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1. Resilience of genetic diversity in forest trees over the Quaternary

Author: Pascal Milesi, Chedly Kastally, Benjamin Dauphin, Sandra Cervantes, Francesca Bagnoli, Katharina B. Budde, Stephen Cavers, Bruno Fady, Patricia Faivre-Rampant, Santiago C. González-Martínez, Delphine Grivet, Felix Gugerli, Véronique Jorge, Isabelle Lesur Kupin, Dario I. Ojeda, Sanna Olsson, Lars Opgenoorth, Sara Pinosio, Christophe Plomion, Christian Rellstab, Odile Rogier, Simone Scalabrin, Ivan Scotti, Giovanni G. Vendramin, Marjana Westergren, Martin Lascoux, Tanja Pyhäjärvi, and On behalf of the GenTree Consortium
Subjects: Science
Abstract: Abstract The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, N e , increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of N e over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes.
Published: 2024
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2. A 14-year series of leaf phenological data collected for European beech (Fagus sylvatica L.) and silver fir (Abies alba Mill.) from their geographic range margins in south-eastern France

Author: Frederic Jean, Hendrik Davi, Sylvie Oddou-Muratorio, Bruno Fady, Ivan Scotti, Caroline Scotti-Saintagne, Julien Ruffault, Valentin Journe, Philippe Clastre, Olivier Marloie, William Brunetto, Marianne Correard, Olivier Gilg, Mehdi Pringarbe, Franck Rei, Jean Thevenet, Norbert Turion, and Christian Pichot
Subjects: Phenology, Forest, Bud development, Leaf senescence, Marginal population, Climate change, Forestry, SD1-669.5
Abstract: Key message Phenology is of increasing interest to climate change science and adaptation ecology. Here, we provide bud development, leafing, and leaf senescence data, collected on 772 European beech and silver fir trees between 2006 and 2019 on Mont Ventoux, France. Dataset access is at https://doi.org/10.15454/TRFMZN . Associated metadata are available at https://metadata-afs.nancy.inra.fr/geonetwork/srv/fre/catalog.search#/metadata/a33c8375-9a90-4bc3-a0d7-19317160b68f .
Published: 2023
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3. Caractériser l’enveloppe climatique future des jardins communs forestiers : une approche essentielle pour mieux raisonner l’adaptation des essences

Author: Gaspard Rihm and Bruno Fady
Subjects: niche climatique, test de provenances, adaptation génétique, plasticité phénotypique, Forestry, SD1-669.5
Abstract: L’adaptation au changement climatique est un enjeu de gestion majeur pour les forêts françaises. Pour décrire et comprendre la variabilité génétique et la plasticité phénotypique des caractères d’intérêt pour l’adaptation, les jardins communs (dont les tests de provenances) sont un outil de choix. Nous décrivons dans ce travail un des réseaux forestier français majeur de tests en jardins communs (GEN4X), son amplitude écologique et, via une approche de modélisation de niche, sa sensibilité à un climat qui va en se réchauffant et s’asséchant au cours du siècle. Une attention particulière a été portée aux dispositifs situés en région méditerranéenne. Messages clés : • Les jardins communs sont des outils pour tester l’adaptation des essences au climat futur • Les conditions climatiques actuelles et futures dans ces jardins ont été évaluées • La zone méditerranéenne préfigure les conditions du futur dans une grande partie de la France
Published: 2023
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4. Fire frequency, as well as stress response and developmental gene control serotiny level variation in a widespread pioneer Mediterranean conifer, Pinus halepensis

