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9 results on '"Istituto di Bioscienze e BioRisorse [Palermo] (IBBR)"'

1. The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Jérémy Marchon, Alan Gray, Sebastian Richter, Christophe Plomion, René Graf, Francesca Bagnoli, Elisabet Martínez-Sancho, Volker Schneck, Frédéric Bernier, Vladimir L. Semerikov, Henry Bignalet, José Alberto Ramírez-Valiente, Ioannis Ganopoulos, Felix Gugerli, Agathe Hurel, Geir Ostreng, Sandro Morganti, Santiago C. González-Martínez, David López-Quiroga, Luc Puzos, William Brunetto, Raquel Benavides, Damien Bouic, Olivier Ambrosio, Filippos A. Aravanopoulos, Mirko Liesebach, Cristina C. Bastias, Veronique Jorge, Outi Savolainen, Stephen Cavers, Célia Michotey, Bernard Dokhelar, Mehdi Pringarbe, Enja Hollenbach, Camilla Avanzi, Silvio Schueler, José M. García del Barrio, Annie Raffin, Bruno Fady, Anna-Maria Farsakoglou, Olivier Gilg, Pascal Milesi, Sonja T. Kujala, Nicolas Mariotte, Florian Knutzen, Nicolas Cheval, F. J. Auñón, Céline Lalanne, Marc Villar, Catherine Bastien, Katri Kärkkäinen, Nicolas Poinot, Fernando Del Caño, Jan-Philipp Kappner, Florence Jean, Birte Pakull, Tanja Pyhäjärvi, Jørn Henrik Sønstebø, Rémi Dourthe, Ermioni Malliarou, Ivan Scotti, Timo Kumpula, Mariaceleste Labriola, Silvia Matesanz, Bernard Issehuth, Martin Lascoux, Jean Thevenet, Christian Rellstab, Marianne Correard, Ricardo Alía, Johannes Lambertz, Anne Eskild Nilsen, Eva Cremer, Christoph Hartleitner, Darius Danusevičius, Lars Opgenoorth, Fernando Valladares, Arnaud Jouineau, Ana M. Cabanillas‐Saldaña, José Climent, Audrey Albet, Jurata Buchovska, Benjamin Dauphin, Sergio San Segundo, Ilaria Spanu, Antonio Mas, Johan Westin, Eduardo Notivol, Juan J. Robledo-Arnuncio, Andrea Piotti, Evangelos Barbas, Robert Kesälahti, Andreas Fera, Mari Mette Tollefsrud, Helge Meischner, Grégoire Le Provost, Eduardo Ballesteros, Tor Myking, Bárbara Carvalho, Jean-Luc Denou, Katrin Heer, Giovanni G. Vendramin, Evangelia V. Avramidou, Norbert Turion, Patrick Fonti, Delphine Grivet, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), 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), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), Unité expérimentale Forêt Pierroton (UEFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Ecologie des Forêts Méditerranéennes (URFM), Aristotle University of Thessaloniki, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Gobierno de Aragon, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Austrian Research Centre for Forests (BFW), Institute of Plant Breeding and Genetic Resources, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIECO GmbH & Co KG, Philipps Universität Marburg = Philipps University of Marburg, Natural Resources Institute Finland (LUKE), University of Oulu, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Unité de Recherche Génomique Info (URGI), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), Skogforsk - Swedish Forestry Research Institute, Horizon 2020. Grant Numbers: 676876, 4540-143AP, 6, 0032 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Comunidad de Madrid, State Secretariat for Education, Research and Innovation (Switzerland), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Museo Nacional de Ciencias Naturales (CSIC), 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), Consiglio Nazionale delle Ricerche (CNR), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigacion Y Tecnologia Agroalimentaria de Aragon, Philipps Universität Marburg, Norwegian Institute of Bioeconomy Research (NIBIO), and Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA)

Subjects
0106 biological sciences, Specific leaf area, Population, Phenotypic variation, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, Leaf functional traits, tree species, Fagus sylvatica, leaf functional traits, Leaf economics spectrum, Leaf size, education, intraspecific variability, Ecology, Evolution, Behavior and Systematics, Global and Planetary Change, education.field_of_study, Ecology, biology, leaf economics spectrum, 010604 marine biology & hydrobiology, Intraspecific variability, Botany, phenotypic variation, Botanik, Interspecific competition, 15. Life on land, biology.organism_classification, Forest genetic resources, Quercus petraea, Sample collection, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, European forests, Tree species
Abstract

