower visitation rates in small plant patches, resulted in low pollen limitation and high selfing rates, while pollinator limitation, arising from low flower visitation rates in large plant patches, resulted in higher pollen limitation and outcrossing rates. Pollinator-mediated selfing and geitonogamy likely alleviates pollen limitation in the case of reduced mate availability, while reduced pollinator availability (intraspecific competition for pollinator services) may result in the maintenance of high outcrossing rates despite reduced seed production.
Published: 2014
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22. Conservation of the endangered Mediterranean tortoise Testudo hermanni hermanni: The contribution of population genetics and historical demography

Author: Giorgio Bertorelle, Raphaël Leblois, Giuseppe Sotgiu, Véronique Arnal, Albert Bertolero, Saliha Zenboudji, Marc Cheylan, Claudine Montgelard, Guillelme Astruc, Joan Lluís Pretus, Mario Lo Valvo, Zenboudji, S., Cheylan, M., Arnal, V., Bertolero, A., Leblois, R., Astruc, G., Bertorelle, G., Pretus, J., LO VALVO, M., Sotgiu, G., Montgelard, C., Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Picampall, the Terres de l'Ebre Ornithological Association, Partenaires INRAE, 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), 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), Università degli Studi di Ferrara (UniFE), Dept Ecol, University of São Paulo (USP), Università degli Studi di Palermo, Association Zirichiltaggi Sardinia Wildlife Conservation, University of Johannesburg (UJ), and Foundation for Research on Biodiversity (FRB: Fondation pour la Recherche sur la Biodiversite) , CORSEPYR project , French National Action Plan (PNA: Plan National d'Action) , French ministery of ecology grants (DREAL-PACA): CNRS contract, Ebro Delta Natural Park , Generalitat de Catalunya, Institut Menorqui d'Estudis (IME) , Spanish Ministry of Science and Technology
Subjects: 0106 biological sciences, 0301 basic medicine, Conservation genetics, Demographic history, Tortoise, [SDV]Life Sciences [q-bio], Population, Endangered species, Settore BIO/05 - Zoologia, Zoology, Biology, 010603 evolutionary biology, 01 natural sciences, Testudo hermanni, 03 medical and health sciences, 14. Life underwater, education, Microsatellites, Conservation genetic, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Testudo hermanni Genetic structure, Conservation issues, education.field_of_study, Ecology, Ambientale, Microsatellite, 15. Life on land, biology.organism_classification, Conservation genetics, Demographic history, Microsatellites, Testudo hermanni, Genetic structure, Conservation issues, 030104 developmental biology, Threatened species, Genetic structure
Abstract: International audience; Estimating the genetic variation and demographic trends of species in decline is of major concern in conservation genetics. This study contributes to understanding how historical and anthropogenic factors shape the distribution of current genetic diversity in one of the most endangered reptiles in Western Europe, the Hermann's tortoise Testudo hermanni hermanni. We used 17 microsatellite loci, chosen from a pyrosequencing library specifically developed for the subspecies to genotype eight populations distributed over about 30 sample localities covering almost the entire geographic distribution of the sub-species. The population genetic results reflect a very strong genetic structure and identify three major clusters among the Hermann's tortoise in the occidental Mediterranean basin: a continental cluster (Albera in Spain, Var in France and continental Italy), an insular cluster (Corsica, Sardinia and Sicily) and a cluster of mixed lineage (Minorca). Each of the eight studied populations is characterized by only one lineage except for Minorca, in which two lineages were identified. In contrast to what most empirical studies predict, the genetic diversity of the Hermann's tortoise is greater on islands than on the continent. Islands can therefore be considered as genetic sanctuaries with high conservation potential for this species, particularly in Corsica. Historical demographic patterns inferred with a generalized stepwise-mutation model (GSM) using maximum likelihood showed significant past demographic changes in only two of the eight sampled populations: a demographic bottleneck was detected in the Albera population (Spain) and a demographic expansion in Corsica (France). In contrast to what was argued in previous studies, these results indicate that the Hermann's tortoise lineage found in Corsica is autochthonous. The origin of both lineages found in Minorca remains speculative. Lastly, our study identifies the six most relevant management units (sensu Moritz, 1994) for conservation purposes on the basis that they represent a significant part of the evolutionary legacy of the species. Some conservation recommendations were proposed, in particular for the most threatened population in Albera.
Published: 2016
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23. Insights into global diatom distribution and diversity in the world's ocean

Author: Daniele Iudicone, Stéphane Audic, Colomban de Vargas, Patrick Wincker, Flora Vincent, Chris Bowler, Shruti Malviya, Julie Poulain, Alaguraj Veluchamy, Eleonora Scalco, Adriana Zingone, Lucie Bittner, Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, 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 des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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 des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Ministero dell'Istruzione dell'Universit a e della Ricerca RITMARE project, Centre National de la Recherche Scientifique, Agnes b., Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, Electricite de France (EDF) Foundation EDF Diversiterre, Fondation pour la Recherche sur la Biodiversite, Prince Albert II de Monaco Foundation, Etienne Bourgois, Groupement de Recherche [GDR3280], Tara schooner, European Molecular Biology Laboratory, Genoscope/Commissariat a l'Energie Atomique, French Government ``Investissements d'Avenir' [ANR-11-BTBR-0008, ANR-10-INBS-09-08, ANR-10-LABX-54], Paris Sciences et Lettres (PSLstar) Research University [ANR-11-IDEX-0001-02], Agence Nationale de la Recherche (ANR) [ANR-10-INBS-09-08, ANR-09-BLAN-0348, ANR-09-GENM-031, ANR-2010-1709-01], European Union [287589], European Research Council [294823], Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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 des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Aquatic Organisms, Databases, Factual, Range (biology), Oceans and Seas, Biodiversity, Tara Oceans, DNA, Ribosomal, 01 natural sciences, diatoms, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Phytoplankton, Photic zone, 14. Life underwater, Ecosystem, biodiversity, Microscopy, Multidisciplinary, biology, choke points, Ecology, 010604 marine biology & hydrobiology, Ocean current, Reproducibility of Results, Chaetoceros, Plankton, biology.organism_classification, 030104 developmental biology, Oceanography, Diatom, PNAS Plus, metabarcoding
Abstract: International audience; Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of similar to 12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.
Published: 2016
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24. Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Author: Urrestarazu Vidart, Jorge, Denancé, Caroline, Ravon, Elisa, Guyader, Arnaud, Guisnel, Rémi, Feugey, Laurence, Poncet, Charles, Lateur, Marc, Houben, Patrick, Ordidge, Matthew, Fernández Fernández, Felicidad, Evans, Kate M., Paprstein, Frantisek, Sedlak, Jiri, Nybom, Hilde, Garkava Gustavsson, Larisa, Miranda Jiménez, Carlos, Gassmann, Jennifer, Kellerhals, Markus, Suprun, Ivan, Pikunova, Anna V., Krasova, Nina G., Torutaeva, Elnura, Dondini, Luca, Tartarini, Stefano, Laurens, François, Durel, Charles Eric, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Department of Agricultural Sciences, University of Bologna, Public University of Navarre, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Plant Breeding & Biodiversity, Centre Wallon de Recherches Agronomiques (CRA-W), School of Agriculture, Policy and Development, University of Reading (UOR), East Malling Research, Tree Fruit Research and Extension Center, Washington State University (WSU), Research and Breeding Institute of Pomology Holovousy Ltd., Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Institute for Plant Production Sciences IPS, Agroscope, North Caucasian Regional Research Institute of Horticulture and Viticulture (NCRRIH&V), All-Russian Research Institute of Fruit Crop Breeding (VNIISPK), Kyrgyz National Agrarian University, INIA, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (RF2004-008-C03-00), Swiss Federal Office for Agriculture, FRB (Fondation pour la Recherche sur la Biodiversite), UK Depart for the Environment Food and Rural Affairs (Defra) (GC0140), Russian Scientific Fund (projet n° 14-1600127), Institute of Advanced Studies (University of Bologna), European Project: 265582, Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), University of Bologna/Università di Bologna, Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), Research and Breeding Institute of Pomology Holovousy (VSUO), AGROCAMPUS OUEST, 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 National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Urrestarazu, Jorge, Denancé, Caroline, Ravon, Elisa, Guyader, Arnaud, Guisnel, Rémi, Feugey, Laurence, Poncet, Charle, Lateur, Marc, Houben, Patrick, Ordidge, Matthew, Fernandez-Fernandez, Felicidad, Evans, Kate M., Paprstein, Frantisek, Sedlak, Jiri, Nybom, Hilde, Garkava-Gustavsson, Larisa, Miranda, Carlo, Gassmann, Jennifer, Kellerhals, Marku, Suprun, Ivan, Pikunova, Anna V., Krasova, Nina G., Torutaeva, Elnura, Dondini, Luca, Tartarini, Stefano, Laurens, Françoi, Durel, Charles-Eric, Universidad Pública de Navarra. Departamento de Producción Agraria, and Nafarroako Unibertsitate Publikoa. Nekazaritza Ekoizpena Saila
Subjects: 0106 biological sciences, 0301 basic medicine, Conservation genetics, Germplasm, Range (biology), [SDV]Life Sciences [q-bio], Plant Science, Population structure, 01 natural sciences, ressource génétique végétale, Parentage analysis, Genetic resources, Phylogeny, 2. Zero hunger, Malus x domestica Borkh, SSR markers, Europe, diversité génétique, Malus, Differentiation, marqueur ssr, Research Article, Gene Flow, Genetic Markers, Parentage analysi, Genotype, pommier, Biology, 03 medical and health sciences, Genetic drift, Genetic variation, Genetic resource, Variability, SSR marker, Genetic association, Genetic diversity, business.industry, Genetic Variation, modèle bayésien, Biotechnology, genetic resources, population structure, variability, differentiation, parentage analysis, 030104 developmental biology, Genetic marker, Evolutionary biology, germplasme, origine géographique, business, 010606 plant biology & botany, Genome-Wide Association Study, Microsatellite Repeats
Abstract: Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies. This work has been partly funded under the EU seventh Framework Programme by the FruitBreedomics project N°265582: “Integrated approach for increasing breeding efficiency in fruit tree crops”. Genotyping of the Spanish collection was partially funded by INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (project grant no RF2004-008-C03-00). Genotyping of the Swiss collection was funded by the Swiss Federal Office for Agriculture. Genotyping of the French collection was funded by the FRB, ‘Fondation pour la Recherche sur la Biodiversité’. Initial genotyping of the UKNFC material was funded by the UK Depart for the Environment Food and Rural Affairs (Defra), grant GC0140. Providing of VNIISPK material (DNA isolation and delivery) have been done with support of Russian Scientific Fund, Project 14- 1600127. JU has been partially supported by an Early Stage Research Fellowship of the Institute of Advanced Studies (University of Bologna).
Published: 2016
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25. Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