Author: Bastien Romero, Ivan Scotti, Bruno Fady, and Anne Ganteaume
Subjects: cone serotiny, fire regime, genetic association, phenotypic plasticity, Pinus halepensis, single nucleotide polymorphisms, Ecology, QH540-549.5
Abstract: Abstract Many plants undergo adaptation to fire. Yet, as global change is increasing fire frequency worldwide, our understanding of the genetics of adaptation to fire is still limited. We studied the genetic basis of serotiny (the ability to disseminate seeds exclusively after fire) in the widespread, pioneer Mediterranean conifer Pinus halepensis Mill., by linking individual variation in serotiny presence and level to fire frequency and to genetic polymorphism in natural populations. After filtering steps, 885 single nucleotide polymorphisms (SNPs) out of 8000 SNPs used for genotyping were implemented to perform an in situ association study between genotypes and serotiny presence and level. To identify serotiny‐associated loci, we performed random forest analyses of the effect of SNPs on serotiny levels, while controlling for tree size, frequency of wildfires, and background environmental parameters. Serotiny showed a bimodal distribution, with serotinous trees more frequent in populations exposed to fire in their recent history. Twenty‐two SNPs found in genes involved in stress tolerance were associated with the presence‐absence of serotiny while 37 found in genes controlling for flowering were associated with continuous serotiny variation. This study shows the high potential of P. halepensis to adapt to changing fire regimes, benefiting from a large and flexible genetic basis of trait variation.
Published: 2023
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5. Marginality indices for biodiversity conservation in forest trees

Author: Nicolas Picard, Maurizio Marchi, Maria Jesus Serra-Varela, Marjana Westergren, Stephen Cavers, Eduardo Notivol, Andrea Piotti, Paraskevi Alizoti, Michele Bozzano, Santiago C. González-Martínez, Delphine Grivet, Filippos A. Aravanopoulos, Giovanni Giuseppe Vendramin, Fulvio Ducci, Bruno Fady, and Ricardo Alía
Subjects: Centre-periphery hypothesis, Environmental indices, Geographical indices, Migration indices, In situ genetic conservation, Marginal populations, Ecology, QH540-549.5
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
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6. Signature of mid‐Pleistocene lineages in the European silver fir (Abies alba Mill.) at its geographic distribution margin

Author: Caroline Scotti‐Saintagne, Thomas Boivin, Marie Suez, Brigitte Musch, Ivan Scotti, and Bruno Fady
Subjects: admixture, conservation, demography, French Pyrenees, genetic diversity, keystone species, Ecology, QH540-549.5
Abstract: Abstract In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight neighboring reference populations in the Massif Central, Alps, and Corsica. We genotyped 1,620 individuals at three chloroplast and ten nuclear microsatellite loci. We analyzed within‐ and among‐population genetic diversity using phylogeographic reconstructions, tests of isolation‐by‐distance, Bayesian population structure inference, modeling of demographic scenarios, and regression analyses of genetic variables with current and past environmental variables. Genetic diversity decreased from east to west suggesting isolation‐by‐distance from the Alps to the Pyrenees and from the Eastern to the Western Pyrenees. We identified two Pyrenean lineages that diverged from a third Alpine–Corsica–Massif Central lineage 0.8 to 1.1 M years ago and subsequently formed a secondary contact zone in the Central Pyrenees. Population sizes underwent contrasted changes, with a contraction in the west and an expansion in the east. Glacial climate affected the genetic composition of the populations, with the western genetic cluster only observed in locations corresponding to the coldest past climate and highest elevations. The eastern cluster was observed over a larger range of temperatures and elevations. All demographic events shaping the current spatial structure of genetic diversity took place during the Mid‐Pleistocene Transition, long before the onset of the Holocene. The Western Pyrenees lineage may require additional conservation efforts, whereas the eastern lineage is well protected in in situ gene conservation units. Due to past climate oscillations and the likely emergence of independent refugia, east–west oriented mountain ranges may be important reservoir of genetic diversity in a context of past and ongoing climate change in Europe.
Published: 2021
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7. WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees

Author: Anne-Christine Monnet, Kévin Cilleros, Frédéric Médail, Marwan Cheikh Albassatneh, Juan Arroyo, Gianluigi Bacchetta, Francesca Bagnoli, Zoltán Barina, Manuel Cartereau, Nicolas Casajus, Panayotis Dimopoulos, Gianniantonio Domina, Aggeliki Doxa, Marcial Escudero, Bruno Fady, Arndt Hampe, Vlado Matevski, Stephen Misfud, Toni Nikolic, Daniel Pavon, Anne Roig, Estefania Santos Barea, Ilaria Spanu, Arne Strid, Giovanni Giuseppe Vendramin, and Agathe Leriche
Subjects: Science
Abstract: Measurement(s) occurrence • Trait • DNA Technology Type(s) Sampling • digital curation • DNA sequencing assay Sample Characteristic - Organism Viridiplantae • trees Sample Characteristic - Environment forest biome Sample Characteristic - Location Mediterranean Region • Europe Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.13553519
Published: 2021
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8. Biodiversity, climate change, and adaptation in the Mediterranean

Author: Didier Aurelle, Séverine Thomas, Cécile Albert, Marc Bally, Alberte Bondeau, Charles‐François Boudouresque, Abigail E. Cahill, François Carlotti, Anne Chenuil, Wolfgang Cramer, Hendrik Davi, Aurélien De Jode, Alexander Ereskovsky, Anne‐Marie Farnet, Catherine Fernandez, Thierry Gauquelin, Pascal Mirleau, Anne‐Christine Monnet, Bernard Prévosto, Vincent Rossi, Stéphane Sartoretto, France Van Wambeke, and Bruno Fady
Subjects: adaptive management, biodiversity, biological adaptation, climate change, marine ecosystems, Mediterranean, Ecology, QH540-549.5
Abstract: Abstract Potential for, and limits to, adaptation to environmental changes are critical for resilience and risk mitigation. The Mediterranean basin is a mosaic of biodiversity‐rich ecosystems long affected by human influence, whose resilience is now questioned by climate change. After reviewing the different components of biological adaptation, we present the main characteristics of marine and terrestrial biodiversity in the Mediterranean basin and of the pressures they face. Taking climatic trends into consideration, we discuss the adaptive potential of a range of ecosystems dominated by species without active dispersal. We argue that the high heterogeneity of Mediterranean landscapes and seascapes constitutes a laboratory for the study of adaptation when environmental conditions change rapidly and may provide opportunities for adaptation and adaptability of species and ecosystems. Adaptive management in the Mediterranean can and should harness the nature‐based solutions offered by both ecological and evolutionary processes for increasing the resilience of ecosystems to climate change.
Published: 2022
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9. Adaptation to drought is coupled with slow growth, but independent from phenology in marginal silver fir (Abies alba Mill.) populations

Author: Katalin Csilléry, Nina Buchmann, and Bruno Fady
Subjects: adaptive divergence, assisted migration, climate change, demography, drought tolerance, phenology, Evolution, QH359-425
Abstract: Abstract Drought is one of the most important selection pressures for forest trees in the context of climate change. Yet, the different evolutionary mechanisms, and their environmental drivers, by which certain populations become more drought tolerant than others is still little understood. We studied adaptation to drought in 16 silver fir (Abies alba Mill.) populations from the French Mediterranean Alps by combining observations on seedlings from a greenhouse experiment (N = 8,199) and on adult tress in situ (N = 315). In the greenhouse, we followed half‐sib families for four growing seasons for growth and phenology traits, and tested their water stress response in a "drought until death" experiment. Adult trees in the field were assessed for δ13C, a proxy for water use efficiency, and genotyped at 357 SNP loci. SNP data was used to generate a null expectation for seedling trait divergence between populations in order to detect the signature of selection, and 31 environmental variables were used to identify the selective environment. We found that seedlings originating from populations with low soil water capacity grew more slowly, attained a smaller stature, and resisted water stress for a longer period of time in the greenhouse. Additionally, adult trees of these populations exhibited a higher water use efficiency as evidenced by their δ13C. These results suggest a correlated evolution of the growth‐drought tolerance trait complex. Population divergence in bud break phenology was adaptive only in the second growing season, and evolved independently from the growth‐drought tolerance trait complex. Adaptive divergence in bud break phenology was principally driven by the inter‐ and intra‐annual variation in temperature at the geographic origin of the population. Our results illustrate the different evolutionary strategies used by populations to cope with drought stress at the range limits across a highly heterogeneous landscape, and can be used to inform assisted migration programs.
Published: 2020
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10. Distribution maps of twenty-four Mediterranean and European ecologically and economically important forest tree species compiled from historical data collections