[Motivation] Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes., [Main types of variable contained] We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope 13C and 15N in leaves., [Spatial location and grain] We surveyed between 18 and 22 populations per species, 141 in total, across Europe., [Time period] Leaf sampling took place between 2016 and 2017., [Major taxa and level of measurement] We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea., [Software format] The data files are in ASCII text, tab delimited, not compressed., All authors acknowledge support from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 676876 (Project GenTree). Laboratory work was also supported by other projects: COMEDIAS (CGL2017- 83170-R, Spanish Ministry of Science, Innovation and Universities), REMEDINAL IV (TE-CM S2018/EMT-4338, Project of the Autonomous Community of Madrid, Spain), SPONFOREST (BIODIVERSA-3, PCIN-2016-055), and International Laboratory of Global Change (LINCGlobal 4540-143AP). The Swiss contribution was supported by the Swiss Secretariat for Education, Research and Innovation (SERI) under contract no. 6.0032. BC was funded by a Scholarship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil).

Published
2021
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2. The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

Author

Opgenoorth, Lars, Dauphin, Benjamin, Benavides, Raquel, Heer, Katrin, Alizoti, Paraskevi, Martínez-Sancho, Elisabet, Alía, Ricardo, Ambrosio, Olivier, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Barbas, Evangelos, Bastias, Cristina C, Bastien, Catherine, Ballesteros, Eduardo, Beffa, Giorgia, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buy, Melanie, Cabanillas-Saldaña, Ana M, Carvalho, Bárbara, Cheval, Nicolas, Climent, José M, Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Del Caño, Fernando, Denou, Jean-Luc, Di Gerardi, Nicolas, Dokhelar, Bernard, Ducousso, Alexis, Nilsen, Anne Eskild, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, García Del Barrio, José M, Gilg, Olivier, González-Martínez, Santiago C, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Hollenbach, Enja, Hurel, Agathe, Issehut, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T, Kumpula, Timo A, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Lejeune, Vincent, Le-Provost, Gregoire, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Meier, Benjamin, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Nievergelt, Daniel, Notivol, Eduardo, Østreng, Geir, Pakull, Birte, Perry, Annika, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A, Rellstab, Christian, Remi, Dourthe, Richter, Sebastian, Robledo-Arnuncio, Juan J, San Segundo, Sergio, Savolainen, Outi, Schueler, Silvio, Schneck, Volker, Scotti, Ivan, Semerikov, Vladimir, Slámová, Lenka, Sønstebø, Jørn Henrik, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, von Arx, Georg, Westin, Johan, Fady, Bruno, Myking, Tor, Valladares, Fernando, Aravanopoulos, Filippos A, Cavers, Stephen, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Philipps Universität Marburg = Philipps University of Marburg, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Aristotle University of Thessaloniki, Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale Forêt Pierroton (UEFP), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), 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), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Biomasse Forestières ORléans (GBFOR), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Unité de Recherche Génomique Info (URGI), Gobierno de Aragon, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), LIECO GmbH & Co KG, Natural Resources Institute Finland (LUKE), University of Oulu, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Austrian Research Centre for Forests (BFW), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), Skogforsk - Swedish Forestry Research Institute, Swiss Secretariat for Education, Research and Innovation (SERI) 6.0032, European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Philipps Universität Marburg, Museo Nacional de Ciencias Naturales (CSIC), Consiglio Nazionale delle Ricerche (CNR), 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), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigacion Y Tecnologia Agroalimentaria de Aragon, Norwegian Institute of Bioeconomy Research (NIBIO), and Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA)

Subjects
crown size, fruit number, Skogsvetenskap, bark thickness, AcademicSubjects/SCI02254, DBH, Forest Science, soil depth, forking index, Botany, Pinus sylvestris, Botanik, Forests, Data Note, stem straightness, Ecology and Environment, Trees, regeneration, branch angle, Fagus, AcademicSubjects/SCI00960, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Picea, height
Abstract

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.

