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4. Forest Genetics Research in the Mediterranean Basin: Bibliometric Analysis, Knowledge Gaps, and Perspectives

Author

Fady, Bruno, Esposito, Edoardo, Abulaila, Khaled, Aleksic, Jelena M., Alia, Ricardo, Alizoti, Paraskevi, Apostol, Ecaterina-Nicoleta, Aravanopoulos, Phil, Ballian, Dalibor, Kharrat, Magda Bou Dagher, Carrasquinho, Isabel, Albassatneh, Marwan Cheikh, Curtu, Alexandru-Lucian, David-Schwartz, Rakefet, de Dato, Giovanbattista, Douaihy, Bouchra, Eliades, Nicolas-George Homer, Fresta, Louis, Gaouar, Semir Bechir Suheil, Illoul, Malika Hachi, Ivetic, Vladan, Ivankovic, Mladen, Kandemir, Gaye, Khaldi, Abdelhamid, Khouja, Mohamed Larbi, Kraigher, Hojka, Lefèvre, François, Mahfoud, Ilène, Marchi, Maurizio, Martín, Felipe Pérez, Picard, Nicolas, Sabatti, Maurizio, Sbay, Hassan, Scotti-Saintagne, Caroline, Stevens, Darrin T, Vendramin, Giovanni Giuseppe, Vinceti, Barbara, and Westergren, Marjana

Published
2022
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6. Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Author

Zhou, Qiujie, Karunarathne, Piyal, Andersson-Li, Lili, Chen, Chen, Opgenoorth, Lars, Heer, Katrin, Piotti, Andrea, Vendramin, Giovanni Giuseppe, Nakvasina, Elena, Lascoux, Martin, Milesi, Pascal, Zhou, Qiujie, Karunarathne, Piyal, Andersson-Li, Lili, Chen, Chen, Opgenoorth, Lars, Heer, Katrin, Piotti, Andrea, Vendramin, Giovanni Giuseppe, Nakvasina, Elena, Lascoux, Martin, and Milesi, Pascal

Abstract

Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi-layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation-by-Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories.

Published
2024
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8. Correction to: Forest Genetics Research in the Mediterranean Basin: Bibliometric Analysis, Knowledge Gaps, and Perspectives

Author

Fady, Bruno, Esposito, Edoardo, Abulaila, Khaled, Aleksic, Jelena M., Alia, Ricardo, Alizoti, Paraskevi, Apostol, Ecaterina-Nicoleta, Aravanopoulos, Phil, Ballian, Dalibor, Kharrat, Magda Bou Dagher, Carrasquinho, Isabel, Albassatneh, Marwan Cheikh, Curtu, Alexandru-Lucian, David-Schwartz, Rakefet, de Dato, Giovanbattista, Douaihy, Bouchra, Eliades, Nicolas-George Homer, Fresta, Louis, Gaouar, Semir Bechir Suheil, Illoul, Malika Hachi, Ivetic, Vladan, Ivankovic, Mladen, Kandemir, Gaye, Khaldi, Abdelhamid, Khouja, Mohamed Larbi, Kraigher, Hojka, Lefèvre, François, Mahfoud, Ilène, Marchi, Maurizio, Martín, Felipe Pérez, Picard, Nicolas, Sabatti, Maurizio, Sbay, Hassan, Scotti-Saintagne, Caroline, Stevens, Darrin T., Vendramin, Giovanni Giuseppe, Vinceti, Barbara, and Westergren, Marjana

Published
2022
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9. Author Correction: WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees

Author

Monnet, Anne-Christine, Cilleros, Kévin, Médail, Frédéric, Albassatneh, Marwan Cheikh, Arroyo, Juan, Bacchetta, Gianluigi, Bagnoli, Francesca, Barina, Zoltán, Cartereau, Manuel, Casajus, Nicolas, Dimopoulos, Panayotis, Domina, Gianniantonio, Doxa, Aggeliki, Escudero, Marcial, Fady, Bruno, Hampe, Arndt, Matevski, Vlado, Misfud, Stephen, Nikolic, Toni, Pavon, Daniel, Roig, Anne, Barea, Estefania Santos, Spanu, Ilaria, Strid, Arne, Vendramin, Giovanni Giuseppe, and Leriche, Agathe