Author: Le Bescot, Noan, Mahé, Frédéric, Audic, Stéphane, Dimier, Céline, Garet, Marie-Jose, Poulain, Julie, Wincker, Patrick, Vargas, Colomban, Siano, Raffaele, Department of ecology, Technische Universität Kaiserslautern (TU Kaiserslautern), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), 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), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Region Bretagne PhD grant, CNRS [GDR3280], Fondation pour la Recherche sur la Biodiversite (FRB), Prince Albert II de Monaco Foundation, ANR (Agence National de la Recherche) [ANR-09-BLAN-0348, ANR-10-INPS-09], French government [ANR-11-BTBR-0008], Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, EDF Foundation Diversiterre, Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences
Abstract: International audience; Dinoflagellates (Alveolata) are one of the ecologically most important groups of modern phytoplankton. Their biological complexity makes assessment of their global diversity and community structure difficult. We used massive V9 18S rDNA sequencing from 106 size-fractionated plankton communities collected across the world's surface oceans during the Tara Oceans expedition (2009-2012) to assess patterns of pelagic dinoflagellate diversity and community structuring over global taxonomic and ecological scales. Our data and analyses suggest that dinoflagellate diversity has been largely underestimated, representing overall approximate to 1/2 of protistan rDNA metabarcode richness assigned at 90% to a reference sequence in the world's surface oceans. Dinoflagellate metabarcode diversity and abundance display regular patterns across the global scale, with different order-level taxonomic compositions across organismal size fractions. While the pico to nano-planktonic communities are composed of an extreme diversity of metabarcodes assigned to Gymnodiniales or are simply undetermined, most micro-dinoflagellate metabarcodes relate to the well-referenced Gonyaulacales and Peridiniales orders, and a lower abundance and diversity of essentially symbiotic Peridiniales is unveiled in the meso-plankton. Our analyses could help future development of biogeochemical models of pelagic systems integrating the separation of dinoflagellates into functional groups according to plankton size classes.
Published: 2016
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26. The reproductive biology of the myrmecophyte, Hirtella physophora, and the limitation of negative interactions between pollinators and ants

Author: Lucie Lusignan, Pierre-Jean G. Malé, Frédéric Petitclerc, Céline Leroy, Jérôme Orivel, Angélique Quilichini, 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, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), 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]), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Fondation pour la Recherche sur la Biodiversite [AAP-IN-2009-050], Programme Convergence Region Guyane from the European Community (BI-Appli) [115/SGAR-DE/2011/052274], 'Investissement d'Avenir' grants (CEBA) [ANR-10-LABX-25-01], 'Investissement d'Avenir' grants (TULIP) [ANR-10-LABX-0041], ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), 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]), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), ANR-10- LABX-25-01,CEBA,Labex CEBA ANR-10- LABX-25-01, and ANR: Labex TULIP,TULIP,ANR-10-LABX-0041
Subjects: 0106 biological sciences, Spatial and temporal segregation, Plant reproductive biology, Pollination, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Myrmecophyte, Pollinator, Pollen, medicine, Hirtella physophora, Ant–pollinator interactions, Ecology, Evolution, Behavior and Systematics, Allomerus decemarticulatus, Ecology, biology, Obligate, Chrysobalanaceae, 15. Life on land, biology.organism_classification, Ant-plant, Insect Science, Floral structure and display, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Myrmecophytism occurs in plants that offer ants a nesting space and, often, food rewards in exchange for protection from predators and competitors. Such biotic protection by ants can, however, interfere with the activity of pollinators leading to potential negative consequences for the plant’s reproduction. In this study, we focused on the association between the understory myrmecophyte, Hirtella physophora (Chrysobalanaceae), and its obligate ant partner, Allomerus decemarticulatus (Myrmicinae). We investigated the reproductive biology of H. physophora and the putative mechanisms that may limit ant–pollinator conflict. Our results show that H. physophora is an obligate outcrosser, self-incompatible, and potentially insect-pollinated species. The reproduction of H. physophora relies entirely on pollen transfer by pollinators that are likely quite specific. Potential interference between flower-visiting insects during pollination may also be lessened by a spatial and temporal segregation of ant and pollinator activities, thus enabling pollen transfer and fruit production.
Published: 2015
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27. Network impact on persistence in a finite population dynamic diffusion model: Application to an emergent seed exchange network

Author: Isabelle Goldringer, Pierre Barbillon, Mathieu Thomas, Stéphane Robin, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Fondation pour la Recherche sur la Biodiversite (FRB), Paris, France, Reseau National des Systemes Complexes, Paris, France, grant 'Contrat Jeunes Scientiques' from the Institut National de la Recherche Agronomique, France, and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)
Subjects: FOS: Computer and information sciences, 0106 biological sciences, Statistics and Probability, Mathematical optimization, Dynamic network analysis, Computer science, [SDV]Life Sciences [q-bio], Population Dynamics, Population, Metapopulation, Context (language use), Network topology, Models, Biological, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Diffusion, 010104 statistics & probability, Sensitivity (control systems), 0101 mathematics, education, Quantitative Biology - Populations and Evolution, Finite-population model, Triticum, Probability, Social network, education.field_of_study, General Immunology and Microbiology, Ecology, business.industry, Other Statistics (stat.OT), Applied Mathematics, Populations and Evolution (q-bio.PE), General Medicine, 15. Life on land, Biological Evolution, Farmer-to-farmer seed diffusion, Statistics - Other Statistics, FOS: Biological sciences, Modeling and Simulation, Seeds, France, General Agricultural and Biological Sciences, business, Sensitivity analysis, Heterogeneous network
Abstract: Dynamic extinction colonisation models (also called contact processes) are widely studied in epidemiology and in metapopulation theory. Contacts are usually assumed to be possible only through a network of connected patches. This network accounts for a spatial landscape or a social organisation of interactions. Thanks to social network literature, heterogeneous networks of contacts can be considered. A major issue is to assess the influence of the network in the dynamic model. Most work with this common purpose uses deterministic models or an approximation of a stochastic Extinction-Colonisation model (sEC) which are relevant only for large networks. When working with a limited size network, the induced stochasticity is essential and has to be taken into account in the conclusions. Here, a rigorous framework is proposed for limited size networks and the limitations of the deterministic approximation are exhibited. This framework allows exact computations when the number of patches is small. Otherwise, simulations are used and enhanced by adapted simulation techniques when necessary. A sensitivity analysis was conducted to compare four main topologies of networks in contrasting settings to determine the role of the network. A challenging case was studied in this context: seed exchange of crop species in the R\'eseau Semences Paysannes (RSP), an emergent French farmers' organisation. A stochastic Extinction-Colonisation model was used to characterize the consequences of substantial changes in terms of RSP's social organisation on the ability of the system to maintain crop varieties.
Published: 2015
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28. Eukaryotic plankton diversity in the sunlit ocean