Published
2021
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3. Biological control of invasive stink bugs: review of global state and future prospects

Author

Gonzalo A. Avila, Guillaume Martel, Raul Alberto Laumann, Gabriele Rondoni, Cesar Rodriguez-Saona, Barbara I. P. Barratt, Michael Rostás, Fernanda Cingolani, Eric Conti, Kim A. Hoelmer, Stefano Colazza, René Sforza, Eric Wajnberg, Luciana Tavella, Salvatore Guarino, Lara Maistrello, Ezio Peri, Pio Federico Roversi, Conti E., Avila G., Barratt B., Cingolani F., Colazza S., Guarino S., Hoelmer K., Laumann R.A., Maistrello L., Martel G., Peri E., Rodriguez-Saona C., Rondoni G., Rostas M., Roversi P.F., Sforza R.F.H., Tavella L., Wajnberg E., Dept. of Pharmaceutical Sciences, University of Perugia, The New Zealand Institute for Plant & Food Research Limited [Auckland] (Plant & Food Research), Better Border Biosecurity (B3), Partenaires INRAE, Centro de Estudios Parasitologicos y de Vectores [La Plata] (CEPAVE), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional de la Plata [Argentine] (UNLP)-Comisión de Investigaciones Científicas [Buenos Aires] (CIC), Università degli studi di Palermo - University of Palermo, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), USDA-ARS : Agricultural Research Service, Embrapa Recursos Genéticos e Biotecnologia [Brasília], Università degli Studi di Modena e Reggio Emilia (UNIMORE), 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), European Biological Control Laboratory (EBCL), United States Department of Agriculture (USDA), Rutgers University System (Rutgers), Georg-August-University [Göttingen], Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Università degli studi di Torino (UNITO), HExapode, PHysiologie, AssISTance et Objets de Service (HEPHAISTOS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia (UNIMORE), Georg-August-University = Georg-August-Universität Göttingen, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA), Università degli studi di Torino = University of Turin (UNITO), and Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
0106 biological sciences, Integrated pest management, Biological pest control, Tachinidae, pre-emptive classical biological control, landscape management, 010603 evolutionary biology, 01 natural sciences, invasive species, Hemiptera, Encyrtidae, invasive specie, Pentatomidae, biocontrol, biocontrol chemical ecology Hemiptera invasive species landscape management pre‐emptive classical biological control semiochemicals parasitoid Pentatomidae risk assessment Tachinidae Scelionidae, parasitoid, Ecology, Evolution, Behavior and Systematics, Bagrada hilaris, biology, semiochemicals, business.industry, Ecology, Pest control, chemical ecology, preemptive classical biological control, risk assessment, semiochemical, biocontrol, chemical ecology, Hemiptera, invasive species, landscape management, preemptive classical biological control, semiochemicals, parasitoid, Pentatomidae, risk assessment, Tachinidae, Scelionidae, biology.organism_classification, 010602 entomology, Settore AGR/11 - Entomologia Generale E Applicata, 13. Climate action, Insect Science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Scelionidae, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Invasive stink bugs (Hemiptera: Pentatomidae) are responsible for high economic losses to agricul-ture on a global scale. The most important species, dating from recent to old invasions, includeBagrada hilaris (Burmeister), Halyomorpha halys (Stal), Piezodorus guildinii (Westwood), Nezara vir-idula (L.), and Murgantia histrionica (Hahn). Bagrada hilaris, H. halys,andN. viridula are nowalmost globally distributed. Biological control of these pests faces a complex set of challenges thatmust be addressed to maintain pest populations below the economic injury level. Several case studiesof classical and conservation biological control of invasive stink bugs are reported here. The mostcommon parasitoids in their geographical area of origin are egg parasitoids (Hymenoptera: Scelion-idae, Encyrtidae, and Eupelmidae). Additionally, native parasitoids of adult stink bugs (Diptera:Tachinidae) have in some cases adapted to the novel hosts in the invaded area and native predatorsare known to prey on the various instars. Improving the efficacy of biocontrol agents is possiblethrough conservation biological control techniques and exploitation of their chemical ecology.Moreover, integration of biological control with other techniques, such as behavioural manipulationof adult stink bugs and plant resistance, may be a sustainable pest control method within organicfarming and integrated pest management programs. However, additional field studies are needed toverify the efficacy of these novel methods and transfer them from research to application.