Published
2021
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10. WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees

Author

Monnet, Anne-Christine, Cilleros, Kévin, Médail, Frédéric, Albassatneh, Marwan Cheikh, Arroyo, Juan, Bacchetta, Gianluigi, Bagnoli, Francesca, Barina, Zoltán, Cartereau, Manuel, Casajus, Nicolas, Dimopoulos, Panayotis, Domina, Gianniantonio, Doxa, Aggeliki, Escudero, Marcial, Fady, Bruno, Hampe, Arndt, Matevski, Vlado, Misfud, Stephen, Nikolic, Toni, Pavon, Daniel, Roig, Anne, Barea, Estefania Santos, Spanu, Ilaria, Strid, Arne, Vendramin, Giovanni Giuseppe, and Leriche, Agathe

Published
2021
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16. The genetic consequences of population marginality: a case study in maritime pine

Author

THERAROZ, Adelaide, primary, GUADANO-PEYROT, Carlos, additional, Archambeau, Juliette, additional, PINOSIO, Sara, additional, BAGNOLI, Francesca, additional, PIOTTI, Andrea, additional, AVANZI, Camilla, additional, VENDRAMIN, Giovanni Giuseppe, additional, ALIA, Ricardo, additional, GRIVET, Delphine, additional, WESTERGREN, Marjana, additional, and GONZALEZ-MARTINEZ, Santiago Cesar, additional

Published
2023
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19. Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Author

Zhou, Qiujie, primary, Karunarathne, Piyal, additional, Andersson-Li, Lili, additional, Chen, Chen, additional, Opgenoorth, Lars, additional, Heer, Katrin, additional, Vendramin, Giovanni Giuseppe, additional, Piotti, Andrea, additional, Nakvasina, Elena, additional, Lascoux, Martin, additional, and Milesi, Pascal, additional

Published
2023
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20. The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Barbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares, Fernando, Cavers, Stephen, Fady, Bruno, Alía, Ricardo, Aravanopoulos, Filippos, Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent, José M., Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna-Maria, del Barrio, José M. García, Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le-Provost, Grégoire, Liesebach, Mirko, Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, Tor, Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A., Ramskogler, Kurt, Robledo-Arnuncio, Juan J., Savolainen, Outi, Schueler, Silvio, Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, and Fonti, Patrick

Published
2020
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21. Author Correction: The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Barbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares, Fernando, Cavers, Stephen, Fady, Bruno, Alía, Ricardo, Aravanopoulos, Filippos, Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent, José M., Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna-Maria, García del Barrio, José M., Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le-Provost, Grégoire, Liesebach, Mirko, Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, Tor, Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A., Ramskogler, Kurt, Robledo-Arnuncio, Juan J., Savolainen, Outi, Schueler, Silvio, Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Veisse, Dominique, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, and Fonti, Patrick

Published
2020
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22. Chloroplast DNA barcoding genes matK and psbA-trnH are not suitable for species identification and phylogenetic analyses in closely related pines

Author

Olsson, Sanna, Giovannelli, Guia, Roig, Anne, Spanu, Ilaria, Vendramin, Giovanni Giuseppe, Fady, Bruno, Office National des Forêts (France), Ministerio de Economía y Competitividad (España), Aix-Marseille Université, Olsson, Sanna, Giovannelli, Guia, Spanu, Ilaria, Vendramin, Giovanni Giuseppe, Fady, Bruno, Olsson, Sanna [0000-0002-1199-4499], Giovannelli, Guia [0000-0003-4776-3219], Spanu, Ilaria [0000-0002-5682-133X], Vendramin, Giovanni Giuseppe [0000-0001-9921-7872], and Fady, Bruno [0000-0003-2379-7617]