Author: Jean-Marc Aury, Daniele Iudicone, Hiroyuki Ogata, Stéphane Audic, Frédéric Mahé, Fabrice Not, Johan Decelle, Gabriel Gorsky, Silvia G. Acinas, Pascal Hingamp, Sarah Romac, Noan Le Bescot, Matthieu Mulot, Sébastien Colin, Eleonora Scalco, Michael E. Sieracki, Marc Picheral, Tara Oceans Coordinators, Nicolas Henry, Stephane Pesant, Micah Dunthorn, Adriana Zingone, Sabrina Speich, Margaux Carmichael, Chris Bowler, Sarah Searson, Céline Dimier, Jeroen Raes, Gipsi Lima-Mendez, Shruti Malviya, Aleš Horák, Eric Karsenti, Ramiro Logares, Olga Flegontova, Julius Lukeš, Shinichi Sunagawa, Flora Vincent, Stefanie Kandels-Lewis, Enrique Lara, Raphael Morard, Stefan Engelen, Peer Bork, Patrick Wincker, Colomban de Vargas, Raffaele Siano, Ian Probert, Jean Weissenbach, Lars Stemmann, Cédric Berney, Samuel Chaffron, Olivier Jaillon, Lionel Guidi, Julie Poulain, Lucie Bittner, Nigel Grimsley, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), 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), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of ecology, Universität Kaiserslautern, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Immunobiologie Cellulaire et Moléculaire des Infections Parasitaires, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Oceanography, University of Hawai‘i [Mānoa] (UHM), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Faculty of Informatics [Brno] (FI / MUNI), Masaryk University [Brno] (MUNI), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Département Electronique, Optronique et Signal (DEOS), Institut Supérieur de l'Aéronautique et de l'Espace (ISAE-SUPAERO), Stazione Zoologica Anton Dohrn (SZN), European Molecular Biology Laboratory [Heidelberg] (EMBL), European Molecular Biology Laboratory [Grenoble] (EMBL), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory, Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Kaiserslautern (TU Kaiserslautern), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratory of Soil Biodiversity, Université de Neuchâtel (UNINE), CNRS [GDR3280], EMBL, Agency for Administration of University and Research Grants (AGAUR) [CONES 2010-0036], Veolia Environment Foundation, EBI [PRJEB402, PRJEB6610], Genoscope/CEA, Lorient Agglomeration, Illumina, UNIMIB, Electricite de France Foundation, Fondation pour la Recherche sur la Biodiversite, Tara schooner, Fund for Scientific Research - The French Ministry of Research, French Government [ANR-11-BTBR-0008, ANR-10-INBS-09-08, ANR-10-LABX-54], French Ministry of Foreign Affairs, UPMC, European Research Council [294823], VIB, Stazione Zoologica Anton Dohrn, Rega Institute, Japan Society for the Promotion of Science [26430184], KU Leuven, PSL* Research University [ANR-11-IDEX-0001-02], World Courier, ANR [POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, PHYTBACK/ANR-2010-1709-01, TARA-GIRUS/ANR-09-PCS-GENM-218], EU FP7 [287589, IHMS/HEALTH-F4-2010-261376], Gordon and Betty Moore Foundation [3790], Prince Albert II de Monaco Foundation, Spanish Ministry of Science and Innovation [CGL2011-26848/BOS], Diversité et Interactions au sein du Plancton Océanique ( DIPO ), Adaptation et diversité en milieu marin ( ADMM ), 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 ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Evolution des Protistes et Ecosystèmes Pélagiques ( EPEP ), 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 ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie Paris-Seine, Institute of Molecular Biology and Swiss Institute of Bioinformatics, University of Zürich [Zürich] ( UZH ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR113-Institut National de la Santé et de la Recherche Médicale ( INSERM ), University of Hawaii at Manoa ( UHM ), Laboratoire d'océanographie de Villefranche ( LOV ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Faculty of Informatics [Masaryk], Masaryk University, Institut de Génomique, Genoscope, Centre National de Séquençage, MARUM, Universität Bremen Postfach, Dynamiques de l'Environnement Côtier ( DYNECO ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Département Electronique, Optronique et Signal ( DEOS ), Institut Supérieur de l'Aéronautique et de l'Espace ( ISAE-SUPAERO ), Stazione Zoologica Napoli, European Molecular Biology Laboratory [Heidelberg] ( EMBL ), European Molecular Biology Laboratory ( EMBL ), Biologie intégrative des organismes marins ( BIOM ), Observatoire océanologique de Banyuls ( OOB ), Information génomique et structurale ( IGS ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Kyoto University [Kyoto], Université Catholique de Louvain ( UCL ), Laboratoire de physique des océans ( LPO ), Institut de Recherche pour le Développement ( IRD ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des Sciences de l'Environnement Marin (LEMAR) ( LEMAR ), Institut de Recherche pour le Développement ( IRD ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de Brest ( UBO ) -Institut Universitaire Européen de la Mer ( IUEM ), Institut de Recherche pour le Développement ( IRD ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Technische Universität Kaiserskautern, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] ( ICM ), Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -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 ), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Lausanne (UNIL), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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)-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)-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, 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), and Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Multidisciplinary, biology, [ SDV ] Life Sciences [q-bio], Ecology, Range (biology), [SDV]Life Sciences [q-bio], fungi, Rhizaria, Biodiversity, 15. Life on land, Ribosomal RNA, Plankton, biology.organism_classification, [ SDE ] Environmental Sciences, Phylogenetics, [SDE]Environmental Sciences, natural sciences, 14. Life underwater, Taxonomic rank, Ribosomal DNA
Abstract: Vargas, Colomban de ... et. al.-- 11 pages, 7 figures, supplementary materials www.sciencemag.org/content/348/6237/1261605/suppl/DC1, Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ∼150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ∼11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts. © 2015, American Association for the Advancement of Science. All rights reserved, We thank the following people and sponsors for their commitment: CNRS (in particular, the GDR3280); EMBL; Genoscope/CEA; UPMC; VIB; Stazione Zoologica Anton Dohrn; UNIMIB; Rega Institute; KU Leuven; Fund for Scientific Research – The French Ministry of Research, the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), and MEMO LIFE (ANR-10-LABX-54); PSL* Research University (ANR-11-IDEX-0001-02); ANR (projects POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCSGENM-217, PHYTBACK/ANR-2010-1709-01, and TARA-GIRUS/ANR-09-PCS-GENM-218); EU FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376); European Research Council Advanced Grant Awards to C. Bowler (Diatomite:294823); Gordon and Betty Moore Foundation grant 3790 to M.B.S.; Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS and TANIT (CONES 2010-0036) grant from the Agency for Administration of University and Research Grants (AGAUR) to S.G.A.; and Japan Society for the Promotion of Science KAKENHI grant 26430184 to H.O. We also thank the following for their support and commitment: A. Bourgois, E. Bourgois, R. Troublé, Région Bretagne, G. Ricono, the Veolia Environment Foundation, Lorient Agglomération, World Courier, Illumina, the Electricité de France Foundation, Fondation pour la Recherche sur la Biodiversité, the Prince Albert II de Monaco Foundation, and the Tara schooner and its captains and crew. We thank MERCATORCORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)
Published: 2015
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29. Asynchrony of taxonomic, functional and phylogenetic diversity in birds