Author: Nadine Wazen, Valentina Garavaglia, Nicolas Picard, Christophe Besacier, and Bruno Fady
Subjects: distribution map, mediterranean forest tree, flora, chorology, biogeography., Agriculture
Abstract: Species distribution maps are often lacking for scientific investigation and strategic management planning at international level. Here, we present the range-wide, natural distribution maps of twenty-four Mediterranean and European forest-tree species of key ecological and economic importance in the Mediterranean basin. Data on the geographic distribution of the twenty-four tree species were compiled from over one hundred published sources, making this contribution one of the most extensive resource available from historical data. Dataset can be accessed at: https://doi.org/10.5281/zenodo.822953. Associated metadata can be accessed at: http://www.fao.org/geonetwork/srv/en/metadata.show?id=56996. These data provide key spatial information to further investigate species occurrence-environment relationships, provide a baseline to assess the future impact of climate change, identify marginal populations with specific genetic resources, among other possible applications.
Published: 2020
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11. Survival and growth of 711 forest tree taxa in eight French arboretums from three different climate regions

Author: Catherine Ducatillion, Thierry Lamant, Richard Bellanger, Valentin Bouttier, Jean-Charles Bastien, Célia Michotey, Laurent Gautier, Bruno Fady, and Brigitte Musch
Subjects: myrtaceae, pinaceae, adaptation, climate change, common garden, ecological restoration, phenotype, Agriculture
Abstract: Arboretums have been used for decades for scientific, educational, horticultural and aesthetic purposes. Recently, climate change concerns have renewed the interest of the scientific community for these invaluable experimental forest systems. Here, we report a dataset from eight scientific arboretums planted in three contrasted French metropolitan bioclimates: Oceanic, Mountain and Mediterranean. In total, 92,236 trees were planted in 3,678 different plots. Originating from a worldwide range of habitats, from sea-level up to 3,670 m in elevation, the collection spans 711 forest tree taxa (species, subspecies and varieties) from 177 genera. Taxa often include several geographic sources (so-called provenances), often simultaneously in different arboretums, making within species analyses possible. Cool-climate temperate Pinaceae (pines, firs, spruces, hemlocks, etc.) are well represented in the Atlantic and Mountain arboretums while Mediterranean arboretums are particularly rich with genera from the Myrtaceae (mostly eucalypts) and the Pinaceae (mostly pines). Data include survival, growth (height and diameter) and health status. Planted between 1969 and 1976, 338 taxa had survived at time of assessment and occurred as at least one individual in one plot. Data can be used to assess species suitability for ecological restoration and afforestation, and to help improve functional niche modeling. Data accessibility: https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/RGMM07.
Published: 2022
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12. Tree Mortality Risks Under Climate Change in Europe: Assessment of Silviculture Practices and Genetic Conservation Networks