Subjects
GenBank, Gene Tree, Pinus, Taxonomy
Abstract

7 Pág. Centro de Investigación Forestal (CIFOR), The largest and most economically important conifer genus Pinus is widespread in the northern hemisphere. Comprehensive phylogenies relying on complete chloroplast gene sequences are now available for the entire genus. However, phylogenetic relationships remain unresolved for certain lineages. One such example, which is also inconsistent in terms of biogeography, is within the subsection Pinus and includes five taxa: Pinus densiflora, P. nigra, P. resinosa, P. sylvestris and P. mugo / uncinata species complex. In this study, we use this clade as an example to explain weak support in phylogenetic studies of closely related pine species and show that some of the most popular genetic markers, namely the chloroplast DNA barcoding sequences matK, psbAtrnH and rbcL, are not recommended for species identification purposes in European pines. In addition, we show that matK and psbA-trnH contain contradicting phylogenetic signals in some of the most economically important pine species., This work was supported by: The French Office National des Forêts “Programme global de conservation des populations françaises de pin de Salzmann”; the French DNA barcoding program “Bibliothèque du Vivant”; the Spanish Ministry of Economy and Competitiveness (MINECO) contract to SO [PTA2015-10836-I]; the Aix-Marseille Université, France (Ecole Doctorale ED251) grant to GG; the short-term scientific mission program of the COST Action FP1202 grant to GG.

Published
2022

29. Marginality indices for biodiversity conservation in forest trees

Author

Picard, Nicolas, primary, Marchi, Maurizio, additional, Serra-Varela, Maria Jesus, additional, Westergren, Marjana, additional, Cavers, Stephen, additional, Notivol, Eduardo, additional, Piotti, Andrea, additional, Alizoti, Paraskevi, additional, Bozzano, Michele, additional, González-Martínez, Santiago C., additional, Grivet, Delphine, additional, Aravanopoulos, Filippos A., additional, Vendramin, Giovanni Giuseppe, additional, Ducci, Fulvio, additional, Fady, Bruno, additional, and Alía, Ricardo, additional

Published
2022
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33. Forest Genetics Research in the Mediterranean Basin: Bibliometric Analysis, Knowledge Gaps, and Perspectives (vol 8, pg 277, 2022)

Author

Fady, Bruno, Esposito, Edoardo, Abulaila, Khaled, Aleksić, Jelena M., Alia, Ricardo, Alizoti, Paraskevi, Apostol, Ecaterina-Nicoleta, Aravanopoulos, Phil, Ballian, Dalibor, Kharrat, Magda Bou Dagher, Carrasquinho, Isabel, Albassatneh, Marwan Cheikh, Curtu, Alexandru-Lucian, David-Schwartz, Rakefet, de Dato, Giovanbattista, Douaihy, Bouchra, Eliades, Nicolas-George Homer, Fresta, Louis, Gaouar, Semir Bechir Suheil, Illoul, Malika Hachi, Ivetić, Vladan, Ivanković, Mladen, Kandemir, Gaye, Khaldi, Abdelhamid, Khouja, Mohamed Larbi, Kraigher, Hojka, Lefevre, Francois, Mahfoud, Ilene, Marchi, Maurizio, Martin, Felipe Perez, Picard, Nicolas, Sabatti, Maurizio, Sbay, Hassan, Scotti-Saintagne, Caroline, Stevens, Darrin T., Vendramin, Giovanni Giuseppe, Vinceti, Barbara, Westergren, Marjana, Fady, Bruno, Esposito, Edoardo, Abulaila, Khaled, Aleksić, Jelena M., Alia, Ricardo, Alizoti, Paraskevi, Apostol, Ecaterina-Nicoleta, Aravanopoulos, Phil, Ballian, Dalibor, Kharrat, Magda Bou Dagher, Carrasquinho, Isabel, Albassatneh, Marwan Cheikh, Curtu, Alexandru-Lucian, David-Schwartz, Rakefet, de Dato, Giovanbattista, Douaihy, Bouchra, Eliades, Nicolas-George Homer, Fresta, Louis, Gaouar, Semir Bechir Suheil, Illoul, Malika Hachi, Ivetić, Vladan, Ivanković, Mladen, Kandemir, Gaye, Khaldi, Abdelhamid, Khouja, Mohamed Larbi, Kraigher, Hojka, Lefevre, Francois, Mahfoud, Ilene, Marchi, Maurizio, Martin, Felipe Perez, Picard, Nicolas, Sabatti, Maurizio, Sbay, Hassan, Scotti-Saintagne, Caroline, Stevens, Darrin T., Vendramin, Giovanni Giuseppe, Vinceti, Barbara, and Westergren, Marjana