Author: Monnet, Anne-Christine, Jiguet, Frédéric, Meynard, Christine, Mouillot, David, Mouquet, Nicolas, Thuiller, Wilfried, Devictor, Vincent, 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), 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), 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), 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 d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), 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), 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), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), 'Fondation pour la Recherche sur la Biodiversite' (FRB), European Research Council under the European Community [281422], European Project: 281422,EC:FP7:ERC,ERC-2011-StG_20101109,TEEMBIO(2012), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)
Subjects: Beta diversity, breeding bird survey, Rao, temporal dynamics, homogenization, species turnover, functional traits, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Article, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Aim: We assessed the temporal trends of taxonomic, functional and phylogenetic diversities in the French avifauna over the last two decades. Additionally, we investigated whether and how this multifaceted approach to biodiversity dynamics can reveal an increasing similarity of local assemblages in terms of species, traits and/or lineages. Location: France. Methods: We analysed a large-scale dataset that recorded annual changes in the abundance of 116 breeding birds in France between 1989 and 2012. We decomposed and analysed the spatio-temporal dynamics of taxonomic, phylogenetic and functional diversities and each of their -, - and -components. We also calculated the trend in the mean specialization of bird communities to track the relative success of specialist versus generalist species within communities during the same period. Results: We found large variation within and among the temporal trends of each biodiversity facet. On average, we found a marked increase in species and phylogenetic diversity over the period considered, but no particular trend was found for functional diversity. Conversely, changes in -diversities for the three facets were characterized by independent and nonlinear trends. We also found a general increase in the local occurrence and abundance of generalist species within local communities. Main conclusions: These results highlight a relative asynchrony of the different biodiversity facets occurring at large spatial scales. We show why a multifaceted approach to biodiversity dynamics is needed to better describe and understand changes in community composition in macroecology and conservation biogeography.
Published: 2014
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30. Pan-Tropical Analysis of Climate Effects on Seasonal Tree Growth

Author: Mélaine Aubry-Kientz, Robert Gliniars, Vivien Rossi, Clément Stahl, Fabien Wagner, Antonio Trabucco, Helmut Dalitz, Damien Bonal, Bruno Hérault, Remote Sensing Div, Sao Jose Dos Campos, Instituto Nacional de Pesquisas Espaciais (INPE), Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Biens et services des écosystèmes forestiers tropicaux : l'enjeu du changement global (Cirad-Es-UPR 105 BSEF), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UMI Modelisat Math & Informat Syst Complexes, Université de Yaoundé, Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Inst Bot, University of Hohenheim, Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Euro-Mediterranean Center on Climate Change (CMCC), Div Forest Nat & Landscape, Université Catholique de Louvain (UCL), Climfor (Fondation pour la Recherche sur la Biodiversite), Guyasim (European structural fundings, PO-Feder), Fapesp (Fundacao de Amparo a Pesquisa do Estado de Sao Paulo) [13/14520-6], Agence Nationale de la Recherche (CEBA) [ANR-10-LABX-0025], Biens et services des écosystèmes forestiers tropicaux : l'enjeu du changement global (UPR BSEF), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université de Yaoundé I, 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)-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), Université Catholique de Louvain = Catholic University of Louvain (UCL), Agence Nationale de la Recherche (CEBA), and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: forêt tropicale, Plant Science, Facteur climatique, Global Change Ecology, K01 - Foresterie - Considérations générales, AMAZON FOREST, Forêt tropicale humide, lcsh:Science, Geography, Ecology, Physical Sciences, Sunlight, Modèle mathématique, Statistics (Mathematics), Carbone, P40 - Météorologie et climatologie, Biostatistics, Arbre, RAIN-FOREST TREE, Precipitation, Teneur en eau du sol, Croissance, Changement climatique, Plant Ecology, Ecology and Environmental Sciences, lcsh:R, DRY SEASON, Biology and Life Sciences, Computational Biology, Modèle de simulation, Global change, 15. Life on land, Température, medicine.disease, Greenhouse gas, lcsh:Q, Adsorption, Énergie solaire, Ecosystem Modeling, Mathematics, Rain, [SDV]Life Sciences [q-bio], Stockage, lcsh:Medicine, Atmospheric sciences, Trees, Tropical climate, Dry season, Principal Component Analysis, Multidisciplinary, U10 - Informatique, mathématiques et statistiques, Variation saisonnière, séquestration du carbone, Community Ecology, Seasons, INTERANNUAL VARIABILITY, Ecosystem Functioning, Zone tropicale, Research Article, F60 - Physiologie et biochimie végétale, Biology, Models, Biological, Ecosystems, FRENCH-GUIANA, Sécheresse, Forest ecology, medicine, Terrestrial Ecology, SEMI-DECIDUOUS FOREST, CARBON DYNAMICS, ARAUCARIA-ANGUSTIFOLIA, EXPERIMENTAL DROUGHT, DENDROMETER BANDS, Tropical Climate, Précipitation, Seasonality, 13. Climate action, Climate model
Abstract: Climate models predict a range of changes in tropical forest regions, including increased average temperatures, decreased total precipitation, reduced soil moisture and alterations in seasonal climate variations. These changes are directly related to the increase in anthropogenic greenhouse gas concentrations, primarily CO2. Assessing seasonal forest growth responses to climate is of utmost importance because woody tissues, produced by photosynthesis from atmospheric CO2, water and light, constitute the main component of carbon sequestration in the forest ecosystem. In this paper, we combine intra-annual tree growth measurements from published tree growth data and the corresponding monthly climate data for 25 pan-tropical forest sites. This meta-analysis is designed to find the shared climate drivers of tree growth and their relative importance across pan-tropical forests in order to improve carbon uptake models in a global change context. Tree growth reveals significant intra-annual seasonality at seasonally dry sites or in wet tropical forests. Of the overall variation in tree growth, 28.7% was explained by the site effect, i.e. the tree growth average per site. The best predictive model included four climate variables: precipitation, solar radiation (estimated with extrasolar radiation reaching the atmosphere), temperature amplitude and relative soil water content. This model explained more than 50% of the tree growth variations across tropical forests. Precipitation and solar radiation are the main seasonal drivers of tree growth, causing 19.8% and 16.3% of the tree growth variations. Both have a significant positive association with tree growth. These findings suggest that forest productivity due to tropical tree growth will be reduced in the future if climate extremes, such as droughts, become more frequent. ispartof: PLoS One vol:9 issue:3 ispartof: location:United States status: published
Published: 2014
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31. Generalization of the Partitioning of Shannon Diversity

Author: Gabriel Lang, Bruno Hérault, Ivan Scotti, Eric Marcon, Vivien Rossi, Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Agence Nationale de la Recherche (CEBA) [ANR-10-LABX-25-01], project Climfor (Fondation pour la Recherche sur la Biodiversite), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Marcon, Eric
Subjects: 0106 biological sciences, Entropy, [SDV]Life Sciences [q-bio], Population Dynamics, lcsh:Medicine, 01 natural sciences, 010104 statistics & probability, Espèce, Community Assembly, Forêt tropicale humide, lcsh:Science, Physics, Multidisciplinary, Shannon's source coding theorem, Ecology, U10 - Informatique, mathématiques et statistiques, Applied Mathematics, Min entropy, Biodiversity, Community Ecology, Maximum entropy probability distribution, P01 - Conservation de la nature et ressources foncières, Biodiversité, Algorithms, Modèle mathématique, Research Article, Ecological Metrics, F40 - Écologie végétale, Tsallis entropy, Environment, Models, Biological, 010603 evolutionary biology, Joint entropy, Rényi entropy, Entropy power inequality, Species Specificity, Mesure, Animals, Applied mathematics, 0101 mathematics, Biology, Community Structure, Ecosystem, Population Density, lcsh:R, Maximum entropy thermodynamics, Computational Biology, Étude de cas, Species Diversity, lcsh:Q, Mathematics
Abstract: Traditional measures of diversity, namely the number of species as well as Simpson's and Shannon's indices, are particular cases of Tsallis entropy. Entropy decomposition, i.e. decomposing gamma entropy into alpha and beta components, has been previously derived in the literature. We propose a generalization of the additive decomposition of Shannon entropy applied to Tsallis entropy. We obtain a self-contained definition of beta entropy as the information gain brought by the knowledge of each community composition. We propose a correction of the estimation bias allowing to estimate alpha, beta and gamma entropy from the data and eventually convert them into true diversity. We advocate additive decomposition in complement of multiplicative partitioning to allow robust estimation of biodiversity.
Published: 2014
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32. Inbreeding depression in a parasitoid wasp with single-locus complementary sex determination

