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1. Les cultures associées céréale / légumineuse : en agriculture 'bas intrants' dans le sud de la France, projet PerfCom - Peuplements Complexes Performants en agriculture à bas intrants

Author: UMR Eco&Sol, ., UMR AGIR, ., UMR Innovation, ., UE DIASCOPE, ., UPR LEVA, ., Biocivam 11, ., ARVALIS Institut du végétal, ., Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Innovation et Développement dans l'Agriculture et l'Agro-alimentaire (UMR Innovation), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-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), Domaine expérimental de Melgueil (MONTP MELGUEIL UE), Institut National de la Recherche Agronomique (INRA), Ecole Supérieure d'Agriculture (Groupe ESA), Biocivam 11, ARVALIS - Institut du végétal [Paris], Projet ANR PerfCom (Programme Systerra), ANR (Agence Nationale de la Recherche - France), ANR-08-STRA-0011,PerfCom,Peuplements Complexes Performants en agriculture bas intrants - Interactions Multitrophiques et Facilitation Intergénotypique(2008), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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)
Subjects: association de cultures, blé dur, [SDV]Life Sciences [q-bio], bas intrant, légumineuse
Abstract: La plupart des recherches qui sont ici présentées, ont été réalisées entre 2009 et 2012 dans le cadre du projet PerfCom financé par le Programme Systerra de l’Agence Nationale de la Recherche (ANR). Elles se sont attachées à estimer les performances agronomiques de peuplements complexes, associant plusieurs espèces (blé dur et légumineuse) ou variétés de blé dur dans une même parcelle agricole, en vue de mieux exploiter les processus écologiques et ressources du sol, notamment N et P, en vue de réduire l’utilisation des intrants fertilisants. Leur objectif était également de comprendre ces processus écologiques sous-jacents.
Published: 2012

2. INCA In-field Nir Spectroscopy for Carbon Accounting

Author: Bellon Maurel, Véronique, Gobrecht, Alexia, INRA, US 1106 InfoSol, ., IRD, UMR Eco&Sols, ., Australian Centre of Precision Agriculture, ., Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-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), University of Sydney, Institut National de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture (IRSTEA), Financement : GESSOL (MEEDDTL), ADEME, Commanditaire : Agence de l'Environnement et de la Maîtrise de l'Energie (France), Type de commande : Commande avec contrat/convention/lettre de saisine, Date de signature : 2010-12-13, and Partenaires : Institut National de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture (IRSTEA), Institut de Recherche pour le Développement (IRD), University of Sydney
Subjects: stock de carbone, capteur portable, [SDV]Life Sciences [q-bio], spectroscopie proche infrarouge
Published: 2012

3. Comparative Analysis of G-Layers in Bast Fiber and Xylem Cell Walls in Flax Using Raman Spectroscopy

Author: Anne-Sophie Blervacq, Myriam Moreau, Anne Duputié, Simon Hawkins, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), ANR-12-ADAP-0011,NoStressWall,NOuvelles informations sur l'effet d'un STRESS hydrique sur la PAROI cellulaire(2012), Université de Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement (LASIRE) - UMR 8516, and Évolution, Écologie et Paléontologie (Evo Eco Paleo) - UMR 8198
Subjects: opposite wood, bast fibers, Raman chemical imaging, flax, G-layer, gravitropic stress, confocal Raman spectroscopy, tension wood, [SDV]Life Sciences [q-bio], Molecular Biology, Biochemistry
Abstract: In a response to gravitropic stress, G-layers (gelatinous layers) were deposited in xylem cell walls of tilted flax plants. G-layers were produced in both tension wood (upper side) as expected but were also observed in opposite wood (lower side). Raman spectral profiles were acquired for xylem G-layers from the tension and opposite side as well as from the G-layer of bast fibers grown under non-tilted conditions. Statistical analysis by principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA) clearly distinguished bast fiber G-layers from xylem G-layers. Discriminating bands were observed for cellulose (380–1150–1376 cm–1), hemicelluloses (517–1094–1126–1452 cm–1) and aromatics (1270–1599–1658 cm–1). PCA did not allow separation of G-layers from tension/opposite-wood sides. In contrast, the two types of xylem G-layers could be incompletely discriminated through PLS-DA. Overall, the results suggested that while the architecture (polymer spatial distribution) of bast fibers G-layers and xylem G-layers are similar, they should be considered as belonging to a different cell wall layer category based upon ontogenetical and chemical composition parameters.
Published: 2023
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4. Shifts in the Ediacaran to Lower Ordovician sedimentary zircon provenances of Northwest Gondwana: the Pyrenean files

Author: Maxime Padel, Sébastien Clausen, Marc Poujol, Jose Javier Alvaro Blasco, Bureau de Recherches Géologiques et Minières (BRGM) [BRGM], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Géosciences Rennes [GR], Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), 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), Instituto de Geociencias [Madrid] (IGEO), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), BRGM (RGF), project CGL2013-48877-P from Spanish MINECO, 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), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Rennes 2 (UR2), and Université de Rennes (UNIV-RENNES)-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: Geodinámica, Gondwana, Pyrenees, Petrología, Geology, Detrital zircon, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, [SDU.STU.ST]Sciences of the Universe [physics]/Earth Sciences/Stratigraphy, Paleogeography, Geología estratigráfica, Rift, Geoquímica, Palaeogeography, Godwana, Orogeny
Abstract: International audience; Detrital zircon grains from Cambrian–Lower Ordovician sandstones and quartzites sampled in the Pyrenees were dated by LA-ICPMS in order to assess their provenance sources. Resulting age distributions are compared to other available datasets from neighbouring margins, such as Morocco, the Iberian Peninsula, southern France and Sardinia. Kolmogorov-Smirnov (K-S) test and Crystallization Age-Depositional Age (CA-DA) diagrams were used to compare zircon populations estimating their possible correlation with the arc/rift/drift geodynamic evolution of the northwestern Gondwana margin. During Terreneuvian times, zircon populations allowed the distinction of i) a southwesternmost edge (Anti-Atlas-Ossa-Morena Rift) mostly influenced by Panafrican and Anti-Atlasian sources (ca. 0.63–0.54), ii) a northeasternmost edge (Sardinia) recording the influence of the Saharan Metacraton and the Arabian Nubian Shield, with an distinct Stenian–Tonian shift (ca. 1.25–0.85Ga) and iii) an intermediate palaeogeographic transect, where lies the Central-Iberian, West Asturian-Leonese and Cantabrian Zones, the Montagne Noire and the Pyrenees sharing similar populations and a chronologically progressive influence from Anti-Atlasian/Panafrican to Saharan Metacraton/Arabian Nubian Shield sources. This gradual modification in zircon percentage populations supports similar trends based on climatically sensitive indicators, biogeographic patterns of Cambrian Epoch 2 archaeocyathan and microfossil assemblages, and laterally correlatable episodes of carbonate production, all of them pointing to a Cambrian setting for the Pyrenean Basin between the Montagne Noire (Occitan Domain) and the Sardinian margins of NW Gondwana. The Terreneuvian zircon patterns recorded in the Pyrenees gradually evolved from Cambrian Epoch 2 to Early Ordovician times, reflecting the geodynamic evolution from Panafrican and Cadomian arc-related to rift-dominant conditions. During Furongian and Ordovician times, the relative percentage of zircon populations led to a more spread age curve, characteristic of extensional settings and pointing to rift (passive margin) conditions.
Published: 2023

5. Going with the flow? Diversification of gastropods reflects drainage evolution in Africa

Author: Bert Van Bocxlaer, Björn Stelbrink, Frank Riedel, Christian Albrecht, Anna Mahulu, Justus-Liebig-Universität Gießen (JLU), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Freie Universität Berlin, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Centre National de la Recherche Scientifique (CNRS)-Université de Lille
Subjects: 0106 biological sciences, Biogeography, Drainage basin, Diversification (marketing strategy), 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 14. Life underwater, Drainage, Ampullariidae, dispersal, biogeography, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, molluscs, 0303 health sciences, geography, Fossil Record, geography.geographical_feature_category, Ecology, biology, East African Rift System, 15. Life on land, biology.organism_classification, fossil record, radiation, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Flow (mathematics), 13. Climate action, Biological dispersal, ddc:570, river basin
Abstract: International audience; Aim: The roles of geodynamics, climatic variability and landscape evolution in shaping aquatic biodiversity patterns on the African continent remain poorly understood. We studied the geographical origin and phylogenetic relationships of an Afrotropical freshwater snail genus to examine the role of drainage evolution on diversification and range evolution. The relevance of fish provinces in bio-regionalization of invertebrates was explored, as well as the evolution of habitat specificity.Location: Africa including Madagascar. Taxon: Lanistes (Gastropoda: Ampullariidae).Methods: Based on a sampling covering the entire geographical range, we reconstructed a fossil-calibrated multi-locus molecular phylogeny using maximum likelihood and Bayesian inference approaches. After applying species delimitation methods, we estimated ancestral areas and habitats and examined rates of diversification through time using lineage through time plots.Results: RAxML and MrBayes analyses resulted in highly congruent topologies and a strongly supported phylogeny. Our BEAST analysis indicate that Lanistes probably originated in the Eocene about 50 Ma and the most recent common ancestor (MRCA) of all 23 Lanistes OTUs in our study may have inhabited an area including the Central African and adjacent Lower Guinean biogeographical regions. A steeper increase in species accumulation from the middle Miocene (c. 15 to 10 Ma), followed by a decrease towards the present was found. Sympatry and jump dispersal were the common cladogenetic events and only a single anagenetic dispersal event was detected. The biogeographical analyses further suggest that Madagascar was colonized from East Africa and that the Zambezi River was colonized at least twice independently. Seven species are confined to rivers and three live exclusively in lakes. The estimation of ancestral habitats suggested that the MRCA of all Lanistes probably evolved in ariverine habitat.Main conclusions: The diversification of Lanistes started in the Eocene and occurred at a constant pace apart from a possible climate-related increase in the Miocene. This study highlights the significance of temporal geographical isolation of river systems and subsequent reconnection in clade diversification and of jump dispersal in range evolution. More comparative analyses across various taxa are needed to obtain a betterunderstanding of African freshwater biodiversity.
Published: 2021

6. Logging residues promote rapid restoration of soil health after clear-cutting of rubber plantations at two sites with contrasting soils in Africa

Author: Thibaut Perron, Aymard Kouakou, Charlotte Simon, Louis Mareschal, Gay Frédéric, Mouman Soumahoro, Daouda Kouassi, Nancy Rakotondrazafy, Bruno Rapidel, Jean-Paul Laclau, Alain Brauman, Agrosystèmes Biodiversifiés (UMR ABSys), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-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), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Société Africaine de Plantations d’Hévéas (SAPH), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Nangui Abrogoua, Société de Caoutchouc de Grand Béréby (SOGB), Cirad Direction Générale (Cirad-DG), This study was carried out as part of the FERTIM project funded by the Institut Français du Caoutchouc (IFC) and by the Michelin, SIPH and SOCFIN companies. This work benefited from the support of the ECOTROP platform of UMR Eco&Sols, with the support of LabEx CeMEB, an ANR 'Investissements d'avenir' program (ANR-10-LABX-0004)., and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)
Subjects: Rubber tree, Clearcutting, Soil biodiversity, [SDV]Life Sciences [q-bio], 010501 environmental sciences, 01 natural sciences, Soil, Soil functions, Soil health, Récupération des sols, couverture du sol, Cover crop, Waste Management and Disposal, Logging residue, 2. Zero hunger, Agroforestry, 04 agricultural and veterinary sciences, Pollution, Legume, soil functions [EN], Restoration, Amélioration des sols, Arénosol, Environmental Engineering, Ferralsol, Déchet d'exploitation forestière, Plantations, Plante à caoutchouc, complex mixtures, Faune du sol, Environmental Chemistry, Ecosystem, Coupe rase, 0105 earth and related environmental sciences, P35 - Fertilité du sol, P34 - Biologie du sol, Q70 - Traitement des déchets agricoles, Disturbance, Soil carbon, 15. Life on land, Carbon, Cote d'Ivoire, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Rubber
Abstract: Soil health is defined as the soil's capacity to deliver ecosystem functions within environmental constraints. On tree plantations, clear-cutting and land preparation between two crop cycles cause severe physical disturbances to the soil and seriously deplete soil organic carbon and biodiversity. Rubber, one of the main tropical perennial crops worldwide, has a plantation life cycle of 25 to 40 years, with successive replanting cycles on the same plot. The aim of this study was to assess the effects of clear-cutting disturbance on three soil functions (carbon transformation, nutrient cycling and structure maintenance) and their restoration after the planting of the new rubber crop, in two contrasting soil situations (Arenosol and Ferralsol) in Côte d'Ivoire. In this 18-month diachronic study, we intensively measured soil functions under different scenarios as regards the management of logging residues and the use or not of a legume cover crop. We investigated the relationship between soil macrofauna diversity and soil heath. At both sites, clear-cutting and land preparation disturbed carbon transformation and nutrient cycling significantly and, to a lesser extent, structure maintenance function. When logging residues were applied, carbon transformation and structure maintenance functions were fully restored within 12 to 18 months after disturbance. By contrast, no restoration of nutrient cycling was observed over the study period. A legume cover crop mainly improved the restoration of carbon transformation. We found a strong relationship (P ≤ 0.001; R2 = 0.62–0.66) between soil macrofauna diversity and soil health. Our overall results were very similar at the two sites, despite their contrasting soil conditions. Keeping logging residues in the plots and sowing a legume in the inter-row at replanting accelerated the restoration of soil functions after major disturbance caused by clear-cutting and land preparation. Our results confirm the necessity of taking soil macrofauna diversity into account in the management of tropical perennial crops.
Published: 2022

7. Evolution of self‐incompatibility in the Brassicaceae: Lessons from a textbook example of natural selection

Author: Durand, Eléonore, Chantreau, Maxime, Le Veve, Audrey, Stetsenko, Roman, Dubin, Manu, Genete, Mathieu, Llaurens, Violaine, Poux, Céline, Roux, Camille, Billiard, Sylvain, Vekemans, Xavier, Castric, Vincent, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, 0301 basic medicine, plant mating systems, sexual reproduction, balancing selection, lcsh:Evolution, Population genetics, Outcrossing, Diversification (marketing strategy), Biology, Balancing selection, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetic variation, dominance/recessivity interactions, Genetics, lcsh:QH359-425, Inbreeding avoidance, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, Natural selection, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], allelic diversification, 030104 developmental biology, Evolutionary biology, Special Issue Review and Syntheses, General Agricultural and Biological Sciences
Abstract: Self‐incompatibility (SI) is a self‐recognition genetic system enforcing outcrossing in hermaphroditic flowering plants and results in one of the arguably best understood forms of natural (balancing) selection maintaining genetic variation over long evolutionary times. A rich theoretical and empirical population genetics literature has considerably clarified how the distribution of SI phenotypes translates into fitness differences among individuals by a combination of inbreeding avoidance and rare‐allele advantage. At the same time, the molecular mechanisms by which self‐pollen is specifically recognized and rejected have been described in exquisite details in several model organisms, such that the genotype‐to‐phenotype map is also pretty well understood, notably in the Brassicaceae. Here, we review recent advances in these two fronts and illustrate how the joint availability of detailed characterization of genotype‐to‐phenotype and phenotype‐to‐fitness maps on a single genetic system (plant self‐incompatibility) provides the opportunity to understand the evolutionary process in a unique perspective, bringing novel insight on general questions about the emergence, maintenance, and diversification of a complex genetic system.
Published: 2020

8. Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition

Author: François Munoz, Florent Arthaud, Julie Crabot, François Massol, Thibault Datry, Franck Jabot, Maxime Dubart, Patrice David, Fabien Laroche, Simon Blanchet, Laboratoire d'ingénierie pour les systèmes complexes (UR LISC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecosystèmes forestiers (UR EFNO), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RiverLy - Fonctionnement des hydrosystèmes (RiverLy), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 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), Station d'écologie théorique et expérimentale (SETE), 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), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-14-CE02-0012,ARSENIC,Adaptation et résilience des réseaux écologiques spatialisés face aux changements d'origine humaine(2014), ANR-17-CE32-0011,NGB,Biosurveillance Next-Gen des changements dans la structure et le fonctionnement des écosystèmes(2017), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Riverly (Riverly), Université Paul-Valéry - Montpellier 3 (UPVM)-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), 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-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), Laboratoire d'ingénierie pour les systèmes complexes [UR LISC], Ecosystèmes forestiers [UR EFNO], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques [CARRTEL], Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture [IRSTEA], Université de Montpellier [UM], Evolution et Diversité Biologique [EDB], Station d'écologie théorique et expérimentale [SETE], Centre d’Ecologie Fonctionnelle et Evolutive [CEFE], Milieux aquatiques, écologie et pollutions [UR MALY], RiverLy - Fonctionnement des hydrosystèmes [RiverLy], Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Université de Montpellier (UM), 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, 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]), Milieux aquatiques, écologie et pollutions (UR MALY), Université Clermont Auvergne (UCA), RiverLy (UR Riverly), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), and 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)
Subjects: 0106 biological sciences, Metacommunity, beta-diversity, Computer science, Ecology (disciplines), [SDV]Life Sciences [q-bio], Beta diversity, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, 01 natural sciences, dispersal limitation, path analysis, MESH: Ecosystem, Ecosystem, Ecology, Evolution, Behavior and Systematics, demographic stochasticity, environmental filtering, Ecology, 010604 marine biology & hydrobiology, Data science, Field (geography), Variable (computer science), Temporal diversity, Community composition, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Although metacommunity ecology has been a major field of research in the last decades, with both conceptual and empirical outputs, the analysis of the temporal dynamics of metacommunities has only emerged recently and still consists mostly of repeated static analyses. Here we propose a novel analysis framework to assess metacommunity processes using path analyses of spatial and temporal diversity turnovers. We detail the principles and practical aspects of this framework and apply it to simulated datasets to illustrate its ability to decipher the respective contributions of entangled drivers of metacommunity dynamics. We then apply it to four real datasets. Empirical results support the view that metacommunity dynamics may be generally shaped by multiple ecological processes acting in concert, with environmental filtering being variable across both space and time. These results reinforce our call to go beyond static analyses of metacommunities that are blind to the temporal part of environmental variability. This article has been peer-reviewed and recommended by Peer Community in Ecology
Published: 2020

9. Acritarch assemblages from the Middle–Upper Ordovician in the Aksu area, northwestern margin of the Tarim Basin, Xinjiang, China

Author: Longlong Shan, Kui Yan, Thomas Servais, Jun Li, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Palynology, 010506 paleontology, [SDE.MCG]Environmental Sciences/Global Changes, Paleontology, Tarim basin, Acritarch, Biostratigraphy, 010502 geochemistry & geophysics, 01 natural sciences, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Margin (machine learning), Ordovician, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, China, Palaeogeography, ComputingMilieux_MISCELLANEOUS, Geology, 0105 earth and related environmental sciences
Abstract: International audience
Published: 2020

10. Stochastic Dynamics of Three Competing Clones: Conditions and Times for Invasion, Coexistence, and Fixation

Author: Sylvain Billiard, Charline Smadi, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'ingénierie pour les systèmes complexes (UR LISC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Systèmes Complexes - Paris Ile-de-France (ISC-PIF), École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-École polytechnique (X)-Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), chair 'Modelisation Mathematique et Biodiversite' European Research Council (NOVEL project) 648321, Univ. Grenoble Alpes, INRAE, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, and Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Sorbonne Université (SU)-École polytechnique (X)-École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)
Subjects: 0106 biological sciences, Genotype, Stochastic modelling, [SDV]Life Sciences [q-bio], Population Dynamics, Population, Population genetics, adaptation, Biology, Bacterial Physiological Phenomena, Models, Biological, 010603 evolutionary biology, 01 natural sciences, nonlinear dynamics, fixation probability, 010104 statistics & probability, Stochastic dynamics, clonal interference, Animals, 0101 mathematics, Quantitative Biology - Populations and Evolution, education, Evolutionary dynamics, Plant Physiological Phenomena, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Stochastic Processes, education.field_of_study, Community, Clonal interference, coexistence, Populations and Evolution (q-bio.PE), Invertebrates, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Fixation (population genetics), fixation time, Evolutionary biology, FOS: Biological sciences
Abstract: In large clonal populations, several clones generally compete which results in complex evolutionary and ecological dynamics: experiments show successive selective sweeps of favorable mutations as well as long-term coexistence of multiple clonal strains. The mechanisms underlying either coexistence or fixation of several competing strains have rarely been studied altogether. Conditions for coexistence have mostly been studied by population and community ecology, while rates of invasion and fixation have mostly been studied by population genetics. In order to provide a global understanding of the complexity of the dynamics observed in large clonal populations, we develop a stochastic model where three clones compete. Competitive interactions can be intransitive and we suppose that strains enter the population via mutations or rare immigrations. We first describe all possible final states of the population, including stable coexistence of two or three strains, or the fixation of a single strain. Second, we give estimate of the invasion and fixation times of a favorable mutant (or immigrant) entering the population in a single copy. We show that invasion and fixation can be slower or faster when considering complex competitive interactions. Third, we explore the parameter space assuming prior distributions of reproduction, death and competitive rates and we estimate the likelihood of the possible dynamics. We show that when mutations can affect competitive interactions, even slightly, stable coexistence is likely. We discuss our results in the context of the evolutionary dynamics of large clonal populations.
Published: 2020

11. Generalized host‐plant feeding can hide sterol‐specialized foraging behaviors in bee–plant interactions

Author: Pierre-Laurent Zerck, Maryse Vanderplanck, Denis Michez, Georges Lognay, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), University of Mons [Belgium] (UMONS), University of Liège, Gembloux Agro-Bio Tech., Laboratoire SAF, Laboratoire Science des Aliments et Formulation, Université de Liège - Gembloux-Université de Liège - Gembloux, and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 0106 biological sciences, Forage (honey bee), Foraging, Zoology, sterols, Generalist and specialist species, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, lcsh:QH540-549.5, Nectar, insects, Osmia cornuta, Ecology, Evolution, Behavior and Systematics, generalization, 030304 developmental biology, Nature and Landscape Conservation, Anthophora plumipes, Original Research, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, biology, physiological constraints, fungi, food and beverages, bee-flower interactions, biology.organism_classification, Brood, behavior and behavior mechanisms, bee–flower interactions, Evolutionary ecology, lcsh:Ecology
Abstract: Host‐plant selection is a key factor driving the ecology and evolution of insects. While the majority of phytophagous insects is highly host specific, generalist behavior is quite widespread among bees and presumably involves physiological adaptations that remain largely unexplored. However, floral visitation patterns suggest that generalist bees do not forage randomly on all available resources. While resource availability and accessibility as well as nectar composition have been widely explored, pollen chemistry could also have an impact on the range of suitable host‐plants. This study focuses on particular pollen nutrients that cannot be synthesized de novo by insects but are key compounds of cell membranes and the precursor for molting process: the sterols. We compared the sterol composition of pollen from the main host‐plants of three generalist bees: Anthophora plumipes, Colletes cunicularius, and Osmia cornuta, as well as one specialist bee Andrena vaga. We also analyzed the sterols of their brood cell provisions, the tissues of larvae and nonemerged females to determine which sterols are used by the different species. Our results show that sterols are not used accordingly to foraging strategy: Both the specialist species A. vaga and the generalist species C. cunicularius might metabolize a rare C27 sterol, while the two generalist species A. plumipes and O. cornuta might rather use a very common C28 sterol. Our results suggest that shared sterolic compounds among plant species could facilitate the exploitation of multiple host‐plants by A. plumipes and O. cornuta whereas the generalist C. cunicularius might be more constrained due to its physiological requirements of a more uncommon dietary sterol. Our findings suggest that a bee displaying a generalist foraging behavior may sometimes hide a sterol‐specialized species. This evidence challenges the hypothesis that all generalist free‐living bee species are all able to develop on a wide range of different pollen types., We compared the sterol composition of pollen from the main host‐plants of three generalist bees: Anthophora plumipes, Colletes cunicularius, and Osmia cornuta, as well as one specialist bee Andrena vaga. We also analyzed the sterols of their brood cell provisions, the tissues of larvae, and nonemerged females to determine which sterols are used by the different species. Our findings suggest that a bee displaying a generalist foraging behavior might sometimes hide a sterol specialized species.
Published: 2020

12. Rubber, rubber and rubber: How 75 years of successive rubber plantations rotations affect topsoil quality?

Author: Phantip Panklang, Alexis Thoumazeau, Rawee Chiarawipa, Sayan Sdoodee, David Sebag, Frédéric Gay, Philippe Thaler, Alain Brauman, Prince of Songkla University (PSU), Land Development Department (LDD), Agrosystèmes Biodiversifiés (UMR ABSys), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-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), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Kasetsart University (KU), DP-Hevea Research Platform in Partnership (HRPP), IFP Energies nouvelles (IFPEN), Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), 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, Phantip Panklang’s PhD scholarship was funded by the Graduate school and Natural Rubber Innovation Research Institute, Prince of Songkla University (PSU), contract No. NAT590338S. We thank Department of National Park (DNP) of Thailand for permission to sample in the forest. This study was also supported by the LMI LUSES (Dynamic of Land Use Changes and Soil Ecosystem Services), the French National Research Agency (ANR) in the framework of the Heveadapt project (ANR-14-CE03-0012) and the HRPP platform, the French Institute for Natural Rubber (IFC), the companies SIPH, SOCFIN and MICHELIN in the framework of the programme 'HeveaBiodiv'. This work benefited from the support of Nancy Rakotondrazafy for nutrient analysis in the ECOTROP platform of UMR Eco&Sols, with the support of LabEx CeMEB and ANR 'Investissements d'avenir' programme (ANR-10-LABX-0004). We are also grateful to Thierry Adatte (Institute of Earth Sciences, University of Lausanne, Switzerland) for his technical and scientific supports in Rock-Eval® analysis, a trademark registered by IFP Energies Nouvelles. The authors also thank Raphaël Chaillé, Céline Venot and all the people involved in field measurements as well as the farmers who allowed us to sample their plots., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and ANR-14-CE03-0012,HEVEADAPT,Comment les plantations familiales peuvent-elles s'adapter aux changements globaux?(2014)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Rotation culturale, successive rotation, F08 - Systèmes et modes de culture, P35 - Fertilité du sol, Soil Science, P34 - Biologie du sol, Couche arable, Development, Hevea brasiliensis, Qualité du sol, Environmental Chemistry, long term, soil quality, rubber plantations, General Environmental Science
Abstract: International audience; Rubber tree plantations (Hevea brasiliensis) cover large areas in the tropics. In historical producing regions like South Thailand, rubber has been planted by smallholders for three successive rotations lasting a total of 75 years. Despite possible consequences on topsoil, the long-term impacts of repeated rubber plantations on soil quality remain unknown. This study aims to better understand how various factors linked to long-term rubber land use and land use change affect topsoil physico-chemical properties and soil organic carbon (SOC) thermal stability. We focus on the effects of three factors: i. deforestation (change from forest to first rubber plantation); ii. the age of the rubber stand (immature vs. mature); and iii. long-term rubber cultivation (first, second or third successive rotation) over a chronosequence in farmers plots. Our results show that soil was deeply degraded after deforestation to a rubber plantation. Long-term rubber cultivation is also detrimental for the soil and has a more negative impact on soil physico-chemical properties and carbon dynamics, than the age of the rubber stand (e.g., on average, decrease of 50% of SOC content between forest and third rotation). At the third rotation, after 50 years of rubber cultivation, the quality of the 0-10 cm soil layer was very low, with an increase in SOC thermal stability. At this stage, logging practices upset the sustainability of the system. These impacts could be limited by less destructive practices during planting.
Published: 2022

13. Raman spectroscopy mapping of changes in the organization and relative quantities of cell wall polymers in bast fiber cell walls of flax plants exposed to gravitropic stress

Author: Anne-Sophie Blervacq, Myriam Moreau, Anne Duputié, Isabelle De Waele, Ludovic Duponchel, Simon Hawkins, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement (LASIRE) - UMR 8516, and Évolution, Écologie et Paléontologie (Evo Eco Paleo) - UMR 8198
Subjects: abiotic stress, [CHIM.POLY]Chemical Sciences/Polymers, flax (Linum usitatissimum L.), bast fibers, cell wall, Raman spectroscopy, chemometric, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract: International audience; Flax is an important fiber crop that is subject to lodging. In order to gain more information about the potential role of the bast fiber cell wall in the return to the vertical position, 6-week-old flax plants were subjected to a long-term (6 week) gravitropic stress by stem tilting in an experimental set-up that excluded autotropism. Stress induced significant morphometric changes (lumen surface, lumen diameter, and cell wall thickness and lumen surface/total fiber surface ratio) in pulling- and opposite-side fibers compared to control fibers. Changes in the relative amounts and spatial distribution of cell wall polymers in flax bast fibers were determined by Raman vibrational spectroscopy. Following spectra acquisition, datasets (control, pulling- and opposite sides) were analyzed by principal component analysis, PC score imaging, and Raman chemical cartography of significant chemical bonds. Our results show that gravitropic stress induces discrete but significant changes in the composition and/or spatial organization of cellulose, hemicelluloses and lignin within the cell walls of both pulling side and opposite side fibers.
Published: 2022

14. Continuous limits of large plant-pollinator random networks and some applications

Author: Sylvain Billiard, Hélène Leman, Thomas Rey, Viet-Chi Tran, Tran, Viet Chi, Laboratoires d'excellence - Centre Européen pour les Mathématiques, la Physique et leurs Interactions - - CEMPI2011 - ANR-11-LABX-0007 - LABX - VALID, Laboratoires d'excellence - Models and algorithms: from the discrete to the continuous - - Bézout2010 - ANR-10-LABX-0058 - LABX - VALID, Modèles multi-échelles et simulation numérique hybride de semi-conducteurs - - MoHyCon2017 - ANR-17-CE40-0027 - AAPG2017 - VALID, APPEL À PROJETS GÉNÉRIQUE 2018 - Modèles statistiques avancés pour les réseaux écologiques - - EcoNet2018 - ANR-18-CE02-0010 - AAPG2018 - VALID, Propagation de processus épidémiques sur des réseaux dynamiques de mouvements d'animaux avec application aux bovins en France - - CADENCE2016 - ANR-16-CE32-0007 - AAPG2016 - VALID, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Unité de Mathématiques Pures et Appliquées (UMPA-ENSL), École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS), Inria Lyon, Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire Paul Painlevé (LPP), Reliable numerical approximations of dissipative systems (RAPSODI ), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire Analyse et Mathématiques Appliquées (LAMA), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université Gustave Eiffel, Chaire Modélisation Mathématique et Biodiversité (MMB)' of Veolia-Ecole Polytechnique-Museum National d'Histoire Naturelle-Fondation X, ANR-11-LABX-0007,CEMPI,Centre Européen pour les Mathématiques, la Physique et leurs Interactions(2011), ANR-10-LABX-0058,Bézout,Models and algorithms: from the discrete to the continuous(2010), ANR-17-CE40-0027,MoHyCon,Modèles multi-échelles et simulation numérique hybride de semi-conducteurs(2017), ANR-18-CE02-0010,EcoNet,Modèles statistiques avancés pour les réseaux écologiques(2018), ANR-16-CE32-0007,CADENCE,Propagation de processus épidémiques sur des réseaux dynamiques de mouvements d'animaux avec application aux bovins en France(2016), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Paul Painlevé - UMR 8524 (LPP), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Institut National de Recherche en Informatique et en Automatique [Inria], Unité de Mathématiques Pures et Appliquées [UMPA-ENSL], Laboratoire Paul Painlevé [LPP], Reliable numerical approximations of dissipative systems [RAPSODI ], and Laboratoire Analyse et Mathématiques Appliquées [LAMA]
Subjects: [MATH.MATH-PR] Mathematics [math]/Probability [math.PR], integro-differential equation, graphon, 92D40, 92D25, 05C90, 60J80, 60F17, 47G20, kinetic limit, Mathematics - Analysis of PDEs, FOS: Mathematics, Quantitative Biology::Populations and Evolution, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], [MATH.MATH-AP] Mathematics [math]/Analysis of PDEs [math.AP], Quantitative Biology - Populations and Evolution, ecological mutualistic community, Probability (math.PR), AMS: 92D40, 92D25, 05C90, 60J80, 60F17, 47G20, Populations and Evolution (q-bio.PE), [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], stationary solution, FOS: Biological sciences, interacting particles, limit theorem, birth and death process, Mathematics - Probability, Analysis of PDEs (math.AP), [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; We study a stochastic individual-based model of interacting plant and pollinator species through a bipartite graph: each species is a node of the graph, an edge representing interactions between a pair of species. The dynamics of the system depends on the between- and within-species interactions: pollination by insects increases plant reproduction rate but has a cost which can increase plant death rate, depending on pollinators density. Pollinators reproduction is increased by the resources harvested on plants. Each species is characterized by a trait corresponding to its degree of generalism. This trait determines the structure of the interactions graph and the quantity of resources exchanged between species. Our model includes in particular nested or modular networks. Deterministic approximations of the stochastic measure-valued process by systems of ordinary differential equations or integro-differential equations are established and studied, when the population is large or when the graph is dense and can be replaced with a graphon. The long-time behaviors of these limits are studied and central limit theorems are established to quantify the difference between the discrete stochastic individual-based model and the deterministic approximations. Finally, studying the continuous limits of the interaction network and the resulting PDEs, we show that nested plant-pollinator communities are expected to collapse towards a coexistence between a single pair of species of plants and pollinators.
Published: 2022