Published
2022

34. High pollen immigration but no gene flow via-seed into a Genetic Conservation Unit of the endangered Picea omorika after disturbance

Author

Aleksić, Jelena M., Mataruga, Milan, Danicić, Vanja, Cvjetković, Branislav, Milanović, Djordjije, Vendramin, Giovanni Giuseppe, Avanzi, Camilla, Piotti, Andrea, Aleksić, Jelena M., Mataruga, Milan, Danicić, Vanja, Cvjetković, Branislav, Milanović, Djordjije, Vendramin, Giovanni Giuseppe, Avanzi, Camilla, and Piotti, Andrea

Abstract

Studying how genetic diversity is transmitted between generations is critical for assessing the survival prospects of fragmented forest tree populations. This is especially urgent in the case of rare, endangered species that are at high risk of extinction and/or exceptionally susceptible to climate change, and are thus to be prioritised for conservation initiatives. We performed the first assessment of gene flow patterns by parentage analysis in the IUCN red-listed Serbian spruce [Picea omorika (Pan.c.) Purk.], within a Genetic Conservation Unit (GCU) which was exposed to fire disturbance 30 years ago. Parentage analysis was based on assigning the parentage of 104 juveniles to all the adult trees (48) present in the 2.8 ha population. All individuals were genotyped at 11 highly informative nuclear microsatellite markers. We found that fire disturbance triggered natural regeneration, usually poor to absent in Serbian spruce, and boosted pollen immigration (66%), which is reported as rather modest among undisturbed populations of this species. Seed immigration was absent, coherently with what was previously hypothesised for natural, undisturbed populations. Thus, the immigration of new gametes into the studied Serbian spruce population was accomplished exclusively through pollen gene flow, at a rate sufficient to counteract, at least in the short term, genetic drift. Furthermore, the abundant post-disturbance pollen immigration most likely accounts for the lack of fine-scale spatial genetic structure (SGS) in the juvenile cohort, contrary to the SGS observed in the adult cohort which is amongst the strongest ever recorded in anemophilous forest tree species. Finally, as generally found in forest trees, individual reproductive success was uneven among individuals, with 25% of local adults siring 70% of the sampled juveniles. Our results on post-disturbance gene flow patterns in the only Serbian spruce population with reportedly abundant regeneration complement the outc

Published
2022

35. Marginality indices for biodiversity conservation in forest trees

Author

Picard, Nicolas, Marchi, Maurizio, Serra-Varela, Maria Jesus, Westergren, Marjana, Cavers, Stephen, Notivol, Eduardo, Piotti, Andrea, Alizoti, Paraskevi, Bozzano, Michele, González-Martínez, Santiago C., Grivet, Delphine, Aravanopoulos, Filippos A., Vendramin, Giovanni Giuseppe, Ducci, Fulvio, Fady, Bruno, Alía, Ricardo, Picard, Nicolas, Marchi, Maurizio, Serra-Varela, Maria Jesus, Westergren, Marjana, Cavers, Stephen, Notivol, Eduardo, Piotti, Andrea, Alizoti, Paraskevi, Bozzano, Michele, González-Martínez, Santiago C., Grivet, Delphine, Aravanopoulos, Filippos A., Vendramin, Giovanni Giuseppe, Ducci, Fulvio, Fady, Bruno, and Alía, Ricardo