Author: Bastien Quaglietti, Chloé Vayssade, Nicolas Ris, Alexandra Auguste, Xavier Fauvergue, Céline de Fazio, Institut Sophia Agrobiotech (ISA), 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)-Institut National de la Recherche Agronomique (INRA), Agence Nationale de la Recherche [ANR-2010-BLAN-1717], and Fondation pour la Recherche sur la Biodiversite [AAP-IN-2009-052]
Subjects: 0106 biological sciences, Male, [SDV]Life Sciences [q-bio], Wasps, lcsh:Medicine, 01 natural sciences, Inbred strain, Ploidy, Inbreeding depression, Natural Selection, Body Size, Inbreeding, Animal Breeding, lcsh:Science, Animal Management, Genetics, 0303 health sciences, détermination du sexe, Multidisciplinary, biology, Ecology, dépression de consanguinité, Agriculture, Gene Pool, [SDE]Environmental Sciences, Haplodiploidy, Female, France, Sex ratio, Research Article, consanguinité, Evolutionary Processes, Outbreeding depression, Longevity, 010603 evolutionary biology, Parasitoid wasp, 03 medical and health sciences, Animals, Parasites, Sex Ratio, Crosses, Genetic, 030304 developmental biology, Ovum, Evolutionary Biology, Genetic Drift, Ecology and Environmental Sciences, lcsh:R, Biology and Life Sciences, venturia canescens, allèle, Sex Determination Processes, biology.organism_classification, Ichneumonidae, Genetic Loci, Evolutionary Ecology, fécondite, Linear Models, Genetic Polymorphism, Veterinary Science, lcsh:Q, Zoology, Entomology, Population Genetics
Abstract: International audience; Inbreeding and inbreeding depression are key processes in small or isolated populations and are therefore central concerns for the management of threatened or (re) introduced organisms. Haplodiploid species of the order Hymenoptera have a particular status with regard to inbreeding depression. Although recessive deleterious alleles that are expressed in males should be purged, an alternative form of inbreeding depression exists in species with single-locus complementary sex determination (sl-CSD). Under sl-CSD, genetically-related parents have a high probability of producing sterile sons instead of fertile daughters. In this article, we study inbreeding depression in Venturia canescens (Hymenoptera: Ichneumonidae), a parasitoid wasp with sl-CSD. We used a crossing design to manipulate relatedness according to three levels: within-family, between-family and between-population. For each level, several fitness components were measured on parents and female offspring. We found a 20% reduction in egg load at emergence for inbred crosses. Inbred crosses also yielded a higher proportion of males, as expected in a species with sl-CSD. Mating probability, presence of daughters among offspring, body size, symmetry and longevity were unaffected by inbreeding.
Published: 2014
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33. Diversity and spatiotemporal dynamics of bacterial communities: Physicochemical and other drivers along an acid mine drainage

Author: Marina Héry, Philippe N. Bertin, Robert Duran, Odile Bruneel, Fabien Javerliat, Béatrice Lauga, Françoise Elbaz-Poulichet, Olivier Bouchez, Aurélie Volant, Noëlle Bru, Angélique Desoeuvre, Corinne Casiot, Anne Fahy, Sophie Delpoux, Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques et de leurs Applications [Pau] (LMAP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), FRB (Fondation pour la recherche sur la Biodiversite) program [AAP-IN-2009039], 'Observatoire de Recherche Mediterraneen de l'Environnement' (OSU-OREME), French Ministry of Education and Research, Direction Generale de l'Armement (DGA), Groupement de recherche: Metabolisme de l'Arsenic chez les Microorganismes [GDR2909CNRS], Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Domaine expérimental d'Auzeville (UE AUZEVILLE), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Virologie et Immunologie Moléculaires (VIM), and Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: Iron, Biodiversity, Biology, Applied Microbiology and Biotechnology, Microbiology, Mining, Microbial ecology, spatial and temporal dynamics, Phylogeny, Environmental gradient, Abiotic component, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Bacteria, Ecology, Sulfates, Water Pollution, arsenic, bacterial diversity, Acidithiobacillus, 15. Life on land, biology.organism_classification, Acid mine drainage, [SDE.ES]Environmental Sciences/Environmental and Society, Microbial population biology, 13. Climate action, [SDE]Environmental Sciences, Biological dispersal, Water Microbiology, Polymorphism, Restriction Fragment Length, Water Pollutants, Chemical, acid mine drainage
Abstract: cited By 15; International audience; Deciphering the biotic and abiotic factors that control microbial community structure over time and along an environmental gradient is a pivotal question in microbial ecology. Carnoulès mine (France), which is characterized by acid waters and very high concentrations of arsenic, iron, and sulfate, provides an excellent opportunity to study these factors along the pollution gradient of Reigous Creek. To this end, biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. Patterns of spatial and temporal variations in bacterial community composition linked to changes in the physicochemical conditions suggested that species-sorting processes were at work in the acid mine drainage. Arsenic, temperature, and sulfate appeared to be the most important factors that drove the composition of bacterial communities along this continuum. Time series investigation along the pollution gradient also highlighted habitat specialization for some major members of the community (Acidithiobacillus and Thiomonas), dispersal for Acidithiobacillus, and evidence of extinction/re-thriving processes for Gallionella. Finally, pyrosequencing revealed a broader phylogenetic range of taxa than previous clone library-based diversity. Overall, our findings suggest that in addition to environmental filtering processes, additional forces (dispersal, birth/death events) could operate in AMD community
Published: 2014
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34. Masculinization of the X Chromosome in the Pea Aphid

Author: N. Prunier-Leterme, Fabrice Legeai, Gaël Le Trionnaire, Denis Tagu, Julie Jaquiéry, Béatrice Segurens, Corinne Da Silva, Denis Roze, Lucie Mieuzet, Claude Rispe, Solenn Stoeckel, Jean-Christophe Simon, Julie Poulain, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Swiss National Science Foundation [PBLAA-122658, PA00P3-139720], INRA-AIP BioRessources (project Poly-Express), Fondation pour la Recherche sur la Biodiversite FRB [AAP-IN-2009-020], Genoscope, ANR [ANR-09-GENM-017-001, ANR-11-BSV7-005-01], ANR-11-BSV7-0005,SPECIAPHID,Génétique de l'adaptation trophique et mécanismes d'isolement reproducteur chez les pucerons(2011), 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), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Inria Rennes – Bretagne Atlantique, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)
Subjects: 0106 biological sciences, Male, Cancer Research, Sexual Selection, Heredity, Genome, Insect, Gene Expression, 01 natural sciences, Natural Selection, Genome Evolution, Genetics (clinical), X chromosome, X-linked recessive inheritance, Dominance (genetics), Genetics, 0303 health sciences, Sex Chromosomes, Chromosome Biology, Genomics, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Female, Research Article, X Chromosome, Evolutionary Processes, lcsh:QH426-470, Biology, 010603 evolutionary biology, Chromosomal Inheritance, 03 medical and health sciences, Reproduction, Asexual, Animals, Allele, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, Alleles, 030304 developmental biology, Allosome, Evolutionary Biology, Autosome, Sexual Conflict, Chromosome, lcsh:Genetics, Aphids, Mutation, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome Expression Analysis
Abstract: Evolutionary theory predicts that sexually antagonistic mutations accumulate differentially on the X chromosome and autosomes in species with an XY sex-determination system, with effects (masculinization or feminization of the X) depending on the dominance of mutations. Organisms with alternative modes of inheritance of sex chromosomes offer interesting opportunities for studying sexual conflicts and their resolution, because expectations for the preferred genomic location of sexually antagonistic alleles may differ from standard systems. Aphids display an XX/X0 system and combine an unusual inheritance of the X chromosome with the alternation of sexual and asexual reproduction. In this study, we first investigated theoretically the accumulation of sexually antagonistic mutations on the aphid X chromosome. Our results show that i) the X is always more favourable to the spread of male-beneficial alleles than autosomes, and should thus be enriched in sexually antagonistic alleles beneficial for males, ii) sexually antagonistic mutations beneficial for asexual females accumulate preferentially on autosomes, iii) in contrast to predictions for standard systems, these qualitative results are not affected by the dominance of mutations. Under the assumption that sex-biased gene expression evolves to solve conflicts raised by the spread of sexually antagonistic alleles, one expects that male-biased genes should be enriched on the X while asexual female-biased genes should be enriched on autosomes. Using gene expression data (RNA-Seq) in males, sexual females and asexual females of the pea aphid, we confirm these theoretical predictions. Although other mechanisms than the resolution of sexual antagonism may lead to sex-biased gene expression, we argue that they could hardly explain the observed difference between X and autosomes. On top of reporting a strong masculinization of the aphid X chromosome, our study highlights the relevance of organisms displaying an alternative mode of sex chromosome inheritance to understanding the forces shaping chromosome evolution., Author Summary Males and females differ in their optimal values for most phenotypic traits, which makes intra-locus genetic conflicts among sexes common. Sex chromosomes have a sex-biased transmission, a pattern which might create favourable conditions for the spread of sexually antagonistic alleles (i.e. alleles beneficial for one sex but deleterious for the other). Yet, expectations for genetic systems with unusual inheritance of sex chromosomes may differ from those derived from standard systems (e.g. XY). Here we demonstrate theoretically that in organisms such as aphids, which alternate sexual and asexual reproduction and display an unusual inheritance of the X chromosome, male-beneficial sexually antagonistic alleles accumulate preferentially on that chromosome, while asexual female-beneficial alleles accumulate on autosomes. Theoretical models suggest that the evolution of sex-biased gene expression may solve such sexual conflicts, by restricting the product of a sexually antagonistic allele to the sex it benefits. We show that in the pea aphid, the genomic location (X versus autosomes) of genes with a sex-biased expression fits predictions derived from this hypothesis. On top of reporting a strong masculinization of the aphid X chromosome, our study highlights the relevance of organisms with an alternative mode of sex chromosome inheritance to understanding the evolutionary forces shaping chromosome evolution.
Published: 2013
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35. The contrasted evolutionary fates of deep-sea chemosynthetic mussels (Bivalvia, Bathymodiolinae)