Published
2021
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4. Author Correction: The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Guillaume Bodineau, Johan Westin, Juan J. Robledo-Arnuncio, Katrin Heer, Cristina C. Bastias, Georg von Arx, Francesca Bagnoli, Fernando Valladares, Bruno Fady, Frédéric Bernier, Christophe Plomion, Kurt Ramskogler, Mehdi Pringarbe, Grégoire Le-Provost, Felix Gugerli, José M. García del Barrio, Vladimir L. Semerikov, Filippos A. Aravanopoulos, Sandro Morganti, Florian Knutzen, Florence Courdier, Tanja Pyhäjärvi, Tor Myking, Bárbara Carvalho, Marc Villar, Catherine Bastien, Katri Kärkkäinen, Olivier Gilg, Pascal Milesi, Christian Rellstab, Mariaceleste Labriola, Lenka Slámová, Mirko Liesebach, Claudio Grefen, Sonja T. Kujala, Outi Savolainen, Stephen Cavers, Dominique Veisse, Birte Pakull, Norbert Turion, Christoph Hartleitner, José Alberto Ramírez-Valiente, Silvio Schueler, Marlène Lefebvre, Ermioni Malliarou, Annie Raffin, Silvia Matesanz, Marianne Correard, Giovanni G. Vendramin, Camilla Avanzi, Eduardo Notivol, Anna-Maria Farsakoglou, Agathe Hurel, Ricardo Alía, Arnaud Jouineau, Alan Gray, Ilaria Spanu, Raquel Benavides, Jean Thevenet, Elisabet Martínez-Sancho, Darius Danusevičius, Lars Opgenoorth, Célia Michotey, Benjamin Dauphin, Santiago C. González-Martínez, Patrick Fonti, Jean-Paul Charpentier, Vincent Lejeune, José Climent, Martin Lascoux, Nicolas Mariotte, Andrea Piotti, Evangelos Barbas, Mari Mette Tollefsrud, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Philipps Universität Marburg, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (CSIC), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Centre for Ecology and Hydrology (CEH), Natural Environment Research Council (NERC), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Aristotle University of Thessaloniki, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale Forêt Pierroton (UEFP), Génétique et Biomasse Forestières ORléans (GBFOR), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIECO GmbH & Co KG, Natural Resources Institute Finland (LUKE), Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Unité de Recherche Génomique Info (URGI), Norwegian Institute of Bioeconomy Research (NIBIO), Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), University of Oulu, Austrian Research Centre for Forests (BFW), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), and Skogforsk - Swedish Forestry Research Institute

Subjects
0106 biological sciences, Statistics and Probability, Data Descriptor, Climate Change, Forests, Library and Information Sciences, 010603 evolutionary biology, 01 natural sciences, Trees, Education, Quercus, Dendrochronology, Fagus, Picea, lcsh:Science, Author Correction, Betula, Forestry, 15. Life on land, Pinus, Wood, Computer Science Applications, Europe, Geography, Populus, lcsh:Q, Forest ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Statistics, Probability and Uncertainty, Tree species, 010606 plant biology & botany, Information Systems
Abstract

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios., Measurement(s)growth ring • wood densityTechnology Type(s)measuring table • calculationFactor Type(s)tree speciesSample Characteristic - OrganismBetula pendula • Fagus sylvatica • Picea abies • Populus nigra • Pinus pinaster • Pinus sylvestris • Quercus petraeaSample Characteristic - LocationEurope Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11294993

Published
2020
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5. A draft genome of sweet cherry ( Prunus avium L.) reveals genome‐wide and local effects of domestication

Author

Michele Morgante, Ioannis Ganopoulos, Filippos A. Aravanopoulos, Gabriella Sonnante, Sara Pinosio, Michele Vidotto, Andrea Zuccolo, Fabio Marroni, Amy Iezzoni, Gabriele Magris, Giovanni G. Vendramin, Nicola Vitulo, Stéphanie Mariette, Marino Palasciano, Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Università degli Studi di Udine - University of Udine [Italie], Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP), University of Verona (UNIVR), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Aristotle University of Thessaloniki, Hellenic Agricultural Organization Demeter (HAO Demeter), Università degli Studi di Bari Aldo Moro, Institute of Applied Genomics [Udine] (IGA), Institute of Applied Genomics, Michigan State University [East Lansing], and Michigan State University System