Abstract

Marginal and peripheral populations are important for biodiversity conservation. Their original situation in a species’ geographic and ecological space often confers them genetic diversity and traits of high adaptive value. Yet theoretical hypotheses related to marginality are difficult to test because of confounding factors that influence marginality, namely environment, geography, and history. There is an urgent need to develop metrics to disentangle these confounding factors. We designed nine quantitative indices of marginality and peripherality that define where margins lie within species distributions, from a geographical, an environmental and a historical perspective. Using the distribution maps of eight European forest tree species, we assessed whether these indices were idiosyncratic or whether they conveyed redundant information. Using a database on marginal and peripheral populations based on expert knowledge, we assessed the capacity of the indices to predict the marginality status of a population. There was no consistent pattern of correlation between indices across species, confirming that the indices conveyed different information related to the specific geometry of the species distributions. Contrasting with this heterogeneity of correlation patterns across species, the relative importance of the indices to predict the marginality status of populations was consistent across species. However, there was still a significant country effect in the marginality status, showing a variation in expert opinion of marginality vis-á-vis the species distribution. The marginality indices that we developed are entirely based on distribution maps and can be used for any species. They pave the way for testing hypotheses related to marginality and peripherality, with important implications in quantitative ecology, genetics, and biodiversity conservation.

Published
2022

37. 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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38. The GenTree Leaf Collection: inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Benavides, Raquel, Carvalho, Bárbara, Bastias, Cristina C., López‐Quiroga, David, Mas, Antonio, Cavers, Stephen, Gray, Alan, Albet, Audrey, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia V., Bagnoli, Francesca, Ballesteros, Eduardo, Barbas, Evangelos, Bastien, Catherine, Bernier, Frédéric, Bignalet, Henry, Bouic, Damien, Brunetto, William, Buchovska, Jurata, Cabanillas‐Saldaña, Ana M., Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Del Caño, Fernando, Denou, Jean‐Luc, Dokhelar, Bernard, Dourthe, Rémi, Farsakoglou, Anna‐Maria, Fera, Andreas, Fonti, Patrick, Ganopoulos, Ioannis, García del Barrio, José M., Gilg, Olivier, González‐Martínez, Santiago C., Graf, René, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issehuth, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan‐Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Le Provost, Gregoire, Liesebach, Mirko, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Martínez‐Sancho, Elisabet, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Myking, Tor, Nilsen, Anne E., Notivol, Eduardo, Opgenoorth, Lars, Østreng, Geir, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez‐Valiente, José A., Rellstab, Christian, Richter, Sebastian, Robledo‐Arnuncio, Juan J., San Segundo, Sergio, Savolainen, Outi, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Semerikov, Vladimir, Henrik Sønstebø, Jørn, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, Fady, Bruno, Valladares, Fernando, Benavides, Raquel, Carvalho, Bárbara, Bastias, Cristina C., López‐Quiroga, David, Mas, Antonio, Cavers, Stephen, Gray, Alan, Albet, Audrey, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia V., Bagnoli, Francesca, Ballesteros, Eduardo, Barbas, Evangelos, Bastien, Catherine, Bernier, Frédéric, Bignalet, Henry, Bouic, Damien, Brunetto, William, Buchovska, Jurata, Cabanillas‐Saldaña, Ana M., Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Del Caño, Fernando, Denou, Jean‐Luc, Dokhelar, Bernard, Dourthe, Rémi, Farsakoglou, Anna‐Maria, Fera, Andreas, Fonti, Patrick, Ganopoulos, Ioannis, García del Barrio, José M., Gilg, Olivier, González‐Martínez, Santiago C., Graf, René, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issehuth, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan‐Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Le Provost, Gregoire, Liesebach, Mirko, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Martínez‐Sancho, Elisabet, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Myking, Tor, Nilsen, Anne E., Notivol, Eduardo, Opgenoorth, Lars, Østreng, Geir, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez‐Valiente, José A., Rellstab, Christian, Richter, Sebastian, Robledo‐Arnuncio, Juan J., San Segundo, Sergio, Savolainen, Outi, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Semerikov, Vladimir, Henrik Sønstebø, Jørn, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, Fady, Bruno, and Valladares, Fernando

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.