15. Detecting human activity areas in Middle Palaeolithic open-air sites in Northern France from faunal remains spatial distribution

Author: Moreau, Gwénaëlle, Auguste, P., Locht, Jean-Luc, Patou-Mathis, Marylène, Université de Liège, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Laboratoire de géographie physique : Environnements Quaternaires et Actuels (LGP), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD)
Subjects: Spatial Analysis, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Geographic Information Systems, Middle Palaeolithic, Human Activity Area, Northern France, Faunal Remains
Abstract: International audience; The detection of Middle Palaeolithic human activity areas represents a methodological challenge at the boundary between two disciplines: archaeology and spatial analysis. During the course of the past decades, with the democratisation of tools such as Geographic Information Systems (GIS), prehistorians have developed a wide diversity of methods for the study of the spatial organization of occupation levels. We must now choose the best adapted method to our spatial problems, our archaeological contexts, but also our set of geographic data, from the existing methods. In this context, we devised a new spatial analysis protocol, highlighting archaeological and spatial criteria that constrained our choice of methods and estimating their reproducibility. The construction and application of our protocol is based on the Middle Palaeolithic open-air sites of Caours and Beauvais, situated in the North of France. On account of the ideal preservation conditions at these sites, they are propitious candidates for spatial analysis. In addition, these sites rank among those with the most abundant faunal remains of the region and our study focuses on this category of remains. The combined use of two methods of spatial analysis-K-means clustering and Kernel Density Estimationenables us, on one hand, to effectively detect human activity areas, their number and their distribution. On the other hand, this protocol contributed to their characterisation and the description of their role for the functioning of the occupation level. For both of the studied sites, we brought to light several areas of butchery activities organized around a combustion zone. In the case of Caours, areas of specific butchery activities, devoted to one or two species, were identified.
Published: 2021

16. Sex allocation, inbreeding, and measures of population differentiation in hermaphroditic metapopulations

Author: John R. Pannell, Samuel Neuenschwander, Charles Mullon, Camille Rouxc, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Evolution of sexual reproduction, media_common.quotation_subject, Population, Metapopulation, Biology, Mating system, 010603 evolutionary biology, 01 natural sciences, Competition (biology), 03 medical and health sciences, Evolutionary biology, Local extinction, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, education, Inbreeding, Sex allocation, 030304 developmental biology, media_common
Abstract: Selection in inbreeding populations is expected to favour female-biased sex ratios in dioecious or gonochoristic species as a result of local mate competition, a prediction that finds strong support in populations in which females have control of the proportion of their sons versus daughters. Local mate competition due to inbreeding should also promote female-biased sex allocation in hermaphrodites, with reduced emphasis on the production of sperm or pollen relative to eggs, ovules or seeds. While inbreeding can be the direct result of the mating system in local populations, it can also result from demographic causes such as population turnover in metapopulations with frequent local extinction and recolonization. This effect of the turnover of demes has previously been analysed under the ‘haystack model’ for species with separate sexes. Here, we use quantitative genetic simulations to ask how population turnover affects the evolution of sex allocation in hermaphroditic metapopulations, and we assess the extent to which different genetic measures of inbreeding and population differentiation, especially FST and Jost’s D, predict the equilibrium sex allocation. We find that population turnover may dramatically enhance the female bias of hermaphroditic metapopulations, particularly where the inter-deme migration rate is low, even where local inbreeding, measured by FIS, is low or absent. In such situations, FST is a good predictor of the equilibrium sex allocation, and much better than Jost’s D. Our study extends predictions for sex allocation in subdivided populations that might experience population turnover to hermaphroditic species, and draws attention in general to the power of Wright’s hierarchical inbreeding statistics to predict the sex allocation in metapopulations at equilibrium.
Published: 2021

17. Genetic mapping of sex and self-incompatibility determinants in the androdioecious plant Phillyrea angustifolia

Author: Pierre Saumitou-Laprade, Cécile Godé, Philippe Vernet, Sylvain Santoni, Amelie Carre, Sophie Gallina, Vincent Castric, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), 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), 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), 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]), and Centre National de la Recherche Scientifique (CNRS)-Université de Lille
Subjects: 0106 biological sciences, 0303 health sciences, Phylogenetic tree, [SDV]Life Sciences [q-bio], Locus (genetics), Context (language use), Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, symbols.namesake, Gene mapping, Genetic linkage, Evolutionary biology, Chromosomal region, Mendelian inheritance, symbols, 030304 developmental biology, Synteny
Abstract: International audience; The diversity of mating and sexual systems in angiosperms is spectacular, but the factors driving their evolution remain poorly understood. In plants of the Oleaceae family, an unusual self-incompatibility (SI) system has been discovered recently, whereby only two distinct homomorphic SI specificities segregate stably. To understand the role of this peculiar SI system in preventing or promoting the diversity of sexual phenotypes observed across the family, an essential first step is to characterize the genetic architecture of these two traits. Here, we developed a high-density genetic map of the androdioecious shrub P. angustifolia based on a F1 cross between a hermaphrodite and a male parent with distinct SI genotypes. Using a double restriction-site associated digestion (ddRAD) sequencing approach, we obtained reliable genotypes for 196 offspring and their two parents at 10,388 markers. The resulting map comprises 23 linkage groups totaling 1,855.13 cM on the sexaveraged map. We found strong signals of association for the sex and SI phenotypes, that were each associated with a unique set of markers on linkage group 12 and 18 respectively, demonstrating inheritance of these traits as single, independent, mendelian factors. The P. angustifolia linkage map shows robust synteny to the olive tree genome overall. Two of the six markers strictly associated with SI in P. angustifolia have strong similarity with a recently identified 741kb chromosomal region fully linked to the SI phenotype on chromosome 18 of the olive tree genome, providing strong cross-validation support. The SI locus stands out as being markedly rearranged, while the sex locus has remained relatively more collinear between the two species. This P. angustifolia linkage map will be a useful resource to investigate the various ways by which the sex and SI determination systems have co-evolved in the broader phylogenetic context of the Oleaceae family.; La diversité des systèmes de reproduction et des types sexuels chez les angiospermes est spectaculaire, mais les facteurs de leur évolution restent mal compris. Chez les plantes de la famille des Oleacées, un système d'auto-incompatibilité (SI) inhabituel a été découvert récemment, dans lequel seules deux spécificités SI distinctes mais parfaitement homomorphes ségrégent de manière stable. Pour comprendre le rôle de ce système SI particulier dans la prévention ou la promotion de la diversité des phénotypes sexuels observés dans la famille des Oléacées, une première étape essentielle est de caractériser l'architecture génétique de ces deux traits. Ici, nous avons développé une carte génétique à haute densité de l'arbuste androdioïque P. angustifolia basée sur un croisement F1 entre un hermaphrodite et un parent mâle avec des génotypes SI distincts. En utilisant une approche de séquençage par double digestion associée à un site de restriction (ddRAD), nous avons obtenu des génotypes fiables pour 196 descendants et leurs deux parents sur 10 388 marqueurs. La carte résultante comprend 23 groupes de liaison totalisant 1 855,13 cM sur la carte moyenne par sexe. Nous avons trouvé de forts signaux d'association pour les phénotypes sexe et SI, qui étaient chacun associés à un ensemble unique de marqueurs sur les groupes de liaison 12 et 18 respectivement, démontrant l'héritage de ces traits comme facteurs mendéliens uniques et indépendants. La carte de liaison de P. angustifolia montre une synténie robuste avec le génome de l'olivier dans son ensemble. Deux des six marqueurs strictement associés au SI chez P. angustifolia présentent une forte similitude avec une région chromosomique de 741 kb récemment identifiée et entièrement liée au phénotype SI sur le chromosome 18 du génome de l'olivier, ce qui fournit une forte validation croisée. Le locus SI se distingue par un réarrangement marqué, tandis que le locus sexuel est resté relativement colinéaire entre les deux espèces. Cette carte de liaison de P. angustifolia sera une ressource utile pour étudier les différentes façons dont les systèmes de détermination du sexe et du SI ont co-évolué dans le contexte phylogénétique plus large de la famille des Oléacées.
Published: 2021

18. Within-host genetic micro-diversity of Mycobacterium tuberculosis and the link with tuberculosis disease features

Author: Oana Dumitrescu, Stéphane Dray, Emilie Westeel, Jean-Luc Berland, Alexia Barbry, Gerard Lina, Laurent Jacob, Elisabeth Hodille, Samuel Venner, Charlotte Genestet, Florence Ader, François Massol, Guislaine Refrégier, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Bactériologie de l'Hôpital de la Croix-Rousse, Hospices Civils de Lyon (HCL), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Fondation Mérieux, Service des Maladies Infectieuses et Tropicales [Lyon], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Baobab, Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), and Institute for Integrative Biology of the Cell [Gif-sur-Yvette] (I2BC)
Subjects: 0303 health sciences, Tuberculosis, biology, 030306 microbiology, Severity symptoms, business.industry, Host (biology), media_common.quotation_subject, respiratory system, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Contagious disease, Mycobacterium tuberculosis, 03 medical and health sciences, Immunology, Medicine, Tuberculosis Disease, business, 030304 developmental biology, Diversity (politics), media_common
Abstract: Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) complex, is still the number one deadly contagious disease. Mtb infection results in a wide spectrum of clinical presentations and severity symptoms, but without proven Mtb genetic determinants. Thanks to a collection of 355 clinical isolates with associated patient’s clinical data, we showed that Mtb micro-diversity within patient isolates is strongly correlated with TB-associated severity scores. Interestingly, this diversity is driven by a selection pressure to adapt to different lifestyles related to the infection site. Taken together, these results provide a new insight to better understand TB pathophysiology. Furthermore, Mtb micro-diversity could be envisioned as a new prognostic tool to improve the management of TB patients.
Published: 2021

19. Further observations on the spores of the Rhynie chert plant Horneophyton lignieri (Kidston & Lang) Barghoorn & Darrah, 1938: Implications for palaeodiversity studies

Author: Cascales-Miñana, B., Servais, T., Capel, E., Steemans, P., Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), ANR-20-CE01-0002,EARTHGREEN,Comprendre le verdissement de la Terre primitive(2020), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo)
Subjects: fungi, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology
Abstract: International audience; The Rhynie chert (Aberdeenshire, Scotland, UK) plant Horneophyton lignieri is likely one of the most studied elements of Lower Devonian floras considering both macro and microremains. Intriguingly, while larger plant fragments are exceptionally fossilized, in situ spores are not necessarily well-preserved in the chert: they are dark brown and intensively torn overall. However, spore masses are often dominated by single spores, which can be taxonomically attributed. Mainly, Horneophyton spores have been described as belonging to Apiculiretusispora type and Emphanisporites cf. decoratus, this last one being currently accepted in general. Here, we document new Horneophyton spore morphologies, that are sometimes quite different. Such morphologies include, but are not restricted to, Ambitisporites, Dibolisporites or Retusotriletes. All these observed spore morphotypes belong to the same palaeobiological entity, as they have been found in the same parent plant. These findings show that the sporangia of a same plant species may deliver diverse taxa of coeval isolated spores. But most importantly, if these spores are found in sediments, they would most probably be identified as different dispersed miospore taxa. This highlights that caution is needed when comparing plant diversity with the dispersed spore fossil record. Moreover, we confirm the presence of Emphanisporites decoratus inside most of the sporangia of Horneophyton lignieri, and its high morphological variability. We further discuss the role of the different states of maturation and preservation, as well as taphonomy-induced features, on observed spore diversity.
Published: 2021

20. Widespread coexistence of self-compatible and self-incompatible phenotypes in a diallelic self-incompatibility system in Ligustrum vulgare (Oleaceae)

Author: Philippe Vernet, Pierre Saumitou-Laprade, Isabelle De Cauwer, Cécile Godé, Chloé Ponitzki, Sylvain Billiard, Angélique Bourceaux, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Florimond Desprez, Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 0106 biological sciences, Pollination, Ligustrum vulgare, Outbreeding depression, Oleaceae, [SDV]Life Sciences [q-bio], Ligustrum, Outcrossing, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Polymorphism (computer science), Genetics, Inbreeding depression, Humans, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, Selfing, Self-Incompatibility in Flowering Plants, Mating system, biology.organism_classification, Plant Breeding, Phenotype, Evolutionary biology, Inbreeding
Abstract: The breakdown of self-incompatibility (SI) in angiosperms is one of the most commonly observed evolutionary transitions. While multiple examples of SI breakdown have been documented in natural populations, there is strikingly little evidence of stable within-population polymorphism with both inbreeding (self-compatible) and outcrossing (self-incompatible) individuals. This absence of mating system polymorphism corroborates theoretical expectations that predict that in/outbreeding polymorphism is possible only under very restricted conditions. However, theory also predicts that a diallelic sporophytic SI system facilitates the maintenance of such polymorphism. We tested this prediction by studying the mating system ofLigustrum vulgareL., an entomophilous hermaphroditic species of the Oleaceae family. Using stigma tests with controlled pollination and paternity assignment of open-pollinated progenies, we confirmed the existence of two self-incompatibility groups in this species. We also demonstrated the existence of self-compatible individuals in different populations of Western Europe arising from a mutation affecting the expression of the pollen component of SI. We then estimated the selfing rate in a garden experiment. Our results finally show that the observed low frequency of self-compatible individuals in natural populations is compatible with theoretical predictions only if inbreeding depression is very high.
Published: 2021

21. Congruent population genetic structures and divergence histories in anther-smut fungi and their host plants Silene italica and the S. nutans species complex