Subjects
0106 biological sciences, 0301 basic medicine, Candidate gene, Plant Science, DNA, Satellite, Biology, Prunus avium, Genes, Plant, 01 natural sciences, Genome, Chromosomes, Plant, Gene flow, 03 medical and health sciences, Prunus, domestication, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Gene, 2. Zero hunger, Genetic diversity, genome structure and evolution, Resistance (ecology), Chromosome Mapping, Genetic Variation, food and beverages, Cell Biology, genetic diversity, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Genetics, Population, 030104 developmental biology, Evolutionary biology, genome assembly, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Plant, 010606 plant biology & botany
Abstract

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety "Big Star*" and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome-wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.

Published
2020
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6. Evolution-based approach needed for the conservation and silviculture of peripheral forest tree populations

Author

Hojka Kraigher, Hassan Sbay, Urs Mühlethaler, Marjana Westergren, Srdjan Stojnic, Fulvio Ducci, Annika Perry, Maria Carolina Varela, Bruno Fady, Matti Rousi, Colin T. Kelleher, Filippos A. Aravanopoulos, Csaba Mátyás, Sanja Perić, Abdelhamid Khaldi, Giovanni G. Vendramin, Paraskevi Alizoti, Magda Bou Dagher Kharrat, Branislav Cvjetković, Tzvetan Zlatanov, Ivaylo Tsvetkov, Martina Tijardović, Koen Kramer, Gerhard Huber, Piero Belletti, Georg von Wühlisch, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Faculty of Agriculture, Forest Science & Natural Environment, Aristotle University of Thessaloniki, Institute of Environmental and Earth Sciences [Sopron] (NRRC), University of West Hungary [Sopron], Institute of Forest Genetics, Johann Heinrich von Thünen Institut, Slovenian Forestry Institute, DISAFA Agricultural Genetics, University of Turin, Faculty of Forestry, University of Banja Luka, Forestry Research Centre, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Bavarian Institute for Forest Seeding and Planting, DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Institut National de Recherche en Génie Rural Eaux et Forêts (INRGREF), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Institution de la Recherche et de l'Enseignement Supérieur Agricoles [Tunis] (IRESA), Faculty of Science, Laboratoire Caractérisation Génomique des Plantes, Université Saint-Joseph de Beyrouth (USJ), Green World Research, Vegetation, Forest, and Landscape Ecology, ALTERRA, Wageningen University and Research [Wageningen] (WUR), Haute école des sciences agronomiques, forestières et alimentaires (HAFL), Croatian Forest Research Institute, Centre for Ecology and Hydrology, Natural resources institute Finland, Université Mohammed V de Rabat, Institute of Lowland Forestry and Environment, University of Novi Sad, Forest Research Institute, Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal] (INIAV), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), COST Action FP1202 ‘‘Strengthening conservation: a key issue for adaptation of marginal/peripheral populations of forest trees to climate change in Europe (MaP-FGR)', projects AMTools (ANR-11-AGRO-005-04) and ERA-NET BiodivERsA 2011– 2012 ‘‘TipTree' (ANR-12-EBID-0003), National Research Institute of Rural Engineering, Water and Forests (INRGREF), Université de Carthage - University of Carthage, Wageningen University and Research Centre [Wageningen] (WUR), Natural Resources Institute Finland, Instituto Nacional de Investigação Agrária e Veterinária (INIAV), Institute of Biosciences and Bioresources (IBBR), and Consiglio Nazionale delle Ricerche [Roma] (CNR)

Subjects
0106 biological sciences, Range (biology), Ecology (disciplines), Bos- en Landschapsecologie, Forest management, forest tree genetics, forest management, Climate change, Context (language use), Conservation, Management, Monitoring, Policy and Law, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, Geographic distribution range, Geographic distribution range, Forest tree genetics, Ecology, Climate change, Forest management, Conservation, Forest and Landscape Ecology, Vegetatie, Nature and Landscape Conservation, Local adaptation, Vegetation, Natural selection, Ecology, business.industry, geographic distribution range, ecology, climate change, conservation, Environmental resource management, Forest tree genetics, Forestry, 15. Life on land, PE&RC, Geography, Sustainability, Vegetatie, Bos- en Landschapsecologie, Vegetation, Forest and Landscape Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany
Abstract