Published
2021

39. Spatial patterns of genus‐level phylogenetic endemism in the tree flora of Mediterranean Europe

Author

Cheikh Albassatneh, Marwan, primary, Escudero, Marcial, additional, Monnet, Anne‐Christine, additional, Arroyo, Juan, additional, Bacchetta, Gianluigi, additional, Bagnoli, Francesca, additional, Dimopoulos, Panayotis, additional, Hampe, Arndt, additional, Leriche, Agathe, additional, Médail, Frédéric, additional, Nikolic, Toni, additional, Ponger, Loïc, additional, Vendramin, Giovanni Giuseppe, additional, and Fady, Bruno, additional

Published
2021
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40. The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Benavides, Raquel, primary, Carvalho, Bárbara, additional, Bastias, Cristina C., additional, López‐Quiroga, David, additional, Mas, Antonio, additional, Cavers, Stephen, additional, Gray, Alan, additional, Albet, Audrey, additional, Alía, Ricardo, additional, Ambrosio, Olivier, additional, Aravanopoulos, Filippos, additional, Auñón, Francisco, additional, Avanzi, Camilla, additional, Avramidou, Evangelia V., additional, Bagnoli, Francesca, additional, Ballesteros, Eduardo, additional, Barbas, Evangelos, additional, Bastien, Catherine, additional, Bernier, Frédéric, additional, Bignalet, Henry, additional, Bouic, Damien, additional, Brunetto, William, additional, Buchovska, Jurata, additional, Cabanillas‐Saldaña, Ana M., additional, Cheval, Nicolas, additional, Climent, José M., additional, Correard, Marianne, additional, Cremer, Eva, additional, Danusevičius, Darius, additional, Dauphin, Benjamin, additional, Del Caño, Fernando, additional, Denou, Jean‐Luc, additional, Dokhelar, Bernard, additional, Dourthe, Rémi, additional, Farsakoglou, Anna‐Maria, additional, Fera, Andreas, additional, Fonti, Patrick, additional, Ganopoulos, Ioannis, additional, García del Barrio, José M., additional, Gilg, Olivier, additional, González‐Martínez, Santiago C., additional, Graf, René, additional, Grivet, Delphine, additional, Gugerli, Felix, additional, Hartleitner, Christoph, additional, Heer, Katrin, additional, Hollenbach, Enja, additional, Hurel, Agathe, additional, Issehuth, Bernard, additional, Jean, Florence, additional, Jorge, Veronique, additional, Jouineau, Arnaud, additional, Kappner, Jan‐Philipp, additional, Kärkkäinen, Katri, additional, Kesälahti, Robert, additional, Knutzen, Florian, additional, Kujala, Sonja T., additional, Kumpula, Timo, additional, Labriola, Mariaceleste, additional, Lalanne, Celine, additional, Lambertz, Johannes, additional, Lascoux, Martin, additional, Le Provost, Gregoire, additional, Liesebach, Mirko, additional, Malliarou, Ermioni, additional, Marchon, Jérémy, additional, Mariotte, Nicolas, additional, Martínez‐Sancho, Elisabet, additional, Matesanz, Silvia, additional, Meischner, Helge, additional, Michotey, Célia, additional, Milesi, Pascal, additional, Morganti, Sandro, additional, Myking, Tor, additional, Nilsen, Anne E., additional, Notivol, Eduardo, additional, Opgenoorth, Lars, additional, Østreng, Geir, additional, Pakull, Birte, additional, Piotti, Andrea, additional, Plomion, Christophe, additional, Poinot, Nicolas, additional, Pringarbe, Mehdi, additional, Puzos, Luc, additional, Pyhäjärvi, Tanja, additional, Raffin, Annie, additional, Ramírez‐Valiente, José A., additional, Rellstab, Christian, additional, Richter, Sebastian, additional, Robledo‐Arnuncio, Juan J., additional, San Segundo, Sergio, additional, Savolainen, Outi, additional, Schneck, Volker, additional, Schueler, Silvio, additional, Scotti, Ivan, additional, Semerikov, Vladimir, additional, Henrik Sønstebø, Jørn, additional, Spanu, Ilaria, additional, Thevenet, Jean, additional, Tollefsrud, Mari Mette, additional, Turion, Norbert, additional, Vendramin, Giovanni Giuseppe, additional, Villar, Marc, additional, Westin, Johan, additional, Fady, Bruno, additional, and Valladares, Fernando, additional