Author: Fabienne Van Rossum, Cécile Godé, Tatiana Giraud, Alodie Snirc, Fanny E. Hartmann, Stéphanie Le Prieur, Amandine Cornille, Jacqui A. Shykoff, Elisabeth Fournier, Pascal Touzet, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Botanic Garden Meise, Fédération Wallonie-Bruxelles, Partenaires INRAE, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Meise Botanic Garden [Belgium] (Plantentuin), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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), 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)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Ecologie Systématique et Evolution [ESE], Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], and Biologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
Subjects: 0106 biological sciences, Sympatry, cryptic speciation, Species complex, Population, host-pathogen interaction, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, approximate Bayesian computation, population genetic structure, education, 030304 developmental biology, genetic divergence, 0303 health sciences, education.field_of_study, biology, coevolution, Host (biology), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Silene nutans, food and beverages, 15. Life on land, biology.organism_classification, Evolutionary biology, Genetic structure, Microbotryum
Abstract: The study of population genetic structure congruence between hosts and pathogens gives important insights into their shared phylogeographic and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (Microbotryumgenus) and of their host plants, theSilene nutansspecies complex, and the morphologically and genetically closeS. italica,which can be found in sympatry. Phylogeographic population genetic structure related to persistence in separate glacial refugia has been recently revealed in theS. nutansplant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic SNPs. We found clear differentiation between fungal populations parasitizingS. nutansandS. italicaplants. The population genetic structure of fungal strains parasitizing theS. nutansplant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages onS. nutanswas congruent with the one previously inferred for the host plant and likely occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of host-pathogen individual pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies are still scarce.
Published: 2021

22. ESR/U-series dating Eemian human occupations of Northern France

Author: Bahain, Jean-Jacques, Farkh, Samer, Falguères, Christophe, Shao, Qingfeng, Voinchet, Pierre, Ghaleb, Bassam, Hérisson, David, Locht, Jean-Luc, Limondin-Lozouet, Nicole, Auguste, Patrick, Dabkowski, Julie, Deschodt, Laurent, Antoine, Pierre, Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Lebanese University [Beirut] (LU), Nanjing Normal University (NNU), Centre de recherche sur la dynamique du système Terre (GEOTOP), École Polytechnique de Montréal (EPM)-McGill University = Université McGill [Montréal, Canada]-Université de Montréal (UdeM)-Université du Québec en Abitibi-Témiscamingue (UQAT)-Université du Québec à Rimouski (UQAR)-Concordia University [Montreal]-Université du Québec à Montréal = University of Québec in Montréal (UQAM), Centre National de la Recherche Scientifique (CNRS), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Anthropologie des techniques, des espaces et des territoires au Pliocène et au Pléistocène (AnTET), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Laboratoire de géographie physique : Environnements Quaternaires et Actuels (LGP), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Université de Montréal (UdeM)-McGill University = Université McGill [Montréal, Canada]-École Polytechnique de Montréal (EPM)-Concordia University [Montreal]-Université du Québec à Rimouski (UQAR)-Université du Québec à Montréal = University of Québec in Montréal (UQAM)-Université du Québec en Abitibi-Témiscamingue (UQAT), Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-Université Paris Nanterre (UPN)-Université Paris 1 Panthéon-Sorbonne (UP1), Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-Université Paris Nanterre (UPN)-Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-Université Paris Nanterre (UPN)-Université Paris 1 Panthéon-Sorbonne (UP1), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), and Hérisson, David
Subjects: [SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Caours, Eemian, Waziers, ESR/U-series, teeth
Abstract: International audience; Palaeolithic sites associated to the Eemian Interglacial (MIS 5e) are very rare in Northern France and their preservation is restricted to very specific geological contexts, in association with carbonated tufa (Caours) or peat deposits (Waziers). In order to check the reliability of ESR/U-series method to date teeth recovered from archaeological levels in so specific geological environments, teeth were sampled on these two Middle Palaeolithic sites and systematic in situ dosimetry was performed using portable gamma spectrometer. The ESR/U-series ages obtained on the Caours site are very homogeneous allowing the calculation of a mean age equal to 125 ± 4 ka, in agreement with the geological age and other available geochronological data (U-series on carbonate, TL on heated flints, OSL on sediments) and despite an relatively heterogeneous dosimetric environment (gamma dose rate ranging between ca 200 to 450 µGy/a). At Waziers, reducing chemical environment linked to the peat lead to very specific U-series data of the analysed teeth (U content lower than 0.1 ppm in all the dental tissues, evidence of leaching in some tissues), but the mean ESR/U-series age, 129 ± 4 ka, is also in agreement with the available geological and palaeoenvironmental data. These two studies confirm the reliability of ESR/U-series method to date with relative accuracy archaeological levels linked to such relatively short climatic event.
Published: 2021

23. Roots take up labeled nitrogen from a depth of 9 m in a wooded savanna in Brazil

Author: Jean-Paul Laclau, Lívia Lanzi Aló, Vânia Regina Pivello, Karel Van den Meersche, Rafael Costa Pinheiro, Vladimir Eliodoro Costa, Jean-Pierre Bouillet, Iraê Amaral Guerrini, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade de São Paulo (USP), Universidade Estadual Paulista (Unesp), UMR Eco&Sols, and Montpellier SupAgro
Subjects: Relation plante eau, SOLOS, Nutrient, Dry season, Transport des substances nutritives, Savane, Tropical savanna, 2. Zero hunger, biology, 15N, Deep roots, Enracinement, Cerrado, 04 agricultural and veterinary sciences, Understory, Physiologie végétale, Miconia, Besoin en eau, Écosystème forestier, Soil horizon, Woody plant, P33 - Chimie et physique du sol, Biogeochemical cycle, Azote, Soil Science, Besoin nutritionnel, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Microbiology, Subsoil, Cycle biogéochimique, Diameter at breast height, 15. Life on land, biology.organism_classification, F61 - Physiologie végétale - Nutrition, Agronomy, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Racine
Abstract: Made available in DSpace on 2021-06-25T11:16:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The savannas (called Cerrado) are the second-largest vegetation formation in Brazil after the Amazon rainforest, with about 2 million km2. Roots have been found in very deep soil layers in Cerrado ecosystems, which suggests a crucial role of deep rooting in the supply of water and nutrients over dry periods. The aim of our study was to gain insight into the complementarity of common Cerrado woody species in taking up mobile nutrients throughout deep soil profiles. In a closed-canopy savanna with dense woody understory, labeled nitrate was injected into the soil at six soil depths (0.1, 1.5, 3.0, 6.0, 9.0, or 12.0 m) with three plots per depth, at two dates (in rainy and dry seasons). Five months after labeled nitrate injection, young leaves were sampled and foliar δ15N was determined in each plot in the three most common woody species (Coussarea hydrangeifolia, Miconia albicans and Xylopia aromatica). The maximum depth of 15N uptake was dependent on the species. X. aromatica trees took up 15N from a maximum depth of 9 m and exploited a much larger soil volume than the two other species, with the uptake of 15N at a horizontal distance of up to 5 m between the trunk and the injection site. The behavior of M. albicans and C. hydrangeifolia was similar, with a strong uptake of 15N only in the 0–1.5 m soil layer, within 2 m horizontally from the injection site. The depth of 15N uptake over the dry season was not related to the diameter at breast height of the woody plants sampled. We show that roots can take up labeled nitrogen from a depth of 9 m in tropical wooded savannas, which suggests an important role of deep-rooted species in closing biogeochemical cycles on highly weathered tropical soils. São Paulo State University (Unesp) School of Agriculture CIRAD UMR Eco&Sols Eco&Sols Univ Montpellier CIRAD INRA IRD Montpellier SupAgro Department of Ecology University of São Paulo (USP) São Paulo State University (Unesp) Institute of Biosciences São Paulo State University (Unesp) School of Agriculture São Paulo State University (Unesp) Institute of Biosciences FAPESP: 2015/25946–0
Published: 2021

24. Palaeobotanical experiences of plant diversity in deep time. II: How to measure and analyse past plant biodiversity

Author: Pardoe, Heather, Cleal, Christopher, Berry, Christopher, Cascales-Miñana, Borja, Davis, Basil, Diez, Jose, Filipova-Marinova, Mariana, Giesecke, Thomas, Hilton, Jason, Ivanov, Dimiter, Kustatscher, Evelyn, Leroy, Suzanne, Mcelwain, Jennifer, Opluštil, Stanislav, Popa, Mihai, Seyfullah, Leyla, Stolle, Ellen, Thomas, Barry, Uhl, Dieter, National Museum of Wales - Cardiff, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire méditerranéen de préhistoire Europe-Afrique (LAMPEA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo)
Subjects: [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

25. The integrative biology of genetic dominance

Author: Sylvain Billiard, Vincent Castric, Violaine Llaurens, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, 0303 health sciences, Genotype, Models, Genetic, Fitness landscape, Inheritance (genetic algorithm), Gene regulatory network, Population genetics, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Wright, Genetics, Population, Phenotype, Evolutionary biology, Evolution of dominance, Epistasis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, ComputingMilieux_MISCELLANEOUS, Genes, Dominant, 030304 developmental biology, Dominance (genetics)
Abstract: Dominance is a basic property of inheritance systems describing the link between a diploid genotype at a single locus and the resulting phenotype. Models for the evolution of dominance have long been framed as an opposition between the irreconcilable views of Fisher in 1928 supporting the role of largely elusive dominance modifiers and Wright in 1929, who viewed dominance as an emerging property of the structure of enzymatic pathways. Recent theoretical and empirical advances however suggest that these opposing views can be reconciled, notably using models investigating the regulation of gene expression and developmental processes. In this more comprehensive framework, phenotypic dominance emerges from departures from linearity between any levels of integration in the genotype-to-phenotype map. Here, we review how these different models illuminate the emergence and evolution of dominance. We then detail recent empirical studies shedding new light on the diversity of molecular and physiological mechanisms underlying dominance and its evolution. By reconciling population genetics and functional biology, we hope our review will facilitate cross-talk among research fields in the integrative study of dominance evolution.
Published: 2021

26. Nutrient deficiency enhances the rate of short-term belowground transfer of nitrogen from Acacia mangium to Eucalyptus trees in mixed-species plantations

Author: Jean-Paul Laclau, G. Le Maire, Andréa de Vasconcelos Ferraz, José Leonardo de Moraes Gonçalves, J.P. Bouillet, Bruno Bordron, Ranieri Ribeiro Paula, Ivanka Rosado de Oliveira, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Universidade Federal do Espirito Santo (UFES), Instituto de Pesquisas e Estudos Florestais (IPEF), IN-SYLVA French network, FAPESP Thematic Project (2010/16623-9), ANR-10-STRA-0004,Intens&Fix,Intensification écologique des écosystèmes de plantations forestières. Modélisation biophysique et évaluation socio-économique de l'association d'espèces fixatrices d'azote(2010), University of Montpellier, UMR Eco&Sols, Universidade Estadual Paulista (Unesp), UFES, Instituto de Pesquisas e Estudos Florestais, Universidade de São Paulo = University of São Paulo (USP), 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 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)
Subjects: 0106 biological sciences, Litière forestière, Carence en substance nutritive, 01 natural sciences, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Acacia mangium, K01 - Foresterie - Considérations générales, Transport des substances nutritives, Absorption de substances nutritives, Eucalyptus, biology, NITROGÊNIO 15, 15N, Forestry, Plant litter, Arbre fixateur d'azote, visual_art, visual_art.visual_art_medium, Bark, Facilitation, Brazil, Randomized block design, Acacia, Management, Monitoring, Policy and Law, 010603 evolutionary biology, Culture en mélange, Fertilité du sol, Nature and Landscape Conservation, Forest floor, Mature trees, P35 - Fertilité du sol, 15. Life on land, biology.organism_classification, F61 - Physiologie végétale - Nutrition, Agronomy, Fertilization, Sol de forêt, Soil fertility, 010606 plant biology & botany, Nitrogen-fixing trees
Abstract: Made available in DSpace on 2021-06-25T10:27:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07-01 While a recent study showed that significant amounts of the nitrogen (N) requirements of young Eucalyptus trees can be provided by nitrogen-fixing trees (NFTs) in mixed-species plantations through short-term belowground N transfer, the consequences of soil fertility on this facilitation process remain unknown. We assessed the effect of fertilization on the percentage of N derived from transfer (%NDFT) from Acacia mangium trees to Eucalyptus trees in mixed-species plantations. A complete randomized block design with two treatments (fertilized vs unfertilized) and three blocks was set up in mixed-species plantations of A. mangium and Eucalyptus in Brazil, with 50% of each species at 2.5 m × 2.5 m spacing. Collection of litterfall and forest floor made it possible to estimate the annual N release from forest floor decomposition between 46 and 58 months after planting, close to harvest age. 15N-NO3- was injected into the stem of one dominant Acacia tree in each plot, 58 months after planting. The x(15N) values of Acacia and Eucalyptus fine roots sampled within 1.8 m of the labelled A. mangium tree were determined at 7, 14, 30 and 60 days after labelling. The x(15N) values in wood, bark, branch and leaf samples were also determined for the 6 labelled Acacia trees and their two closest Eucalyptus neighbours, just before and 60 days after labelling. The amount of N released from forest floor decomposition was 31% higher in fertilized (F+) than in unfertilized (F-) plots. Sixty days after labelling, the aboveground compartments of Eucalyptus trees were significantly 15N enriched in both treatments. The x(15N) values of Acacia fine roots were higher than background values from 7 days after labelling onwards in F+ and 30 days after labelling in F-. The x(15N) values of Eucalyptus fine roots were higher than background values in both treatments, from 30 days after labelling onwards. Mean %NDFT values were 18.0% in F+ and 33.9% in F- over the first 60 days after labelling, and 22.8% in F+ and 67.7% in F- from 30 to 60 days after labelling. Fertilization decreased short-term transfer belowground of N from Acacia trees to Eucalyptus trees. Our study suggests that belowground facilitation processes providing N from NFTs to Eucalyptus trees in mixed-species plantations are more pronounced in low-fertility soils than in nutrient-supplied stands. USP ESALQ Forest Science Department Eco&Sols INRA CIRAD IRD Montpellier SupAgro University of Montpellier CIRAD UMR Eco&Sols UNESP School of Agriculture São Paulo State University ‘Julio de Mesquita Filho,’ Department of Forest Science and Wood UFES IPEF Instituto de Pesquisas e Estudos Florestais UNESP School of Agriculture São Paulo State University ‘Julio de Mesquita Filho,’
Published: 2021

27. Revised Cambrian stratigraphy in the Franconian Forest (Frankenwald), Germany, reveals typical West Gondwanan succession in the Saxothuringian Belt

Author: Ulf Linnemann, Stefan Meier, Thomas Wotte, Stefan Höhn, Thomas Servais, Hans-Georg Herbig, Ed Landing, Gerd Geyer, Senckenberg Naturhistorische Sammlungen Dresden, Museum für Mineralogie und Geologie, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDE.MCG]Environmental Sciences/Global Changes, Stratigraphy, 05 social sciences, Lithostratigraphy, Geology, 06 humanities and the arts, Ecological succession, Volcanism, 0603 philosophy, ethics and religion, 050105 experimental psychology, Sedimentary depositional environment, Paleontology, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, 060302 philosophy, 0501 psychology and cognitive sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Chronostratigraphy, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

28. Molecular and morphological recognition of species boundaries in the neglected ant genus Brachymyrmex (Hymenoptera: Formicidae): toward a taxonomic revision