The fate of peripheral forest tree populations is of particular interest in the context of climate change. These populations may concurrently be those where the most significant evolutionary changes will occur; those most facing increasing extinction risk; the source of migrants for the colonization of new areas at leading edges; or the source of genetic novelty for reinforcing standing genetic variation in various parts of the range. Deciding which strategy to implement for conserving and sustainably using the genetic resources of peripheral forest tree populations is a challenge. Here, we review the genetic and ecological processes acting on different types of peripheral populations and indicate why these processes may be of general interest for adapting forests and forest management to climate change. We particularly focus on peripheral populations at the rear edge of species distributions where environmental challenges are or will become most acute. We argue that peripheral forest tree populations are “natural laboratories” for resolving priority research questions such as how the complex interaction between demographic processes and natural selection shape local adaptation; and whether genetic adaptation will be sufficient to allow the long-term persistence of species within their current distribution. Peripheral populations are key assets for adaptive forestry which need specific measures for their preservation. The traditionally opposing views which may exist between conservation planning and sustainable forestry need to be reconciled and harmonized for managing peripheral populations. Based on existing knowledge, we suggest approaches and principles which may be used for the management and conservation of these distinctive and valuable populations, to maintain active genetic and ecological processes that have sustained them over time.

Published
2016
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7. Local adaptation in european firs assessed through extensive sampling across altitudinal gradients in southern Europe

Author

Dragos Postolache, Louise Brousseau, Martin Lascoux, Bruno Fady, Peter Zhelev, Thomas Källman, Andrea Piotti, Sascha Liepelt, Andreas D. Drouzas, Cristina Leonarduzzi, Giovanni G. Vendramin, Anna M. Roschanski, Flaviu Popescu, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Institute of Biosciences and Bioresources (IBBR), Consiglio Nazionale delle Ricerche [Roma] (CNR), Scuola Superiore Sant’Anna, National Institute of Forest Research and Development, Institutul de Cercetari si Amenajari Silvice (ICAS), Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, School of Biology, Aristotle University of Thessaloniki, Institute of Biosciences and BioResources (IBBR, Faculty of Biology, Conservation Biology, University of Giessen and Marburg Lung Center (UGMLC), Leibniz Institute of Plant Genetics and Crop Plant Research, University of Forestry (UF), Funding was provided by the ERAnet BiodivERsA project ‘LinkTree’ (ANR-08-Biodiversa- 006-06), the ERAnet BiodivERsA project 'TipTree' (ANR-12-EBID-0003) and COST Action FP 1202. GGV was also supported by a grant by the Italian MIUR project ‘Biodiversitalia’ (RBAP10A2T4), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), and Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)

Subjects
0106 biological sciences, 0301 basic medicine, arbre forestier, Heredity, Climate, Biodiversité et Ecologie, lcsh:Medicine, Population genetics, Forests, europe du sud, Mechanical Treatment of Specimens, 01 natural sciences, Trees, Evolutionsbiologi, abies cephalonica, Gene Frequency, Natural Selection, Homogenizing, lcsh:Science, phenotypic and genetic divergence, Milieux et Changements globaux, abies alba, Expressed Sequence Tags, Adaptive traits, Multidisciplinary, Natural selection, Geography, Ecology, Altitude, Simulation and Modeling, Sampling (statistics), Adaptation, Physiological, Terrestrial Environments, Genetic Mapping, Phenotype, Abies, Research Article, Evolutionary Processes, DNA, Plant, Genotype, Local adaptation, [SDE.MCG]Environmental Sciences/Global Changes, Variant Genotypes, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, 010603 evolutionary biology, Ecosystems, Biodiversity and Ecology, 03 medical and health sciences, Evolutionary Adaptation, Genetic variation, Genetics, Computer Simulation, modélisation, Evolutionary Biology, Population Biology, lcsh:R, Ecology and Environmental Sciences, Genetic Variation, Biology and Life Sciences, Bayes Theorem, 15. Life on land, Genetic divergence, 030104 developmental biology, Specimen Preparation and Treatment, Genetic Loci, lcsh:Q, adaptation au changement climatique, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Population Genetics
Abstract

Background: Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. Methods: A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). Results: HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. Conclusion: Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.