Published
2021
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41. Functional Relationships of Wood Anatomical Traits in Norway Spruce

Author

Piermattei, Alma, primary, von Arx, Georg, additional, Avanzi, Camilla, additional, Fonti, Patrick, additional, Gärtner, Holger, additional, Piotti, Andrea, additional, Urbinati, Carlo, additional, Vendramin, Giovanni Giuseppe, additional, Büntgen, Ulf, additional, and Crivellaro, Alan, additional

Published
2020
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43. The genetic structure of the European black pine (Pinus nigra Arnold) is shaped by its recent Holocene demographic history

Author

Giovannelli, Guia, Scotti-Saintagne, Caroline, Scotti, Ivan, Roig, Anne, Spanu, Ilaria, Vendramin, Giovanni Giuseppe, Guibal, Frederic, and Fady, Bruno

Subjects
structure génétique des populations, taxonomie, Demographic inference, nuclear genes, organelle genes, gene flow, admixture, taxonomy, organite, gène nucléaire, diversité génétique, holocène, pinus nigra, Milieux et Changements globaux, inférence, cycle géologique
Abstract

Fragmentation acting over geological times confers wide, biogeographical scale, genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a major European forest tree and to resolve its demographic history, we describe and model its spatial genetic structure and gene 30 genealogy. We then test which Pleistocene event, whether recent or ancient, could explain its widespread but patchy geographic distribution using population genetic data, environmental data and realistic demographic timed scenarios. The taxon of interest is a conifer forest tree, Pinus nigra (Arnold), the European black pine, whose populations are located in the mountains of southern Europe and North Africa, most frequently at mid35 elevation. We used a set of different genetic markers, both neutral and potentially adaptive, and either bi-parentally or paternally inherited, and we sampled natural populations across the entire range of the species. We analysed the data using frequentist population genetic methods as well as Bayesian inference methods to calibrate realistic, demographic timed scenarios. Species with geographically fragmented distribution areas are expected to display strong among40 population genetic differentiation and low within-population genetic diversity. Contrary to these expectations, we show that the current diversity of Pinus nigra and its weak genetic spatial structure are best explained as resulting from late Pleistocene or early Holocene fragmentation of one ancestral population into seven genetic lineages, which we found to be the main biogeographical contributors of the natural black pine forests of today. Gene flow among the different lineages is strong across forests 45 and many current populations are admixed between lineages. We propose to modify the currently accepted international nomenclature made of five subspecies and name these seven lineages using regionally accepted subspecies-level names.

Published
2019

44. A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability

Author

Cheikh Albassatneh, Marwan, primary, Escudero, Marcial, additional, Ponger, Loic, additional, Monnet, Anne-Christine, additional, Arroyo, Juan, additional, Nikolic, Toni, additional, Bacchetta, Gianluigi, additional, Bagnoli, Francesca, additional, Dimopoulos, Panayotis, additional, Leriche, Agathe, additional, Médail, Frédéric, additional, Roig, Anne, additional, Spanu, Ilaria, additional, Vendramin, Giovanni Giuseppe, additional, Hampe, Arndt, additional, and Fady, Bruno, additional

Published
2019
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50. Genome sequencing reveals microgeographic adaptation in the widespread Amazonian tree species Eperua falcata (Aublet.): A Bayesian framework

Author

Brousseau, Louise, Vendramin, Giovanni Giuseppe, Scotti, Ivan, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche [Roma] (CNR), Ecologie des Forêts Méditerranéennes (URFM), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

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