Author: Claudia M. Ortiz-Sepulveda, Fernando Fernández, Andrés D. Meneses, Bert Van Bocxlaer, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional de Colombia [Bogotà] (UNAL), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo)
Subjects: 0106 biological sciences, Morphometrics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Identification key, Subspecies, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Brachymyrmex, 010602 entomology, Monophyly, Taxon, Evolutionary biology, Taxonomy (biology), Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Brachymyrmex is a neglected genus of Formicinae because of its small body size, soft mesosoma, and superficially monotonous external morphology. These features have complicated the documentation of morphological variation, resulting in poorly defined and incompletely described species. Consequently, the taxonomy of the genus is complex and problematic, which has impeded research and conservation efforts. Here, we integrate molecular and morphological data to recognize species boundaries in Brachymyrmex and to guide its long-overdue revision. Specifically, we (1) redefine the limits of all described species, subspecies, and varieties based on intra-and interspecific morphological variation in workers; (2) document this variation quantitatively by constructing morphospace occupation and statistically analyzing measurements; (3) synthesize our findings on diagnostic traits in a dichotomous, illustrated identification key; and (4) examine the significance of our morphological identification system with molecular evidence from four gene fragments (EF1aEF1, EF1aEF2, WG, and COI). We recognize 40 species, of which four are new to science: Brachymyrmex bahamensis, Brachymyrmex bicolor, Brachymyrmex iridescens, and Brachymyrmex sosai. Furthermore, Brachymyrmex attenuatus and Brachymyrmex bonariensis are raised to species, and we propose 25 new synonyms. Morphometrics indicated that even poorly distinguishable species pairs show statistically significant differences in some traits, and that taxonomically problematic cases relate to taxa that demonstrate large intraspecific trait variance. Our molecular analysis supports the monophyly of the genus based on increased taxon sampling, and of the 19 species that were included 18 were retrieved as monophyletic. The single case of incongruence was also flagged in morphological analyses and requires extended geographic sampling before it can be resolved. In conclusion, the molecular work corroborates the morphologically recognized species boundaries. We also document the presence of worker dimorphism and putative worker-queen intercastes in several Brachymyrmex species, which indicates that the genus may present a promising study system to understand caste evolution in ants.
Published: 2019

29. Functional integration for enrolment constrains evolutionary variation of phacopid trilobites despite developmental modularity

Author: Rémi Laffont, Ahmed Yacine Khaldi, Morgane Oudot, Catherine Crônier, Nicolas Navarro, Pascal Neige, Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Laboratoire de Paléontologie stratigraphique et paléo-environnements, Université d'Oran 1 Ahmed Ben Bella [Oran], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 0106 biological sciences, 010506 paleontology, Cephalon, Developmental modularity, Modularity (biology), Biology, Diversification (marketing strategy), 010603 evolutionary biology, 01 natural sciences, Pygidium, Paleontology, Enrollment, Functional integration, Stabilizing selection, Clade, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Phacopidae, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], biology.organism_classification, Trilobite, Evolutionary biology, Trilobites, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology
Abstract: 17 pages; International audience; Modularity and integration are variational properties expressed at various levels of the biological hierarchy. Mismatches among these levels, for example developmental modules that are integrated in a functional unit, could be informative of how evolutionary processes and trade‐offs have shaped organismal morphologies as well as clade diversification. In the present study, we explored the full, integrated and modular spaces of two developmental modules in phacopid trilobites, the cephalon and the pygidium, and highlight some differences among them. Such contrasts reveal firstly that evolutionary processes operating in the modular spaces are stronger in the cephalon, probably due to a complex regime of selection related to the numerous functions ensured by this module. Secondly, we demonstrate that the same pattern of covariation is shared among species, which also differentiate along this common functional integration. This common pattern might be the result of stabilizing selection acting on the enrolment and implying a coordinate variation between the cephalon and the pygidium in a certain direction of the morphospace. Finally, we noticed that Austerops legrandi differs slightly from other species in that its integration is partly restructured in the way the two modules interact. Such a divergence can result from the involvement of the cephalon in several vital functions that may have constrained the response of the features involved in enrolment and reorganized the covariation of the pygidium with the cephalon. Therefore, it is possible that important evolutionary trade‐offs between enrolment and other functions on the cephalon might have partly shaped the diversification of trilobites.
Published: 2019

30. The floristic relationship between the upland and lowland Carboniferous wetlands of Variscan Euramerica — Evidence from some medullosalean pteridosperm fronds

Author: Christopher J. Cleal, Borja Cascales-Miñana, National Museum of Wales - Cardiff, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 010506 paleontology, Frond, Wetland, 010502 geochemistry & geophysics, 01 natural sciences, Swamp, Carboniferous, ComputingMilieux_MISCELLANEOUS, Migration, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, biology, Ecology, Coal swamps, Paleontology, 15. Life on land, Medullosales, biology.organism_classification, QE701-760, Upland, Habitat, Upland and lowland, Alethopteris, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Geology
Abstract: International audience; Alethopteris grandinii represents remains of fronds of a medullosalean pteridosperm (probably a small tree) that rapidly migrated across the lowland wetland habitats of Variscan Euramerica in middle Asturian (late Moscovian) times. This was probably caused by changing drainage patterns within the lowland coal swamps, in response to climate and landscape changes. However, these medullosaleans had first appeared rather earlier, in early Bolsovian (early Moscovian) times, in upland wetland habitats. These upland habitats may have pre-adapted these plants to the changed condition in the lowland coal swamps.
Published: 2019

31. The Furongian (late Cambrian) Biodiversity Gap: Real or apparent?

Author: David A. T. Harper, Per Ahlberg, Thomas Servais, Timothy P. Topper, Borja Cascales-Miñana, Yuandong （张元动） Zhang, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 010506 paleontology, Paleozoic, [SDE.MCG]Environmental Sciences/Global Changes, Stratigraphy, Fauna, Biodiversity, Marine life, 010502 geochemistry & geophysics, 01 natural sciences, Paleontology, Naturvetenskap, 14. Life underwater, Palaeogeography, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Taxon, Geography, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Facies, Ordovician, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Natural Sciences, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Cambrian GOBE Biodiversit yPalaeoenvironments Extinctions Radiations
Abstract: Two major, extended diversifications punctuated the evolution of marine life during the Early Palaeozoic. The interregnum, however, between the Cambrian Explosion and the Great Ordovician Biodiversification Event, is exemplified by the Furongian Gap when there was a marked drop in biodiversity. It is unclear whether the gap is apparent, due to sampling failure or lack of rock, or real — associated with unique and fluctuating environments, a distinctive palaeogeography and extreme climates during the late Cambrian. Indications suggest that there has been little attention paid to this interval compared with those below and above, while some of the classical areas for Cambrian research, such as Bohemia, have poor coverage through the Furongian. Moreover, based on information available in databases and the literature, together with the ghost ranges of many higher taxa through the Furongian, data suggest that biodiversity in this stage has been significantly underestimated. Emphasis, to date, has been placed on widespread, deeper-water dark shale facies of the interval, with generally low diversity faunas, whereas shallow-water communities have often been neglected.
Published: 2019

32. Mediterranean Temporary Lagoon: Proposal for a definition of this endangered habitat to improve its conservation

Author: Mathilde Latron, Aubin Allies, Olivier Argagnon, Nadine Bosc, Karine Faure, Hugo Fontes, Patrick Grillas, James Molina, Rutger De Wit, Guillaume Papuga, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Conservatoire Botanique National Méditerranéen de Porquerolles, Agence de l'eau Rhône Méditérranée Corse, Institut de recherche de la Tour du Valat, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), 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), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), 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 [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Tour du Valat, Research Institute for the conservation of Mediterranean Wetlands, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), and 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)
Subjects: Habitat directive, Ecology, [SDE.MCG]Environmental Sciences/Global Changes, coastal lagoon, conservation, Conservation, Habitat Directive, Coastal lagoon, [SDE.ES]Environmental Sciences/Environmental and Society, wetland, salt pan, Salt pan, Water Framework Directive, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Wetland, Water framework directive, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Nature and Landscape Conservation
Abstract: International audience; Coastal lagoons have been recognised as a priority habitat for conservation and have benefited from several conservation plans. Under the Mediterranean climate, some of these lagoons might dry out during summer due to drought events. We propose the term Mediterranean Temporary Lagoons (MTLs) for these ephemeral water bodies and discuss their definition and characteristics. This term emerged in France among its coastal zone managers, who now commonly use it for conservation purposes. It is used in both natural systems as well as most artificial salt ponds in abandoned saltworks. In Europe, two directives have integrated lagoons as key targets to be preserved. Nonetheless, a certain discrepancy in the different definitions of lagoons has constrained joint actions. Indeed, while institutional definitions were originally derived from the scientific concept, their legislative and managerials meanings have been gradually modified and nowadays often differ from the original concept to create difficulties in the field. In addition, while it has been recommended to consider MTLs as a coastal lagoon habitat in the European Habitat Directive, its interpretation among EU member states is unsettled. Thus, clarifying lagoon habitats' terminology is required to ensure better management, monitoring and planning, and coordinate conservation actions. We discuss the inclusion of MTLs in habitat 1150 by confronting scientific and institutional literature and propose a new framework to better delimitate lagoon habitat around the Mediterranean basin, integrating MTLs. MTLs represent a specific habitat that hosts a pool of stenoecious macrophytes of conservation interest like Althenia filiformis, Riella helicophylla or Tolypella salina.
Published: 2022

33. Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies

Author: Abir Hafsi, Stéphane Robin, Pierre François Duyck, Frédéric Chiroleu, Benoit Facon, Virginie Ravigné, François Massol, Julien Chiquet, Maud Charlery De La Masseliere, Maxime Dubart, Enric Frago, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-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)-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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Agronomique Néo-Calédonien (IAC), Thicenters work used images acquired within the framework of the CNES Kalideos device (Reunion site), which benefited from the 'Programme Investissements d'Avenir' EQUIPEX of the French 'Agence Nationale de la Recherche' on project GEOSUD bearing the reference ANR-10-EQPX-0020. The images also required financial support the French Ministry of Agriculture and field data transmitted by the `Syndicat du Sucre de la Reunion' and the 'SAFER de la Reunion'. BF, FC, FM, JC, MD, SR and VR received the financial support of the French 'Agence Nationale de la Recherche' project NGB (ANR-17-CE32-0011). EF, FC, PFD and VR were funded by the European Union (European Regional Development Fund, ERDF contract GURDT I2016-1731-0006632), the Conseil Regional de La Reunion and the Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD). AH was funded by the 'Ministere de l'Enseignement superieur et de la Recherche Scientifique de la Tunisie'., ANR-10-EQPX-0020,GEOSUD,GEOSUD : Infrastructure nationale d'imagerie satellitaire pour la recherche sur l'environnement et les territoires et ses applications à la gestion et aux politiques publiques(2010), ANR-17-CE32-0011,NGB,Biosurveillance Next-Gen des changements dans la structure et le fonctionnement des écosystèmes(2017), This work is dedicated to Serge Quilici who has been leading prolific research on the tephritids of Reunion his whole career. Cirad technicians Jim Payet and Serge Glenac made this study possible through their invaluable expertise with fly rearing and ecology. We also thank them as well as Antoine Franck, Christophe Simiand and Patrick Turpin for collecting field data over the years. Thomas Brequigny contributed to measuring larval traits during his internship. Thicenters work used images acquired within the framework of the CNES Kalideos device (Reunion site), which benefited from the 'Programme Investissements d'Avenir' EQUIPEX of the French 'Agence Nationale de la Recherche' on project GEOSUD bearing the reference ANR-10-EQPX-0020. The images also required financial support the French Ministry of Agriculture and field data transmitted by the `Syndicat du Sucre de la Reunion' and the 'SAFER de la Reunion'. BF, FC, FM, JC, MD, SR and VR received the financial support of the French 'Agence Nationale de la Recherche' project NGB (ANR-17-CE32-011). EF, FC, PFD and VR were funded by the European Union (European Regional Development Fund, ERDF contract GURDT I2016-1731-0006632), the Conseil Regional de La Reunion and the Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD). AH was funded by the 'Ministere de l'Enseignement superieur et de la Recherche Scientifique de la Tunisie'. This study used the facilities provided by the Plant Protection Platform (3P, IBISA), Saint-Pierre, Reunion, France., Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), 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, pecialisation, [SDV]Life Sciences [q-bio], Facteur climatique, Generalist and specialist species, 01 natural sciences, specialization, Abundance (ecology), preference, preferences, media_common, U10 - Informatique, mathématiques et statistiques, Ecology, Tephritidae, food and beverages, Plants, phytophagous insects, Sympatric speciation, Drosophila, L20 - Écologie animale, niche modelling, performance, Assembly rules, Plante hôte, media_common.quotation_subject, Distribution des populations, Biology, 010603 evolutionary biology, Competition (biology), Animals, Ecology, Evolution, Behavior and Systematics, Ecological niche, Host (biology), 010604 marine biology & hydrobiology, fungi, facteurs abiotiques, 15. Life on land, H10 - Ravageurs des plantes, Environmental niche modelling, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Modélisation, Compétition interspécifique, Écologie animale, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Adaptation, community ecology
Abstract: This work is dedicated to Serge Quilici who has been leading prolific research on the tephritids of Reunion his whole career. This article has been reviewed and recommended by Peer Community in Ecology, https://doi.org/10.24072/pci.ecology.100080. The peer review history for this article is available at https://publo ns.com /publo n/10.1111/ele.13825.; International audience; The relative importance of ecological factors and species interactions for shaping species distributions is still debated. The realised niches of eight sympatric tephritid fruit flies were inferred from field abundance data using joint species distribution modelling and network inference, on the whole community and separately on three host plant groups. These estimates were then confronted the fundamental niches of seven fly species estimated through laboratory-measured fitnesses on host plants. Species abundances depended on host plants, followed by climatic factors, with a dose of competition between species sharing host plants. The relative importance of these factors mildly changed among the three host plant groups. Despite overlapping fundamental niches, specialists and generalists had almost distinct realised niches, with possible competitive exclusion of generalists by specialists on Cucurbitaceae. They had different assembly rules: Specialists were mainly influenced by their adaptation to host plants, while generalist abundances varied regardless of their fundamental host use.
Published: 2021

34. Network analysis highlights increased generalisation and evenness of plant-pollinator interactions after conservation measures

Author: Marta Galloni, François Massol, Laura Bortolotti, Gherardo Bogo, Natasha de Manincor, Alessandro Fisogni, Marino Quaranta, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Fisogni A., Massol F., de Manincor N., Quaranta M., Bogo G., Bortolotti L., Galloni M., Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Foraging, Population, Modularity, Context (language use), Biology, Biodiversity conservation, 010603 evolutionary biology, 01 natural sciences, Pollinator, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Nature and Landscape Conservation, education.field_of_study, Ecology, Community structure, food and beverages, 15. Life on land, Native plant, Interaction rewiring, Population reinforcement, Species evenness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Protected area, 010606 plant biology & botany, Specialization
Abstract: The decline of pollinators may alter the complex system of interactions that they establish with flowering plants, with potential negative consequences on both partners. Within this context, network analysis may be a useful tool to study ecological properties of plant-pollinator interactions and to evaluate the outcomes of conservation actions. Three conservation measures were implemented within the European LIFE + PP-ICON project to support the local pollinator community of a population of the rare plant Dictamnus albus in a protected area near Bologna, Italy. Artificial nesting sites were installed to support solitary bees, populations of native plants were reinforced to increase foraging resources for pollinators, and colonies of bumblebees reared from wild queens were released in the study area. In this work we evaluate the effects of these conservation actions on plant-pollinator networks over a period of four years, comparing a pre- (2011–2012) and a post-conservation (2013–2014) action period. The overall network generalisation increased after the implementation of conservation measures and interactions were more evenly distributed. Module composition significantly changed between the two periods, showing a marked rewiring of interactions. D. albus was a module hub both before and after conservation actions, thus emerging as an important node within its own module. In addition, some plant and pollinator species directly targeted by conservation measures became module connectors, highlighting their increased importance in linking different modules. Finally, the reinforcement of plant and pollinator populations led to increased flower visitation. These results indicate that conservation actions affected species both directly and indirectly and that the network of interactions has potentially increased its robustness and resilience towards possible species loss. This study highlights ways in which network analysis can be used to measure changes in plant-pollinator interactions in response to conservation actions.
Published: 2021