Published
2016
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8. Adapting through glacial cycles: insights from a long-lived tree (Taxus baccata)

Author

Santiago C. González-Martínez, Elisa Berganzo, Miquel Riba, Francesca Bagnoli, Giovanni G. Vendramin, Jacques-Louis de Beaulieu, Diana Krajmerová, Marta Dubreuil, Maria Mayol, Cristina Vettori, Ladislav Paule, Lucie Vincenot, Concetta Burgarella, Ivana Romšáková, Centre de Recerca Ecològica i Aplicacions Forestals, Univ. Autònoma de Barcelona (CREAF), université de Barcelone, Departamento de Sistemas y Recursos forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), 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 la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institute of Biosciences and BioResources, Plant Genetics Institute, UOS Florence, Consiglio Nazionale delle Ricerche [Roma] (CNR), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institute of Biosciences and Bioresources (IBBR), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, demography, Physiology, Climate, Interglacial, Adaptation, Biological, Plant Science, 01 natural sciences, microsatellites, Ice Cover, Glacial period, 0303 health sciences, education.field_of_study, Ecology, DNA, Chloroplast, Approximate Bayesiancomputation (ABC), interglacial, Europe, Phylogeography, Genetic structure, Taxus, Approximate Bayesian computation, Demographic history, Environment-dependent selection, Climate Change, Population, Biology, 010603 evolutionary biology, Evolutionary hisory, environment-dependent selection, 03 medical and health sciences, Evolutionary history, Taxus baccata, education, Microsatellites, 030304 developmental biology, Demography, Genetic diversity, Environment_x0002_dependent seection, Genetic Variation, Microsatellite, 15. Life on land, Chloroplast DNA(cpDNA), Genetic divergence, chloroplast DNA (cpDNA), approximate Bayesian computation (ABC), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Quaternary, evolutionary history, Microsatellite Repeats
Abstract

Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity. © 2015 New Phytologist Trust.

Published
2015
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9. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq

Author

M. Bou Dagher-Kharrat, Giovanni G. Vendramin, Marie-Joe Karam, Sara Pinosio, François Lefèvre, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), laboratoire de Caractérisation Génomique des Plantes, Université Saint-Joseph de Beyrouth (USJ), Applied Genomics Institute (IGA), Institute of Biosciences and Bioresources (IBBR), Consiglio Nazionale delle Ricerche [Roma] (CNR), This project was supported by the Agropolis Fondation (Montpellier, France) under the reference ID 'BIOFIS' 1001-001, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), and Consiglio Nazionale delle Ricerche (CNR)

Subjects
0106 biological sciences, Genetic Markers, DNA, Plant, Molecular Sequence Data, SNP, Single-nucleotide polymorphism, Computational biology, Biology, 01 natural sciences, Genome, Polymorphism, Single Nucleotide, DNA sequencing, 03 medical and health sciences, chemistry.chemical_compound, Cedrus atlantica, next generation sequencing, RADseq, SSR, transcriptome, Molecular marker, Genetics, Genotyping, Cedrus, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Contig, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Restriction site, chemistry, Microsatellite, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Plant, 010606 plant biology & botany, Biotechnology
Abstract

We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of[i] Cedrus atlantica[/i], a conifer tree species. With each method, Illumina(®) reads from one individual were used to generate de novo assemblies. SNPs from the RADseq data set were detected in a panel of one single individual and three pools of three individuals each. We developed a flexible script to estimate the ascertainment bias in SNP detection considering the pooling and sampling effects on the probability of not detecting an existing polymorphism. Gene Ontology (GO) and transposable element (TE) search analyses were applied to both data sets. The RADseq and the mRNAseq assemblies represented 0.1% and 0.6% of the genome, respectively. Genome complexity reduction resulted in 17% of the RADseq contigs potentially coding for proteins. This rate was doubled in the mRNAseq data set, suggesting that RADseq also explores noncoding low-repeat regions. The two methods gave very similar GO-slim profiles. As expected, the two assemblies were poor in TE-like sequences (

Published
2014
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