Author: Baptiste Faure, Sarah Samadi, Nicolas Puillandre, Corinne Cruaud, Justine Thubaut, Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Biotope [Mèze], 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), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Fondation pour la Recherche sur la Biodiversite [FRB AAP-IN-2009-009], Consortium National de Recherche en Genomique, ``Service de Systematique Moleculaire' of the Museum National d'Histoire Naturelle [CNRS UMS 2700, 2005/67], CNRS, Museum National d'Histoire Naturelle, INRA, CEA (Genoscope), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], chemosynthetic ecosystem, Biology, 01 natural sciences, Deep sea, 03 medical and health sciences, Phylogenetics, Polyphyly, evolution, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Nature and Landscape Conservation, Original Research, Chemosynthesis, 0303 health sciences, deep-sea, Ecology, 010604 marine biology & hydrobiology, Bathymodiolinae, Species diversity, Bivalvia, biology.organism_classification, Habitat, [SDE]Environmental Sciences, Hydrothermal vent
Abstract: International audience; Bathymodiolinae are giant mussels that were discovered at hydrothermal vents and harboring chemosynthetic symbionts. Due to their close phylogenetic relationship with seep species and tiny mussels from organic substrates, it was hypothesized that they gradually evolved from shallow to deeper environments, and specialized in decaying organic remains, then in seeps, and finally colonized deep-sea vents. Here, we present a multigene phylogeny that reveals that most of the genera are polyphyletic and/or paraphyletic. The robustness of the phylogeny allows us to revise the genus-level classification. Organic remains are robustly supported as the ancestral habitat for Bathymodiolinae. However, rather than a single step toward colonization of vents and seeps, recurrent habitat shifts from organic substrates to vents and seeps occurred during evolution, and never the reverse. This new phylogenetic framework challenges the gradualist scenarios from shallow to deep. Mussels from organic remains tolerate a large range of ecological conditions and display a spectacular species diversity contrary to vent mussels, although such habitats are yet underexplored compared to vents and seeps. Overall, our data suggest that for deep-sea mussels, the high specialization to vent habitats provides ecological success in this harsh habitat but also brings the lineage to a kind of evolutionary dead end.
Published: 2013
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36. Pelagic cephalopods in the western Indian Ocean: New information from diets of top predators

Author: Richard Sabatié, Michel Potier, Sébastien Jaquemet, Yves Cherel, Evgeny V. Romanov, Frédéric Ménard, UMR 212 EME 'écosystèmes marins exploités' (EME), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM), Laboratoire d'Ecologie Marine (ECOMAR), Université de La Réunion (UR), IRD - Botany Department, Rhodes University, ARDA CAP RUN, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), Rhodes University, Grahamstown, 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), IOSSS project (European Fisheries Funds) [UE-FEP 2007-2013, 31122/DRAM/2009], La Reunion Regional Council [DAE4/20090164], BIOPS project, and Fondation pour la Recherche sur la Biodiversite [CD-AOOI-07-013]
Subjects: 0106 biological sciences, Diet composition, Scombridae, Bigeye tuna, Oceanography, 010603 evolutionary biology, 01 natural sciences, Pelagic fish, Trophic ecology, 14. Life underwater, Ommastrephidae, Squid, Beaks, biology, 010604 marine biology & hydrobiology, Swordfish, Pelagic zone, Octopod, biology.organism_classification, Neon flying squid, Cephalopod, Fishery, [SDE]Environmental Sciences, Thunnus, Sooty tern
Abstract: Using a combination of diverse large predatory fishes and one seabird, we collected information on the cephalopod fauna of the western Indian Ocean. We analyzed the stomach contents of 35 fishes representing ten families (Xiphiidae, Istiophoridae, Scombridae, Carangidae, Coryphaenidae, Alepisauridae, Dasyatidae, Carcharhinidae, Alopiidae and Sphyrnidae) and of the sooty tern Onychoprion fuscata of the Mozambique Channel from 2000 to 2010. Both fresh and accumulated beaks were used for identifying cephalopod prey. Cephalopods were important prey for twelve predators; swordfish Xiphias gladius had the highest cephalopod proportion; sooty tern (O. fuscata) and bigeye tuna (Thunnus obesus) had high proportions too. We recovered 23 cephalopod families and identified 38 species. Ten species from four Teuthida families (Ommastrephidae, Onychoteuthidae, Histioteuthidae and Ancistrocheiridae) and two Octopoda families (Argonautidae and Bolitaenidae) occurred very frequently in the stomach contents, while Sepiida were rare. Ommastrephidae were the most cephalopod food sources: the purpleback flying squid Sthenoteu this oualaniensis was the most prevalent prey by far, Ornithoteuthis volatilis was important for eleven predators and few but large specimens of the neon flying squid Ommastrephes bartramii were recovered in the stomachs of swordfish in the Indian South Subtropical Gyre province only. Predators' groups were identified based on cephalopod prey composition, on depth in which they forage, and on prey size. Surface predators' diets were characterized by lower cephalopod diversity but greater average numbers of cephalopod prey, whereas the deep-dwelling predators (swordfish and bigeye tuna) preyed on larger specimens than surface predators (O. fuscata or yellowfin tunas Thunnus albacares). Our findings emphasized the usefulness of a community of marine predators to gain valuable information on the biology and the distribution of the cephalopod forage fauna that are discussed with regard to biogeographic province, marine predator, fishing gear to catch the large pelagic fishes, and size of the beaks recovered in the stomachs.
Published: 2013
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37. A review of mate-finding Allee effects in insects: from individual behavior to population management

Author: Fauvergue, Xavier, Institut Sophia Agrobiotech (ISA), 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)-Institut National de la Recherche Agronomique (INRA), ANR,ANR-2010-BLAN-1717 'Sextinction', and Fondation pour la Recherche sur la Biodiversite , AAP-IN-2009-052 'Vortex'
Subjects: small populations, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, demographic Allee effect, density dependence, [SDV.BA]Life Sciences [q-bio]/Animal biology, low density, biological control, invasion, mating failure
Abstract: International audience; Like other animals and plants, insects may find it difficult to survive and reproduce in small populations, to the extent that their long-term persistence may be jeopardized. The Allee effect is a theoretical framework that formalizes this decrease in survival or reproduction in small populations, and the resulting decrease in population growth and persistence. Mating failure in low-density populations is likely to generate an Allee effect and, therefore, has a major effect on the functioning of small populations. Here, I review mate-finding Allee effects in insect species, and their consequences for individual mating success, population dynamics, and population management. I focus, in particular, on the comparison of theoretical expectations with observational data. Several studies have reported some degree of mating failure at low density. However, almost none of the datasets available allow comparison with the predictions of classical mate-searching models. A few studies at the population level have reported the co-occurrence of mating failure at low density and a demographic Allee effect, but no study has yet clearly demonstrated a causal relationship between mating failure and lower rates of population growth. Thus, although the theoretical development of management tactics based on Allee effects is considered promising, the current lack of evidence supporting this strategy limits its potential relevance. I call here for a more rigorous approach to the study of mate-finding Allee effects and propose new approaches for this purpose.
Published: 2013
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38. Toward trait-based mortality models for tropical forests