35. Accessing partners in a dioecious insect-pollinated species : the case of Silene dioica

Author: Barbot, Estelle, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Mathilde Dufaÿ, and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: Sexual dimorphism, Succès reproducteur, Sexual selection, Pollinators, Floral traits, Mating success, Traits floraux, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Silène dioïque – Reproduction
Abstract: In insect-pollinated plant species, mating success is conditioned by pollinators, which ensure pollentransfer. Floral traits that play a role in pollinator attraction and/or traits that optimize pollen export or depositionby pollinators are expected to be under sexual selection. Indeed, this component of natural selection acts on traitsthat impact mate and/or gamete acquisition. Because of anisogamy, the theory predicts that reproductive successacquired via the male function should depend more strongly on access to partners than reproductive success acquiredvia the female function, resulting in different selection patterns between sexual functions. However, in angiosperms,few studies (i) have estimated selection on floral traits in both sexes or in both sexual functions, and (ii) have explicitlyaddressed sexual selection in terms of sexual partner’s diversity. The aim of this thesis is to understand selectionpatterns on floral traits in a dioecious insect-pollinated species, Silene dioica, using various experimental methods.In the introduction section, studies on sexual selection in animals are confronted with those focusing on selection onfloral traits, in order to define a conceptual framework for sexual selection studies on insect-pollinated plant species.In the first chapter, approaches that are classically used when studying sexual selection in animals are combinedwith those classically used when characterizing pollinator-mediated selection on floral traits, in order to identifytraits undergoing sexual selection. The second chapter focuses on two floral traits implicated in pollinator attraction,flower number and odor emission. Both traits were independently exacerbated using phenotypic manipulations.This method allowed us to dissociate the effect of fertility selection from pollinator-mediated selection, as both canact jointly on floral traits. Furthermore, selection pressures exerted on floral traits by diurnal versus nocturnalpollinators are characterized using an exclusion treatment. In the third chapter, the effects of demographic andecological context in terms of pollen availability for females are characterized in natura, by estimating pollen load. Inconclusion, results of these chapters are discussed all together in order to understand how sexual selection patternson floral traits agree with the theory and how it depends on spatio-temporal variations. Our results indicate thatfemale floral traits are mainly under fecundity selection, while selection on male floral traits seems to be furtherassociated to pollinator attraction. Moreover, males are more limited in their reproductive success by sexual partner’sdiversity, compared to females. This is emphasized by strong sexual selection on flowering phenology to increaseaccess to females. In perspective, the methodological implications of estimating sexual selection patterns are discussed.; L’accès à la reproduction chez les plantes zoogames est conditionné par les pollinisateurs, qui assurentles transferts de pollen entre individus. En ce sens, les traits floraux liés à l’attraction des pollinisateurs et/ou quioptimisent le prélèvement ou le dépôt de pollen par les pollinisateurs devraient être sous sélection sexuelle. Cettecomposante de la sélection naturelle agit en effet sur les traits qui affectent l’accès aux partenaires sexuels et/ou auxgamètes du sexe opposé. En raison de l’anisogamie, la théorie prédit que le succès reproducteur acquis via la fonctionmâle devrait dépendre plus fortement de l’accès aux partenaires que le succès reproducteur acquis via la fonctionfemelle, résultant en des patrons de sélection différents entre fonctions sexuelles. Cependant, rares sont les étudesportant sur les plantes (i) qui ont estimé la sélection sur les traits floraux chez les deux sexes ou fonctions sexuelles, ou(ii) qui se sont intéressées explicitement à la sélection sexuelle en termes de diversité de partenaires reproducteurs. Cetravail de thèse vise ainsi principalement à comprendre les patrons de sélection sur les traits floraux chez une espècedioïque entomophile, Silene dioica, à l’aide de diverses méthodes expérimentales. En introduction, les études portantsur la sélection sexuelle chez les animaux sont confrontées à celles portant sur la sélection sur les traits floraux, afinde tenter de définir un cadre conceptuel dans lequel étudier la sélection sexuelle chez les plantes zoogames. Dansle premier chapitre, les approches classiquement utilisées pour étudier la sélection sexuelle chez les animaux sontassociées à celles classiquement utilisées pour étudier la sélection médiée par les pollinisateurs, afin d’identifier lestraits sous sélection sexe-spécifique. Le second chapitre se focalise sur deux traits floraux probablement importantspour l’attraction des pollinisateurs, le nombre de fleurs et l’émission d’odeur, exacerbés à l’aide de manipulationsphénotypiques. Cette méthode permet ainsi de dissocier la sélection de fécondité de la sélection liée à l’attractiondes pollinisateurs, deux composantes de la sélection naturelle agissant potentiellement sur les traits floraux. Parailleurs, les pressions de sélection exercées sur les traits floraux par les pollinisateurs diurnes versus nocturnes sontcaractérisées, via une manipulation de l’accès des plantes aux deux cohortes de pollinisateurs. Dans le troisièmechapitre, les effets du contexte démographique et écologique en termes d’accès au pollen sont caractérisés in natura,par le biais de la charge pollinique. En conclusion, les résultats de ces chapitres sont abordés en synergie afin decomprendre comment les patrons de sélection sexe-spécifiques sur les traits floraux s’accordent avec la théorie etcomment ils dépendent du contexte spatio-temporel. Il ressort de l’ensemble de ces résultats que les traits florauxfemelles sont principalement sous sélection de fécondité, tandis que la sélection sur les traits floraux mâles sembleêtre davantage liée au moins partiellement à l’attraction des pollinisateurs. Par ailleurs, les mâles sont plus limitésdans leur succès reproducteur par la diversité des partenaires reproducteurs, comparés aux femelles, ce qui semblese manifester par une forte sélection sexuelle sur la phénologie de floraison pour augmenter l’accès aux femelles.En perspective, les implications de l’approche utilisée dans la caractérisation des patrons de sélection sexuelle sontdiscutées.
Published: 2021

36. Truncated bimodal latitudinal diversity gradient in early Paleozoic phytoplankton

Author: Zacaï, Axelle, Monnet, Claude, Pohl, Alexandre, Beaugrand, Grégory, Mullins, Gary, Kroeck, David M., Servais, Thomas, Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Centre National de la Recherche Scientifique (CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut national des sciences de l'Univers (INSU - CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), and Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord])
Subjects: [SDE.MCG]Environmental Sciences/Global Changes, SciAdv r-articles, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Oceanography, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Research Articles, Research Article
Abstract: The apparently unimodal latitudinal diversity gradient of Paleozoic phytoplankton is shown to be a truncated bimodal gradient., The latitudinal diversity gradient (LDG)—the decline in species richness from the equator to the poles—is classically considered as the most pervasive macroecological pattern on Earth, but the timing of its establishment, its ubiquity in the geological past, and explanatory mechanisms remain uncertain. By combining empirical and modeling approaches, we show that the first representatives of marine phytoplankton exhibited an LDG from the beginning of the Cambrian, when most major phyla appeared. However, this LDG showed a single peak of diversity centered on the Southern Hemisphere, in contrast to the equatorial peak classically observed for most modern taxa. We find that this LDG most likely corresponds to a truncated bimodal gradient, which probably results from an uneven sediment preservation, smaller sampling effort, and/or lower initial diversity in the Northern Hemisphere. Variation of the documented LDG through time resulted primarily from fluctuations in annual sea-surface temperature and long-term climate changes.
Published: 2021

37. Projet Collectif de Recherches PALEHAUTS. Enrichissement du cadre chronostratigraphique et archéologique des sites paléolithiques historiquement et récemment découverts en Hauts-de-France. Rapport d’étape 2020. Bilan de la deuxière année de triennale

Author: Emilie Goval, Emmanuelle Allart, Pierre Antoine, Auguste, P., Jean-Jacques Bahain, Paule Coudret, Sylvie Coutard, Rudy Debiak, Pascal Depaepe, Laurent Deschodt, Jean-Pierre Fagnart, Philippe Feray, Caroline Font, David Hérisson, Marina Pagli, Jessica Lacarriere, Jean‑luc Locht, Bertrand Masson, Olivier Moine, Clément Paris, Noémie Sévêque, Luc Vallin, Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Ministère de la Culture et de la Communication, Laboratoire de géographie physique : Environnements Quaternaires et Actuels (LGP), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Institut national de recherches archéologiques préventives (Inrap), Conseil général de la Somme - Centre archéologique départemental, Ministère de la Culture et de la Communication (MCC), Centre National de la Recherche Scientifique (CNRS), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Anthropologie des techniques, des espaces et des territoires au Pliocène et au Pléistocène (AnTET), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Ministère de la Culture, Hérisson, David, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-Université Paris Nanterre (UPN)-Université Paris 1 Panthéon-Sorbonne (UP1), Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-Université Paris Nanterre (UPN)-Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-Université Paris Nanterre (UPN)-Université Paris 1 Panthéon-Sorbonne (UP1), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), and Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory
Abstract: Ce rapport de décompose en deux sections, la première rassemble la documentation administrative, la seconde rappelle la problématique générale du projet et présente les résultats obtenus lors de l’année en cours et le bilan. Sauf mention contraire en tête de chapitre les textes et la mise en page sont réalisés par Emilie Goval.
Published: 2021

38. Contribution to a physiological and genetic theory of plant evolution : mutation load, mating systems and mutation rate evolution in class-structured populations

Author: Lesaffre, Thomas, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sylvain Billiard, and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo)
Subjects: Mutation rate evolution, Class-structured populations, Mating systems, Dépression de consanguinité, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Theoretical population genetics, Fardeau génétique, Mutation load
Abstract: In Angiosperms, there exists a strong association between life-history and mating system. Indeed, most predominantly selfing species are annual while the majority of perennials are outcrossers. This association is the starting point of the work presented in this thesis. In the first chapter, I study the joint evolution of lifespan and selfing assuming that inbreeding depression affects survival between flowering seasons and is fixed by a parameter. Under these assumptions, lifetime inbreeding depression increases as lifespan increases therefore preventing the evolution of self-fertilisation in a wider parameter range. When it occurs, it induces the evolution of shorter lifespans. These results are in agreement with the empirically observed pattern. In chapter two, I relax the assumption that inbreeding depression is fixed by a parameter, by assuming an explicit genetic basis. Far from generating higher inbreeding depression in more long-lived species, deleterious mutations affecting survival result in a decrease of inbreeding depression with longevity at mutation-selection equilibrium. Yet, increased inbreeding depression is empirically observed in long-lived species. In the following chapters, I explore two hypotheses to explain this increase. In chapter two, I study the more general idea that variations in the fitness effects of mutations with longevity, of which mutations affecting survival are a mere special case, may generate increased inbreeding depression in longer-lived species. In chapter three, I model the consequences of inheritable somatic mutations accumulating during growth for the evolution of the mutation rate and the resulting inbreeding depression in plants. As for chapter four, it is devoted to a theoretical evaluation of indirect inbreeding depression estimation methods. I end this manuscrit by proposing leads and ideas for the development of a physiological and genetic theory of plant evolution.; Chez les Angiospermes, il existe une forte association entre histoire de vie et système de reproduction. En effet, la plupart des espèces autofécondantes sont annuelles alors que la majorité des espèces pérennes sont allofécondantes. Cette association est le point de départ du travail réalisé dans cette thèse. Dans le premier chapitre, je m'intéresse à la coévolution entre longévité et autofécondation sous l'hypothèse que la dépression de consanguinité affecte la survie des individus entre les saisons de floraison et qu'elle est fixée par un paramètre. Sous ces hypothèses, l'évolution de l'autofécondation est d'autant plus empêchée que la longévité de l'espèce considérée augmente, car la dépression de consanguinité subie à l'échelle de l'existence complète des individus devient plus forte. Lorsqu'elle se produit néanmoins, elle induit une diminution de la longévité à l'équilibre évolutif. Ces résultats sont en accord avec le patron empirique observé. Dans le chapitre deux, je lève l'hypothèse d'une dépression de consanguinité fixée par un paramètre en donnant une base génétique explicite à cette dernière. Je montre que des mutations affectant la survie, loin de générer une augmentation de la dépression de consanguinité avec la longévité, aboutissent à une diminution de cette dernière. Partant du constat qu'une augmentation de la dépression de consanguinité est pourtant bien observée chez les espèces pérennes, j'explore deux hypothèses pour expliquer cette augmentation. Dans le chapitre deux, j'étudie l'idée plus générale selon laquelle des variations des effets sélectifs des mutations avec la longévité, dont des mutations affectant la survie ne sont qu'un cas particulier, pourraient générer ce patron. Dans le chapitre trois, je m'intéresse aux conséquences de l'accumulation de mutations somatiques pour l'évolution du taux de mutation et la dépression de consanguinité résultante chez les plantes. Le chapitre quatre est quant à lui consacré à une évaluation théorique des méthodes d'estimation de la dépression de consanguinité. Je termine ce manuscrit en proposant des pistes pour l'élaboration d'une théorie physiologique et génétique de l'évolution végétale.
Published: 2021

39. Nutrient supply modulates species interactions belowground: dynamics and traits of fine roots in mixed plantations of Eucalyptus and Acacia mangium

Author: Jean-Paul Laclau, Jean-Pierre Bouillet, Agnès Robin, Ranieri Ribeiro Paula, Amandine Germon, Christophe Jourdan, Joannès Guillemot, José Leonardo de Moraes Gonçalves, I.R. Oliveira, Bruno Bordron, Rafael Costa Pinheiro, Universidade de São Paulo (USP), UMR Silva, Universidade Estadual Paulista (Unesp), Univ Montpellier, UMR Eco&Sols, Alto Universitário, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), and Universidade Federal do Espirito Santo (UFES)
Subjects: 0106 biological sciences, Interaction sol racine, forêt tropicale, Plant Science, 01 natural sciences, Système racinaire, Interactions biologiques, Nutrient, Acacia mangium, 2. Zero hunger, Eucalyptus, biology, 04 agricultural and veterinary sciences, Ferralsol soil, Culture associée, Facilitation, Architecture racinaire, Relation plante sol, Randomized block design, Soil Science, Acacia, Fertilité du sol, Culture en mélange, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Taille des racines, Topsoil, Competition, P35 - Fertilité du sol, P34 - Biologie du sol, Sowing, Mixed-species plantations, 15. Life on land, biology.organism_classification, F61 - Physiologie végétale - Nutrition, Agronomy, Fertilization, 040103 agronomy & agriculture, Sol de forêt, 0401 agriculture, forestry, and fisheries, Soil fertility, F04 - Fertilisation, 010606 plant biology & botany
Abstract: Made available in DSpace on 2021-06-25T10:21:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-01 Aims: Belowground interactions are still poorly understood in mixed-species forests. We investigated the effects of soil fertility on belowground processes in mixed planted forests. Methods: The dynamics and traits of Eucalyptus and Acacia mangium fine roots (diameter < 2 mm) in plantations with 50% of each species were studied in a randomized block design established in a nutrient depleted soil. Stands with NPK fertilization applied at planting (F+) were compared to unfertilized stands (F-). Results: In the 0–15 cm soil layer, Eucalyptus root mass density (RMD) was higher than Acacia RMD by 50% in F+ and 10% in F-, considering both ages. At 34 months of age, Eucalyptus RMD was 94% higher near Acacia trees than near Eucalyptus trees in F-. In this layer, Eucalyptus specific root length (SRL) was 21% higher than Acacia SRL at 16 months of age and was 10% higher in F- than in F+ at 34 months of age. The cumulative Eucalyptus fine root length production between 16 and 34 months was 66% higher in F- than in F+ in the 0–1 m soil layer. Conclusions: Fertilization increased the competition between species and led to a partial exclusion of Acacia fine roots from the nutrient-rich topsoil. Soil exploration by Eucalyptus roots in the vicinity of Acacia trees was higher in F- than in F+, which suggests that unfertilized trees benefited from facilitation through higher soil N availability and direct N transfer from Acacia trees. ESALQ Forest Science Department Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo Université de Lorraine AgroParisTech INRAE UMR Silva School of Agriculture São Paulo State University (UNESP) Eco&Sols CIRAD INRA IRD Montpellier SupAgro Univ Montpellier CIRAD UMR Eco&Sols ESALQ Soil Science Department Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo UFES Centro de Ciências Agrárias e Engenharias Alto Universitário, S/N Guararema School of Agriculture São Paulo State University (UNESP)
Published: 2021

40. Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene

Author: Alex Widmer, Raquel Tavares, Aline Muyle, Maeva Mollion, Sylvain Glémin, Hélène Martin, Sophie Gallina, Alexandre Sérgio Silva, Niklaus Zemp, Gabriel A. B. Marais, Thomas Bataillon, Pascal Touzet, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), University of California [Irvine] (UC Irvine), University of California (UC), Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Aarhus University [Aarhus], 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), Uppsala University, ANR-11-BSV7-013-03, Agence Nationale de la Recherche, 31003A-182675, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, French Research Ministry, HFSPO LT000496/2018-L, Postdoctoral fellowships, ANR-11-BSV7-0013,TRANS,Les transitions de systèmes de reproduction chez les angiosperms et leurs conséquences génomiques(2011), University of California [Irvine] (UCI), University of California, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), 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), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 0106 biological sciences, Biologisk systematik, Dioecy, Population, Adaptation, Biological, Population genetics, Flowers, Biological Systematics, AcademicSubjects/SCI01180, 010603 evolutionary biology, 01 natural sciences, Population genomics, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Allee effect, 03 medical and health sciences, Genetics, Selection, Genetic, education, Silene, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Discoveries, 030304 developmental biology, 0303 health sciences, Genetic diversity, education.field_of_study, Phylogenetic inertia, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Reproduction, AcademicSubjects/SCI01130, Genetic Variation, population genetics, selection efficacy, 15. Life on land, biology.organism_classification, Biological Evolution, Evolutionary biology, Species richness, sexual systems, RNA-seq, angiosperms, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister clades, raising the hypothesis that dioecy may be an evolutionary dead-end. This hypothesis has been recently challenged by macroevolutionary analyses that detected no or even positive effect of dioecy on diversification. However, the possible genetic consequences of dioecy at the population level, which could drive the long-term fate of dioecious lineages, have not been tested so far. Here, we used a population genomics approach in the Silene genus to look for possible effects of dioecy, especially for potential evidence of evolutionary handicaps of dioecy underlying the dead-end hypothesis. We collected individual-based RNA-seq data from several populations in 13 closely related species with different sexual systems: seven dioecious, three hermaphroditic, and three gynodioecious species. We show that dioecy is associated with increased genetic diversity, as well as higher selection efficacy both against deleterious mutations and for beneficial mutations. The results hold after controlling for phylogenetic inertia, differences in species census population sizes and geographic ranges. We conclude that dioecious Silene species neither show signs of increased mutational load nor genetic evidence for extinction risk. We discuss these observations in the light of the possible demographic differences between dioecious and self-compatible hermaphroditic species and how this could be related to alternatives to the dead-end hypothesis to explain the rarity of dioecy.
Published: 2021

41. Increased hydraulic constraints in Eucalyptus plantations fertilized with potassium

Author: Jean-Christophe Domec, Ivan Cornut, Agnès Robin, Cassio Hamilton Abreu-Junior, Guerric Le Maire, Bruno Bordron, Jean-Pierre Bouillet, Amandine Germon, Yann Nouvellon, José Leonardo de Moraes Gonçalves, Verónica Asensio, Joannès Guillemot, Patricia Battie-Laclau, Juan Sinforiano Delgado Rojas, Jean-Paul Laclau, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centro de Energia Nuclear na Agricultura (CENA ), University of São Paulo (USP), Universidade Estadual de Campinas (UNICAMP), Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Duke University [Durham], Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Fundaçao de Amparo à Pesquisa do Estado de S~ao Paulo, Grant/Award Number: #2013/25998-4, ANR-18-PRIM-0006,SWATCH,Effet du changement climatique sur les stratégies d'amélioration de l'utilisation en eau des bassin versants et des systèmes agrosylvopastoraux Méditerranéens(2018), UMR Eco&Sols, Montpellier SupAgro, Edafotec SL, UMR INRAe-ISPA 1391, Duke University, Université Paris-Saclay, and Universidade Estadual Paulista (Unesp)
Subjects: 0106 biological sciences, 0301 basic medicine, hydraulic conductance, Physiology, potassium fertilization, Plant Science, 01 natural sciences, transpiration, Trees, water stress, Human fertilization, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, F01 - Culture des plantes, Evapotranspiration, Huber value, water potential, Biomass, Transpiration, 2. Zero hunger, Biomass (ecology), Eucalyptus, Surface foliaire, Forestry, Throughfall, Bilan hydrique, Eucalyptus grandis, Stress dû à la sécheresse, F60 - Physiologie et biochimie végétale, Fertilisation, 03 medical and health sciences, Xylem, Sève, allometry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Fertilizers, Absorption d'eau, TRANSPIRAÇÃO VEGETAL, tree height, Water, Plant Transpiration, 15. Life on land, Évapotranspiration, Plant Leaves, 030104 developmental biology, Agronomy, 13. Climate action, Soil water, Potassium, Environmental science, tropical forest plantation, Water use, F04 - Fertilisation, 010606 plant biology & botany
Abstract: Made available in DSpace on 2021-06-25T10:32:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Fertilization is commonly used to increase growth in forest plantations, but it may also affect tree water relations and responses to drought. Here, we measured changes in biomass, transpiration, sapwood-to-leaf area ratio (As:Al) and sap flow driving force (ΔΨ) during the 6-year rotation of tropical plantations of Eucalyptus grandis under controlled conditions for throughfall and potassium (K) fertilization. K fertilization increased final tree height by 8 m. Throughfall exclusion scarcely affected tree functioning because of deep soil water uptake. Tree growth increased in K-supplied plots and remained stable in K-depleted plots as tree height increased, while growth per unit leaf area increased in all plots. Stand transpiration and hydraulic conductance standardized per leaf area increased with height in K-depleted plots, but remained stable or decreased in K-supplied plots. Greater Al in K-supplied plots increased the hydraulic constraints on water use. This involved a direct mechanism through halved As:Al in K-supplied plots relative to K-depleted plots, and an indirect mechanism through deteriorated water status in K-supplied plots, which prevented the increase in ΔΨ with tree height. K fertilization in tropical plantations reduces the hydraulic compensation to growth, which could increase the risk of drought-induced dieback under climate change. CIRAD UMR Eco&Sols Eco&Sols Univ Montpellier CIRAD INRAe IRD Montpellier SupAgro Department of Forest Sciences Universidade de São Paulo “Luiz de Queiroz” College of Agriculture (USP-ESALQ) Center of Nuclear Energy in Agriculture Universidade de São Paulo (USP-CENA) Edafotec SL NIPE UNICAMP Bordeaux Sciences Agro UMR INRAe-ISPA 1391 Nicholas School of the Environment Duke University Ecologie Systématique Evolution Univ. Paris-Sud CNRS AgroParisTech Université Paris-Saclay School of Agricultural Sciences UNESP—São Paulo State University School of Agricultural Sciences UNESP—São Paulo State University
Published: 2021

42. Networking agrobiodiversity management to foster biodiversity-based agriculture. A review

Author: Mathieu Thomas, Didier Bazile, Juliette Mariel, Christian Leclerc, Selim Louafi, Sophie Caillon, Martine Antona, Vanesse Labeyrie, Christophe Le Page, Örjan Bodin, Jacques Baudry, François Massol, Gestion des ressources renouvelables et environnement [UPR GREEN], Savoirs, ENvironnement et Sociétés [SENS], Biodiversité agroécologie et aménagement du paysage [UMR BAGAP], Centre d’Ecologie Fonctionnelle et Evolutive [CEFE], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales [UMR AGAP], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Gestion des ressources renouvelables et environnement (UPR GREEN), Savoirs, ENvironnement et Sociétés (SENS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut de Recherche pour le Développement (IRD), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO 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), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Département Systèmes Biologiques (Cirad-BIOS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), INRAE, CNRS, Stockholm University, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), 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)-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), 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), and 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)
Subjects: 0106 biological sciences, agrobiodiversité, F08 - Systèmes et modes de culture, [SDV]Life Sciences [q-bio], Réseaux sociaux, Biodiversity, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, 01 natural sciences, Social networks, [SHS]Humanities and Social Sciences, Agriculture durable, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Intensive farming, Corporate governance, 04 agricultural and veterinary sciences, Management, governance, Agroécosystème, Conservation de la diversité biologique, Management system, agriculture de conservation, P01 - Conservation de la nature et ressources foncières, Environmental Engineering, Participatory approaches, Analyse de réseau, gestion des ressources naturelles, Social-ecological interactions, Agrobiodiversity, Agroecology, Environmental planning, Sustainable development, business.industry, 15. Life on land, approches participatives, Crop diversity, 13. Climate action, Agriculture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Agricultural biodiversity, Business, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Biodiversity-based agriculture is the main form of agriculture practiced by smallholder farmers, who produce half the world's food, especially in the Global South. This form of agriculture relies on planned biodiversity intentionally managed by farmers and on the associated biodiversity that spontaneously colonizes the agroecosystem. In recent decades, there have been increasing calls from researchers and society to support biodiversity-based agriculture as an alternative paradigm to today's industrial agriculture. Building adapted governance and management systems for enhancing farmers' access to agrobiodiversity is a key challenge for the development of biodiversity-based agriculture. To achieve this, a better understanding of how farmer's access agrobiodiversity is needed, and in particular, how this access is affected by interactions between farmers and with institutions, i.e., social networks. In this article, we first review the literature on the role of social networks in farmers' access to agrobiodiversity, in the form of crop diversity and associated biodiversity, and the related knowledge to manage this diversity. This review points at a major knowledge gap concerning how the composition and structure of these networks affect farmers' access to agrobiodiversity. Then, we review literature on social-ecological networks to identify how this framework developed for environmental management could contribute in getting a better understanding of the role of social networks' structure and composition in farmers' access to agrobiodiversity. Based on this review, we propose a social-ecological network framework dedicated to crop diversity. Finally, we present potential applications of this framework to develop new participatory approaches for agrobiodiversity management and governance, adapted to biodiversity-based agriculture.
Published: 2021

43. The genomic architecture of competitive response of Arabidopsis thaliana is highly flexible among plurispecific neighborhoods

Author: Cyril Libourel, Etienne Baron, Juliana Lenglet, Laurent Amsellem, Dominique Roby, Fabrice Roux, Laboratoire des Interactions Plantes Microbes Environnement [LIPME], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 0106 biological sciences, Arabidopsis thaliana, Range (biology), plant-plant interactions, media_common.quotation_subject, Population, Context (language use), Genetic Variation, GWAS, Local population, plurispecific interactions, Plant Science, 010603 evolutionary biology, 01 natural sciences, Competition (biology), SB1-1110, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, food, Stellaria media, education, Relative species abundance, 030304 developmental biology, media_common, Original Research, 2. Zero hunger, 0303 health sciences, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Plant culture, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 15. Life on land, biology.organism_classification, food.food, Genetic architecture, local population, Evolutionary biology, [SDE]Environmental Sciences, genetic variation, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Plants are daily challenged by multiple abiotic and biotic stresses. A major biotic constraint corresponds to competition with other plant species. Although plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a genome wide association study (GWAS) to estimate the extent of genetic variation of competitive response in 12 plant species assemblages, based on three competitor species (Poa annua, Stellaria media, and Veronica arvensis). Based on five phenotypic traits, we detected strong crossing reaction norms not only between the three bispecific neighborhoods but also among the plurispecific neighborhoods. The genetic architecture of competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, most of the enriched biological processes underlying competitive responses largely differ among neighborhoods. While the RNA related processes might confer a broad range response toolkit for multiple traits in diverse neighborhoods, some processes, such as signaling and transport, might play a specific role in particular assemblages. Altogether, our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of candidate genes associated with diverse and unexpected processes leading to developmental and stress responses.
Published: 2021

44. Ozone Pollution Alters Olfaction and Behavior of Pollinators

Author: Manon Opsommer, Margot Brondani, Magali Proffit, Maryse Vanderplanck, Mathilde Dufay, Martine Hossaert-McKey, Benoit Lapeyre, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Zoologie [Mons], University of Mons [Belgium] (UMONS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 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), Bio-inspired Chemistry and Ecological Innovations (ChimEco), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), CNRS, ANSES (2018/1/138), ANR-16-IDEX-0006,MUSE,MUSE(2016), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université Paul-Valéry - Montpellier 3 (UPVM)-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), 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, 0301 basic medicine, Pollination, Physiology, Clinical Biochemistry, behavioral response, Air pollution, Olfaction, RM1-950, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Biochemistry, Article, 03 medical and health sciences, Pollinator, medicine, Molecular Biology, Ozone pollution, Ecology, atmospheric pollution, Cell Biology, Attraction, ozone, 030104 developmental biology, Behavioral response, Odor, 13. Climate action, Environmental science, Therapeutics. Pharmacology, pollinators, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, plant VOC perception, plant-pollinator interactions
Abstract: Concentration of air pollutants, particularly ozone (O3), has dramatically increased since pre-industrial times in the troposphere. Due to the strong oxidative potential of O3, negative effects on both emission and lifetime in the atmosphere of plant volatile organic compounds (VOCs) have already been highlighted. VOCs alteration by O3 may potentially affect the attraction of pollinators that rely on these chemical signals. Surprisingly, direct effects of O3 on the olfaction and the behavioral response of pollinators have not been investigated so far. We developed a comprehensive experiment under controlled conditions to assess O3 physiological and behavioral effects on two pollinator species, differing in their ecological traits. Using several realistic concentrations of O3 and various exposure times, we investigated the odor antennal detection and the attraction to VOCs present in the floral scents of their associated plants. Our results showed, in both species, a clear effect of exposure to high O3 concentrations on the ability to detect and react to the floral VOCs. These effects depend on the VOC tested and its concentration, and the O3 exposure (concentration and duration) on the pollinator species. Pollination systems may, therefore, be impaired in different ways by increased levels of O3, the effects of which will likely depend on whether the exposure is chronic or, as in this study, punctual, likely causing some pollination systems to be more vulnerable than others. While several studies have already shown the negative impact of O3 on VOCs emission and lifetime in the atmosphere, this study reveals, for the first time, that this impact alters the pollinator detection and behavior. These findings highlight the urgent need to consider air pollution when evaluating threats to pollinators.
Published: 2021

45. A factor analysis approach to modelling the early diversification of terrestrial vegetation

Author: Philippe Gerrienne, Christopher J. Cleal, Borja Cascales-Miñana, E. Capel, Thomas Servais, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), National Museum of Wales - Cardiff, Université de Liège, and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo)
Subjects: 010506 paleontology, Flora, [SDE.MCG]Environmental Sciences/Global Changes, Devonian, Diversification (marketing strategy), 010502 geochemistry & geophysics, Oceanography, 01 natural sciences, Plant radiation, Carboniferous, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Earth-Surface Processes, Plant evolution, Ecology, Terrestrialization, Paleontology, Macrofossil, Vegetation, 15. Life on land, Plant macrofossil, Early land plants, Terrestrial ecosystem, Factor analysis, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Geology
Abstract: International audience; Data from a new comprehensive macrofossil-based compilation of early plant genera are analyzed via a Q-mode factor analysis. This compilation ranges from the Silurian to the earliest Carboniferous and illustrates the key vegetation changes that took place during the configuration of early terrestrial ecosystems. Results reveal that four factors can be used to explain more than 90% of the variance in the data. These factors are interpreted as the major phases of the early land plant evolution: a first Eotracheophytic flora (Silurian-Lochkovian) dominated by basal eutracheophytes and rhyniophytoids, an early Eophytic Flora (Early Devonian) dominated by zosterophylls, a transitional late Eophytic Flora (Middle Devonianearliest Carboniferous) dominated by lycopsids and cladoxylopsids, and finally, the earliest phase of the Palaeophytic Flora (Late Devonian-earliest Carboniferous) dominated by the first seed plants. These floras present different but complementary diversity patterns, which help us to understand the overall trajectory of changes in plant diversity. Results further show how the maximum peaks of diversity appear linked to the rise of each new flora but, interestingly, these diversifications are not associated with any exponential declines of the previously dominant one. This new four-phase diversification model reflects the early steps of Earth's greening.
Published: 2021