Author: Mélaine Aubry-Kientz, Christopher Baraloto, Bruno Hérault, Vivien Rossi, Charles Ayotte-Trépanier, Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Project Climfor (Fondation pour la Recherche sur la Biodiversite), project Guyasim (European structural fundings, PO-Feder), French Ministry of Agriculture (MAAP), 'Investissement d'Avenir' grant [ANR-10-LABX-0025], CIRAD, and CNRS
Subjects: 0106 biological sciences, Light, Rain, [SDV]Life Sciences [q-bio], lcsh:Medicine, Plant Science, 01 natural sciences, Trees, Bayes' theorem, K01 - Foresterie - Considérations générales, Tropical climate, Densité, Biomass, Community Assembly, Forêt tropicale humide, lcsh:Science, Hauteur, Likelihood Functions, Port de la plante, Biomass (ecology), Multidisciplinary, Ecology, U10 - Informatique, mathématiques et statistiques, Plants, French Guiana, Tree (data structure), Community Ecology, Modèle mathématique, Research Article, Markov Model, F40 - Écologie végétale, P40 - Météorologie et climatologie, Mortalité, Theoretical ecology, Biology, 010603 evolutionary biology, Ecosystems, Écologie forestière, Species Specificity, Ecosystem, Arbre forestier, Changement climatique, Tropical Climate, Uncertain data, Community, Plant Ecology, lcsh:R, Computational Biology, Bayes Theorem, Modèle de simulation, 15. Life on land, Probability Theory, lcsh:Q, Ecosystem Modeling, Mathematics, 010606 plant biology & botany
Abstract: Tree mortality in tropical forests is a complex ecological process for which modelling approaches need to be improved to better understand, and then predict, the evolution of tree mortality in response to global change. The mortality model introduced here computes an individual probability of dying for each tree in a community. The mortality model uses the ontogenetic stage of the tree because youngest and oldest trees are more likely to die. Functional traits are integrated as proxies of the ecological strategies of the trees to permit generalization among all species in the community. Data used to parametrize the model were collected at Paracou study site, a tropical rain forest in French Guiana, where 20,408 trees have been censused for 18 years. A Bayesian framework was used to select useful covariates and to estimate the model parameters. This framework was developed to deal with sources of uncertainty, including the complexity of the mortality process itself and the field data, especially historical data for which taxonomic determinations were uncertain. Uncertainty about the functional traits was also considered, to maximize the information they contain. Four functional traits were strong predictors of tree mortality: wood density, maximum height, laminar toughness and stem and branch orientation, which together distinguished the light-demanding, fast-growing trees from slow-growing trees with lower mortality rates. Our modelling approach formalizes a complex ecological problem and offers a relevant mathematical framework for tropical ecologists to process similar uncertain data at the community level.
Published: 2013
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39. An APETALA3 homolog controls both petal identity and floral meristem patterning in Nigella damascena L. (Ranunculaceae)

Author: Halima Morin, Odrade Nougué, Patrick Laufs, Céline Ridel, Domenica Manicacci, Catherine Damerval, Florian Jabbour, Beatriz Gonçalves, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Fondation pour la Recherche sur la Biodiversite [AAS-IN-2009-040], Ministere de l'Education Nationale de la Recherche et de Technologie, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), and Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF)
Subjects: 0106 biological sciences, perianth architecture, homeotic transformation, B-function genes, [SDV]Life Sciences [q-bio], Meristem, Stamen, Ranunculaceae, MADS Domain Proteins, Plant Science, Flowers, 01 natural sciences, Sepal, 03 medical and health sciences, Gene Expression Regulation, Plant, Botany, Genetics, Gene Silencing, Nigella damascena, reproductive and urinary physiology, 030304 developmental biology, Plant Proteins, 0303 health sciences, biology, fungi, food and beverages, Cell Biology, biology.organism_classification, floral meristem patterning, Sexual dimorphism, Evolutionary biology, Microscopy, Electron, Scanning, Petal, petal identity, Perianth, 010606 plant biology & botany
Abstract: Flower architecture mutants provide a unique opportunity to address the genetic origin of flower diversity. Here we study a naturally occurring floral dimorphism in Nigella damascena (Ranunculaceae), involving replacement of the petals by numerous sepal-like and chimeric sepal/stamen organs. We performed a comparative study of floral morphology and floral development, and characterized the expression of APETALA3 and PISTILLATA homologs in both morphs. Segregation analyses and gene silencing were used to determine the involvement of an APETALA3 paralog (NdAP3-3) in the floral dimorphism. We demonstrate that the complex floral dimorphism is controlled by a single locus, which perfectly co-segregates with the NdAP3-3 gene. This gene is not expressed in the apetalous morph and exhibits a particular expression dynamic during early floral development in the petalous morph. NdAP3-3 silencing in petalous plants perfectly phenocopies the apetalous morph. Our results show that NdAP3-3 is fully responsible for the complex N. damascena floral dimorphism, suggesting that it plays a role not only in petal identity but also in meristem patterning, possibly through regulation of perianth organ number and the perianth/stamen boundary.
Published: 2013
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40. A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes

Author: Nicolas Mouquet, Emmanuel J. P. Douzery, David Mouillot, Christine N. Meynard, 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), Centre National de la Recherche Scientifique (CNRS), Ecologie des systèmes marins côtiers (Ecosym), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), bioinformatics cluster of the Institut des Sciences de l'Evolution de Montpellier (ISE-M), computer grid of University Montpellier 2, Agence Nationale de la Recherche [ANR-08-EMER-011, BIOSYS06_136906, ANR-09-PEXT-01102], Fondation pour la Recherche sur la Biodiversite, Fondation TOTAL, Institut Universitaire de France, FABIO, BIODIVMED, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Meynard, Christine
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Mediterranean climate, Genes, RAG-1, Origin of Life, Marine and Aquatic Sciences, 01 natural sciences, Marine Conservation, Mediterranean sea, Macroecology, Phylogeny, 0303 health sciences, Multidisciplinary, Méditerranée, biogeography, phylogénie, poisson, biodiversité, ADN, taxonomie, histoire, Crétacé, faune sauvage, distribution spatiale, salinité, Ecology, Cytochrome b, Marine Ecology, Fishes, Biodiversity, Agricultural sciences, Biogeography, Medicine, Research Article, Fish Proteins, Rhodopsin, Science, Marine Biology, Biology, 010603 evolutionary biology, DNA, Mitochondrial, DNA, Ribosomal, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Mediterranean Sea, Animals, 14. Life underwater, 030304 developmental biology, Evolutionary Biology, Cytochrome c oxidase subunit I, Species diversity, Paleontology, Phylogeography, Evolutionary biology, Evolutionary Ecology, Earth Sciences, Sciences agricoles
Abstract: International audience; The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing nonendemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically ,100–80 Mya, and most Perciformes families originated 80–50 Mya. Two important clade origin events were detected. The first at 100–80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot.
Published: 2012
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41. Water availability is the main climate driver of neotropical tree growth

Author: Bruno Hérault, Damien Bonal, Clément Stahl, Vivien Rossi, Fabien Wagner, Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), project Climfor (Fondation pour la Recherche sur la Biodiversite), and project Guyasim (European structural fundings, PO-Feder)
Subjects: 0106 biological sciences, Atmospheric Science, 010504 meteorology & atmospheric sciences, Epidemiology, Rain, Amazonian, [SDV]Life Sciences [q-bio], lcsh:Medicine, F62 - Physiologie végétale - Croissance et développement, Plant Science, Atmospheric sciences, 01 natural sciences, Trees, Global Change Ecology, Geoinformatics, Tropical climate, Dry season, K01 - Foresterie - Considérations générales, AMAZON FOREST, Forêt tropicale humide, lcsh:Science, Plant Growth and Development, Climatology, Multidisciplinary, Ecology, Geography, U10 - Informatique, mathématiques et statistiques, Temperature, Plants, Terrestrial Environments, 6. Clean water, Community Ecology, Plant Physiology, Seasons, Research Article, Computer Modeling, Wet season, VEGETATION DYNAMICS, TROPICAL RAIN-FOREST, Dendrology, FRENCH-GUIANA, DRY-FOREST, EXPERIMENTAL DROUGHT, MODEL SELECTION, CARBON BALANCE, WET FOREST, RESPONSES, Rainforest, 010603 evolutionary biology, Ecosystems, Environmental Epidemiology, Plant-Environment Interactions, medicine, Environmental Systems Modeling, Croissance, Arbre forestier, Biology, 0105 earth and related environmental sciences, Changement climatique, Tropical Climate, Population Biology, Plant Ecology, lcsh:R, Computational Biology, Water, Modèle de simulation, 15. Life on land, Seasonality, medicine.disease, 13. Climate action, Computer Science, Earth Sciences, Environmental science, Climate model, lcsh:Q, Ecosystem Modeling, Ecological Environments, Climate Modeling
Abstract: • Climate models for the coming century predict rainfall reduction in the Amazonian region, including change in water availability for tropical rainforests. Here, we test the extent to which climate variables related to water regime, temperature and irradiance shape the growth trajectories of neotropical trees. • We developed a diameter growth model explicitly designed to work with asynchronous climate and growth data. Growth trajectories of 205 individual trees from 54 neotropical species censused every 2 months over a 4-year period were used to rank 9 climate variables and find the best predictive model. • About 9% of the individual variation in tree growth was imputable to the seasonal variation of climate. Relative extractable water was the main predictor and alone explained more than 60% of the climate effect on tree growth, i.e. 5.4% of the individual variation in tree growth. Furthermore, the global annual tree growth was more dependent on the diameter increment at the onset of the rain season than on the duration of dry season. • The best predictive model included 3 climate variables: relative extractable water, minimum temperature and irradiance. The root mean squared error of prediction (0.035 mm x d(-1)) was slightly above the mean value of the growth (0.026 mm x d(-1)). • Amongst climate variables, we highlight the predominant role of water availability in determining seasonal variation in tree growth of neotropical forest trees and the need to include these relationships in forest simulators to test, in silico, the impact of different climate scenarios on the future dynamics of the rainforest.
Published: 2012
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42. The biology of small, introduced populations, with special reference to biological control

Author: Ruth A. Hufbauer, Xavier Fauvergue, Elodie Vercken, Thibaut Malausa, Institut Sophia Agrobiotech (ISA), 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)-Institut National de la Recherche Agronomique (INRA), Dept Bioagr Sci & Pest Management, Colorado State University [Fort Collins] (CSU), Agence Nationale de la Recherche [ANR-2010-BLAN-1717], Fondation pour la Recherche sur la Biodiversite, and National Science Foundation [0541673, 0949619]
Subjects: 0106 biological sciences, Empirical data, [SDV]Life Sciences [q-bio], NEW-ZEALAND, biological invasions, inbreeding, Metapopulation, Introduced species, ECO-EVOLUTIONARY DYNAMICS, adaptation, Biology, HOUNDSTONGUE CYNOGLOSSUM-OFFICINALE, 010603 evolutionary biology, 01 natural sciences, Allee effect, 03 medical and health sciences, symbols.namesake, Synthesis, Genetic drift, Genetics, Population growth, demographic and environmental stochasticity, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Management science, Ecology, metapopulation, Small population size, classical biological control, CONTROL AGENT, DEVELOPMENTAL MORTALITY, PROPAGULE PRESSURE, COMPLEMENTARY SEX DETERMINATION, DEMOGRAPHIC STOCHASTICITY, genetic demographic interactions, genetic drift, MELINUS DEBACH HYMENOPTERA, ENVIRONMENTAL STOCHASTICITY, [SDE]Environmental Sciences, symbols, genetic × demographic interactions, Adaptation, General Agricultural and Biological Sciences
Abstract: International audience; Populations are introduced into novel environments in different contexts, one being the biological control of pests. Despite intense efforts, less than half introduced biological control agents establish. Among the possible approaches to improve biological control, one is to better understand the processes that underpin introductions and contribute to ecological and evolutionary success. In this perspective, we first review the demographic and genetic processes at play in small populations, be they stochastic or deterministic. We discuss the theoretical outcomes of these different processes with respect to individual fitness, population growth rate, and establishment probability. Predicted outcomes differ subtly in some cases, but enough so that the evaluating results of introductions have the potential to reveal which processes play important roles in introduced populations. Second, we attempt to link the theory we have discussed with empirical data from biological control introductions. A main result is that there are few available data, but we nonetheless report on an increasing number of well-designed, theory-driven, experimental approaches. Combining demography and genetics from both theoretical and empirical perspectives highlights novel and exciting avenues for research on the biology of small, introduced populations, and great potential for improving both our understanding and practice of biological control.
Published: 2012
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43. Accelerated evolution of sex chromosomes in aphids, an X0 system

Author: Jean-Christophe Simon, Fabrice Legeai, Claude Rispe, Lucie Mieuzet, Solenn Stoeckel, Julie Jaquiéry, Département d'écologie et évolution [Lausanne] (DEE), Université de Lausanne (UNIL), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), AGROCAMPUS OUEST, 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), INRA-AIP BioRessources, Departement INRA Sante des Plantes et Environnement, Genoscope, Fondation pour la Recherche sur la Biodiversite, ANR GW-Aphid, Swiss National Science Foundation [PBLAA-122658], Université de Lausanne = University of Lausanne (UNIL), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique
Subjects: Genetic Markers, Male, 0106 biological sciences, POSITIVE SELECTION, Genotype, Evolution of sexual reproduction, ADAPTIVE PROTEIN EVOLUTION, EFFECTIVE POPULATION-SIZE, Biology, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, X chromosome, 03 medical and health sciences, Effective population size, ACYRTHOSIPHON-PISUM, Genetics, Animals, inheritance, MICROSATELLITE VARIABILITY, PHYLOGENETIC ANALYSIS, DROSOPHILA-SIMULANS, X:A ratio, Allele, sex chromosome, NUCLEOTIDE DIVERSITY, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Allosome, 0303 health sciences, Autosome, GENETIC DRIFT, PEA APHID, Genetic Variation, genetic diversity, Sex Determination Processes, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Evolutionary biology, Aphids, faster-X effect, Female, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Sex linkage, effective population size, Microsatellite Repeats
Abstract: International audience; Sex chromosomes play a role in many important biological processes, including sex determination, genomic conflicts, imprinting and speciation. In particular, they exhibit several unusual properties such as inheritance pattern, hemizygosity and reduced recombination, which influence their response to evolutionary factors (e.g. drift, selection, demography). Here, we examine the evolutionary forces driving X chromosome evolution in aphids, an XO system where females are homozygous (XX) and males hemizygous (X0) at sex chromosomes. We show by simulations that the unusual mode of transmission of the X chromosome in aphids coupled to cyclical parthenogenesis results in similar effective population sizes and predicted levels of genetic diversity for X chromosomes and autosomes under neutral evolution. These results contrast with expectations from standard XX/XY or XX/X0 systems (where the effective population size of the X is 3/4 of that of autosomes) and have deep consequences for aphid X chromosome evolution. We then localized 52 microsatellites markers on the X and 351 on autosomes. We genotyped 167 individuals with 356 of these loci and found similar levels of allelic richness on the X and on the autosomes, as predicted by our simulations. In contrast, we detected higher dN and dN/dS ratio for X-linked genes compared to autosomal genes, a pattern compatible with either positive or relaxed selection. Given that both types of chromosomes have similar effective population sizes and that the single copy of the X chromosome of male aphids exposes its recessive genes to selection, some degree of positive selection seems to best explain the higher rates of evolution of X-linked genes. Overall, this study highlights the particular relevance of aphids to study the evolutionary factors driving sex chromosomes and genome evolution.
Published: 2011
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44. Tree size and climatic water deficit control root to shoot ratio in individual trees globally.

Author: Ledo A, Paul KI, Burslem DFRP, Ewel JJ, Barton C, Battaglia M, Brooksbank K, Carter J, Eid TH, England JR, Fitzgerald A, Jonson J, Mencuccini M, Montagu KD, Montero G, Mugasha WA, Pinkard E, Roxburgh S, Ryan CM, Ruiz-Peinado R, Sochacki S, Specht A, Wildy D, Wirth C, Zerihun A, and Chave J
Subjects: Climate, Plant Roots physiology, Plant Shoots physiology, Trees anatomy & histology, Water physiology
Published: 2018
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44 results on '"Fondation pour la Recherche sur la Biodiversite"'

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