46. A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities

Author: Michael J. Hickerson, François Massol, Isaac Overcast, Andrew J. Rominger, Catherine E. Wagner, Brent C. Emerson, Christine E. Parent, Megan Ruffley, Luke J. Harmon, Ben Peter, Rampal S. Etienne, James Rosindell, Bob Week, Henrik Krehenwinkel, Rosemary G. Gillespie, Jairo Patiño, D. Luke Mahler, Paulo A. V. Borges, Massol, François, City University of New York [New York] (CUNY), City College of New York [CUNY] (CCNY), University of Idaho [Moscow, USA], Imperial College London, Universidade dos Açores, Instituto de Productos Naturales y Agrobiologia = Institute of Natural Products and Agrobiology (IPNA), University of Groningen [Groningen], University of California [Berkeley] (UC Berkeley), University of California (UC), Trier University, University of Toronto, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Universidad de La Laguna [Tenerife - SP] (ULL), Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, University of Wyoming (UW), American Museum of Natural History (AMNH), The University of New Mexico [Albuquerque], Etienne group, Fundação de Amparo à Pesquisa do Estado de São Paulo, National Science Foundation (US), City University of New York, University of Idaho, Santa Fe Institute (US), Natural Environment Research Council (UK), University of California [Berkeley], University of California, and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo)
Subjects: 0106 biological sciences, Range (biology), Population genetics, Insular biogeography, Population, Biodiversity, Comparative phylogeography, Context (language use), Community genetic diversity, Biology, 010603 evolutionary biology, 01 natural sciences, Models, Biological, 03 medical and health sciences, Abundance (ecology), Genetics, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Community ecology, education, Relative species abundance, Community Genetic Diversity, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, Comparative Phylogeography, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, education.field_of_study, Genetic diversity, Community, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, 15. Life on land, Biota, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Geography, Community Phylogenetics, Community phylogenetics, Community Ecology, Species richness, Population Genetics, Biotechnology
Abstract: Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce Massive Eco-evolutionary Synthesis Simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: i) species richness and abundances; ii) population genetic diversities; and iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community assembly models. MESS is unique in generating predictions of community-scale genetic diversity, and in characterizing joint patterns of genetic diversity, abundance, and trait values. MESS unlocks the full potential for investigation of biodiversity processes using multi-dimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine with supervised machine learning to fit the parameters of the model to real data and infer processes underlying how biodiversity accumulates, using communities of tropical trees, arthropods, and gastropods as case studies that span a range of data availability scenarios, and spatial and taxonomic scales., Funding was provided by grants from FAPESP (BIOTA, 2013/50297-0 to MJH and AC Carnaval), the Synthesis Centre of iDiv (DFG FZT 118), NASA through the Dimensions of Biodiversity Program (DOB 1343578) and the National Science Foundation (DEB-1253710 to MJH; DEB 1745562 to AC Carnaval; DBI 1927319 to AJR). IO was supported by the Mina Rees Dissertation Fellowship in the Sciences provided by the Graduate Center of the City University of New York. MR was supported by the Bioinformatics and Computational Biology Fellowship through the Institute for Bioinformatics and Evolutionary Studies at the University of Idaho. AJR was supported by the Santa Fe Institute Omidyar Fellowship. JR was supported by fellowships from the Natural Environment Research Council (NERC) (NE/I021179, NE/L011611/1). RSE was supported by an NWO-VICI grant. This work is a contribution to Imperial College’s Grand Challenges in Ecosystems and the Environment initiative, through JR.
Published: 2021

47. An introgression breakthrough left by an anthropogenic contact between two ascidians

Author: Nicolas Bierne, Frédérique Viard, Alan Le Moan, Charlotte Roby, Claire Daguin-Thiébaut, Christelle Fraïsse, Adaptation et diversité en milieu marin (AD2M), 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), Tjarno Marine Biological Laboratory, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 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), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, anthropogenic hybridization, population genomics, media_common.quotation_subject, tunicates, [SDE.MCG]Environmental Sciences/Global Changes, Allopatric speciation, Introgression, 010603 evolutionary biology, 01 natural sciences, Population genomics, 03 medical and health sciences, introgression hotspots, Genetics, Animals, Humans, Ciona intestinalis, non-indigenous species, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, media_common, 0303 health sciences, Genome, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genomics, biology.organism_classification, Biological Evolution, Ciona, Speciation, Taxon, Evolutionary biology, Genetic structure, Hybridization, Genetic, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biological introductions
Abstract: This zenodo archive contains the vcf files and the R scripts used for thestatistical analyses of the paper "An introgression breakthrough left by an anthropogenic contact between two ascidians" published in Molecular Ecology in 2021. The fastq files processed by the stacks reference pipeline to produce the vcf files in this archive are available on NCBI under the bioproject "PRJNA759193". The analyses of the paper available here are divided in three parts: Analyses of the fine-scale population structure of Ciona intestinalis across the English Channel, the Iroise Sea, and the Bay of biscay Genotype file: Ciona_data1_finescale.vcf.gz Genotype file pruned for physical linkage: Ciona_dataset1_fine_scale_maf_thin.vcf R script file for pop. structure : Finescale_structure_dataset1.R Analyses of the large-scale population structure of C. instestinalis, C. robusta and C. roulei across the Atlantic and the Mediteranean sea Genotype file: Ciona_data2_Largescale.vcf.gz Genotype file pruned for physical linkage: Ciona_dataset2_largescale_maf_thin.vcf R script file for pop. structure : Largescale_structure_dataset2.R Linux + R script file for phylogeny: Phylogeny.R Analyse of introgression from C. robusta into C. intestinalis background: Genotype file: Ciona_data2_Largescale.vcf.gz Ancestry informative genotype: Ciona_diagnistic_SNPs_order.vcf R script for admixture across all chromosome: Ancestry_chromosome.R R script for HMM to detect introgression breakthrough from ancestry informative SNPs: HMM_log10FST+1_3norm_introgression_hotspot.R* *this script is a modified version of the script by Marques et al. (2016) available here: https://github.com/marqueda/HMM-detection-of-genomic-islands
Published: 2021

48. Using self–organizing maps and machine learning models to assess mollusc community structure in relation to physicochemical variables in a West Africa river–estuary system

Author: Antoine Chikou, Bert Van Bocxlaer, Thierry Backeljau, Olaniran Hamed Odountan, Prudenciène Ablawa Agboho, Tatenda Dalu, Zinsou Cosme Koudenoukpo, Luc Janssens de Bistoven, University of Abomey Calavi (UAC), Centre de Recherche Entomologique de Cotonou (CREC), Ministère de la Santé, South African Institute for Aquatic Biodiversity (SAIAB), South African Institute for Aquatic Biodiversity, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Royal Belgian Institute of Natural Sciences (RBINS), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), National Research Foundation [South Africa] (NRF), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and ANR-17-CE02-0015,EVOLINK,Lier les processus micro- et macro-évolutifs impliqués dans les mollusques dulcicoles du Rift Est Africain(2017)
Subjects: 0106 biological sciences, Artificial neural network, Fauna, Drainage basin, General Decision Sciences, 010501 environmental sciences, 010603 evolutionary biology, 01 natural sciences, Modelling, Sphaerium, Mollusc community, 14. Life underwater, Biology, QH540-549.5, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, Brackish water, biology, Ecology, Community structure, Estuary, 15. Life on land, Freshwater biodiversity, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Chemistry, 13. Climate action, Indicator species, Tropical river systems, Environmental science, Radix natalensis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The poor understanding of changes in mollusc ecology along rivers, especially in West Africa, hampers the implementation of management measures. We used a self–organizing map, indicator species analysis, linear discriminant analysis and a random forest model to distinguish mollusc assemblages, to determine the ecological preferences of individual mollusc species and to associate major physicochemical variables with mollusc assemblages and occurrences in the Sô River Basin, Benin. We identified four mollusc assemblages along an upstream–downstream gradient. Dissolved oxygen (DO), biochemical oxygen demand (BOD), salinity, calcium (Ca), total nitrogen (TN), copper (Cu), lead (Pb), nickel (Ni), cadmium (Cd) and mercury (Hg) were the major physicochemical variables responsible for structuring these mollusc assemblages. However, the physicochemical factors responsible for shaping the distribution of individual species varied per species. Upstream sites (assemblage I) showed high DO and low BOD and mineral compounds (i.e., TN, salinity, and Ca), which are primarily responsible for structuring the occurrences of bivalves (Afropisidium pirothi, Etheria elliptica, Sphaerium hartmanni) and the gastropod Lanistes varicus. Sites along the middle reach (assemblage II) were characterised by a high degree of organic pollution but low heavy metal pollution; we detected no specific mollusc indicator species. Downstream sites (assemblage III) displayed high mineral and heavy metal concentrations and a fauna without specific indicator species. Finally, downstream sites associated with brackish water (assemblage IV) displayed important levels of organic and heavy metal pollution. These sites are dominated by diverse gastropods (i.e., Bulinus spp., Gabbiella africana, Indoplanorbis exustus, Pachymelania fusca, Radix natalensis, Stenophysa marmorata and Tympanotonos fuscatus). Our results highlight that mollusc communities in the Sô River Basin are structured by key physicochemical variables related to the river–estuary continuum. Habitats that are progressively more downstream are confronted with increasing anthropogenic stress. Conservation and management plans should focus on downstream habitats.
Published: 2021

49. A CNN-based approach for the estimation of canopy heights and wood volume from GEDI waveforms

Author: Fayad, Ibrahim, Ienco, Dino, Baghdadi, Nicolas, Gaetano, Raffaele, Alvares, Clayton, Stape, Jose, Ferraço Scolforo, Henrique, Le Maire, Guerric, AgroParisTech, Universidade Estadual Paulista (UNESP), Estrada Limeira, UMR Eco&Sols, Montpellier SupAgro, Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), French Space Study Center (CNES), National Research Institute for Agriculture, Food and the Environment (INRAE), 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 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)
Subjects: Lidar, Eucalyptus, Cartographie, Dominant height, [SDE]Environmental Sciences, K01 - Foresterie - Considérations générales, Convolutional neural networks, Dendrométrie, Couvert forestier, U30 - Méthodes de recherche, Observation satellitaire, Brazil, GEDI, Wood volume
Abstract: Made available in DSpace on 2022-04-28T19:44:02Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-11-01 Full waveform (FW) LiDAR systems have proven their effectiveness to map forest biophysical variables in the last two decades, owing to their ability of measuring, with high accuracy, forest vertical structures. The Global Ecosystem Dynamics Investigation (GEDI) system on board the International Space Station (ISS) is the latest FW spaceborne LiDAR instrument for the continuous observation of Earth's forests. FW systems rely on very sophisticated pre-processing steps to generate a priori metrics in order to leverage their capabilities for the accurate estimation of the aforementioned forest characteristics. The ever-expanding volume of acquired GEDI data, which to date comprises more than 25 billion acquired unfiltered shots, and along with the pre-processed data, amounting to more than 90 TB of data, raises new challenges in terms of adapted preprocessing methods for the suitable exploitation of such a huge and complex amount of LiDAR data. To overcome the issues related to the generation of relevant metrics from GEDI data, we propose a new metric-free approach to estimate canopy dominant heights (Hdom) and wood volume (V) of Eucalyptus plantations over five different regions in Brazil. To avoid metric computation, we leverage deep learning techniques and, more in detail, convolutional neural networks with the aim to analyze the GEDI Level 1B geolocated waveforms. Performance comparisons were conducted between four convolutional neural network (CNN) variants using GEDI waveform data (either untouched, or subsetted) and a metric based Random Forest regressor (RF). Additionally, we tested if our framework can improve the generalization of the models to different distant regions. First, the models were trained using data from all the study regions. Cross validated results showed that the CNN based models compared well against their RF counterpart for both Hdom and V. The RMSE on the estimation of Hdom from the CNN based models varied between 1.54 and 1.94 m with a coefficient of determination (R2) between 0.86 and 0.91, while the RF model produced an accuracy on Hdom estimates of 1.45 m (R2 = 0.92). For V, CNN based estimations ranged from 27.76 to 33.33 m3.ha−1 (R2 between 0.82 and 0.88), while for RF, the RMSE was 27.61 m3.ha−1 (R2 = 0.88). Next, model generalization was assessed by means of a spatial transfer experiment. For Hdom, both the CNN and RF approaches showed similar performances to a global model, however, the CNN based approach showed higher variability on the estimation accuracy, and the variability was related to the forest structure between the trained and tested data (similar tree heights yield better accuracies). For the estimation of V, considering both approaches, the accuracy was dependent on the allometric relationship between Hdom and V in the training and testing regions while lower accuracies on V were obtained when the testing and training regions exhibited a different allometric relationship. French National Research Institute for Agriculture Food and the Environment (INRAE) CIRAD CNRS TETIS Univ Montpellier AgroParisTech, 34093 Montpellier CEDEX 5 Unesp Faculdade de Ciências Agronômicas Suzano SA Estrada Limeira, 391, 13465-970 CIRAD UMR Eco&Sols Eco&Sols Univ Montpellier CIRAD INRAE IRD Montpellier SupAgro Unesp Faculdade de Ciências Agronômicas
Published: 2021

50. Simultaneous genotyping of snails and infecting trematode parasites using high‐throughput amplicon sequencing

Author: Tine Huyse, Cyril Hammoud, Bert Van Bocxlaer, Stephen Mulero, Jérôme Boissier, Dirk Verschuren, Christian Albrecht, Royal Museum for Central Africa [Tervuren] (RMCA), Universiteit Gent = Ghent University [Belgium] (UGENT), Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Justus-Liebig-Universität Gießen (JLU), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Universiteit Gent = Ghent University (UGENT), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), ANR-18-CE35-0001,HySWARM,Hybrid Swarm: rôle de l'hybridation dans les capacités invasives, l'épidémiologie et le diagnostic de la schistosomiase(2018), and ANR-17-CE02-0015,EVOLINK,Lier les processus micro- et macro-évolutifs impliqués dans les mollusques dulcicoles du Rift Est Africain(2017)
Subjects: Genotype, 030231 tropical medicine, Gastropoda, Zoology, Snail, high-throughput amplicon sequencing, Host-Parasite Interactions, 03 medical and health sciences, 0302 clinical medicine, biology.animal, schistosomiasis, Multiplex polymerase chain reaction, parasitic diseases, Genetics, diagnostics, Biomphalaria glabrata, Parasite hosting, Animals, Parasites, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Genotyping, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, biology, co-infections, Reproducibility of Results, biology.organism_classification, Hygrophila (gastropod), Schistosoma mansoni, Trematoda, community ecology, Biotechnology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Several methodological issues currently hamper the study of entire trematode communities within populations of their intermediate snail hosts. Here we develop a new workflow using high-throughput amplicon sequencing to simultaneously genotype snail hosts and their infecting trematode parasites. We designed primers to amplify four snail and five trematode markers in a single multiplex PCR. While also applicable to other genera, we focused on medically and economically important snail genera within the superorder Hygrophila and targeted a broad taxonomic range of parasites within the class Trematoda. We tested the workflow using 417 Biomphalaria glabrata specimens experimentally infected with Schistosoma rodhaini, two strains of Schistosoma mansoni and combinations thereof. We evaluated the reliability of infection diagnostics, the robustness of the workflow, its specificity related to host and parasite identification, and the sensitivity to detect co-infections, immature infections and changes of parasite biomass during the infection process. Finally, we investigated its applicability in wild-caught snails of other genera naturally infected with a diverse range of trematodes. After stringent quality control the workflow allows the identification of snails to species level, and of trematodes to taxonomic levels ranging from family to strain. It is sensitive to detect immature infections and changes in parasite biomass described in previous experimental studies. Co-infections were successfully identified, opening the possibility to examine parasite-parasite interactions such as interspecific competition. Together, these results demonstrate that our workflow provides a powerful tool to analyse the processes shaping trematode communities within natural snail populations.
Published: 2021

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