Author: Cathleen Petit-Cailleux, Hendrik Davi, François Lefèvre, Pieter Johannes Verkerk, Bruno Fady, Marcus Lindner, and Sylvie Oddou-Muratorio
Subjects: climate change stresses, tree mortality, ecophysiology, genetic resources, conservation strategy, management practices, Evolution, QH359-425, Ecology, QH540-549.5
Abstract: General Context: Climate change can positively or negatively affect abiotic and biotic drivers of tree mortality. Process-based models integrating these climatic effects are only seldom used at species distribution scale.Objective: The main objective of this study was to investigate the multi-causal mortality risk of five major European forest tree species across their distribution range from an ecophysiological perspective, to quantify the impact of forest management practices on this risk and to identify threats on the genetic conservation network.Methods: We used the process-based ecophysiological model CASTANEA to simulate the mortality risk of Fagus sylvatica, Quercus petraea, Pinus sylvestris, Pinus pinaster, and Picea abies under current and future climate conditions, while considering local silviculture practices. The mortality risk was assessed by a composite risk index (CRIM) integrating the risks of carbon starvation, hydraulic failure and frost damage. We took into account extreme climatic events with the CRIMmax, computed as the maximum annual value of the CRIM.Results: The physiological processes' contributions to CRIM differed among species: it was mainly driven by hydraulic failure for P. sylvestris and Q. petraea, by frost damage for P. abies, by carbon starvation for P. pinaster, and by a combination of hydraulic failure and frost damage for F. sylvatica. Under future climate, projections showed an increase of CRIM for P. pinaster but a decrease for P. abies, Q. petraea, and F. sylvatica, and little variation for P. sylvestris. Under the harshest future climatic scenario, forest management decreased the mean CRIM of P. sylvestris, increased it for P. abies and P. pinaster and had no major impact for the two broadleaved species. By the year 2100, 38–90% of the European network of gene conservation units are at extinction risk (CRIMmax=1), depending on the species.Conclusions: Using a process-based ecophysiological model allowed us to disentangle the multiple drivers of tree mortality under current and future climates. Taking into account the positive effect of increased CO2 on fertilization and water use efficiency, average mortality risk may increase or decrease in the future depending on species and sites. However, under extreme climatic events, our process-based projections are as pessimistic as those obtained using bioclimatic niche models.
Published: 2021
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13. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource

Author: Elena Mosca, Fernando Cruz, Jèssica Gómez-Garrido, Luca Bianco, Christian Rellstab, Sabine Brodbeck, Katalin Csilléry, Bruno Fady, Matthias Fladung, Barbara Fussi, Dušan Gömöry, Santiago C. González-Martínez, Delphine Grivet, Marta Gut, Ole Kim Hansen, Katrin Heer, Zeki Kaya, Konstantin V. Krutovsky, Birgit Kersten, Sascha Liepelt, Lars Opgenoorth, Christoph Sperisen, Kristian K. Ullrich, Giovanni G. Vendramin, Marjana Westergren, Birgit Ziegenhagen, Tyler Alioto, Felix Gugerli, Berthold Heinze, Maria Höhn, Michela Troggio, and David B. Neale
Subjects: Abies alba, annotation, conifer genome, genome assembly, chloroplast genome, Genetics, QH426-470
Abstract: Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species’ future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.
Published: 2019
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14. What is a tree in the Mediterranean Basin hotspot? A critical analysis

Author: Frédéric Médail, Anne-Christine Monnet, Daniel Pavon, Toni Nikolic, Panayotis Dimopoulos, Gianluigi Bacchetta, Juan Arroyo, Zoltán Barina, Marwan Cheikh Albassatneh, Gianniantonio Domina, Bruno Fady, Vlado Matevski, Stephen Mifsud, and Agathe Leriche
Subjects: Plant biogeography, Mediterranean region, Threatened trees, Tree definition, Tree distributions, Ecology, QH540-549.5
Abstract: Abstract Background Tree species represent 20% of the vascular plant species worldwide and they play a crucial role in the global functioning of the biosphere. The Mediterranean Basin is one of the 36 world biodiversity hotspots, and it is estimated that forests covered 82% of the landscape before the first human impacts, thousands of years ago. However, the spatial distribution of the Mediterranean biodiversity is still imperfectly known, and a focus on tree species constitutes a key issue for understanding forest functioning and develop conservation strategies. Methods We provide the first comprehensive checklist of all native tree taxa (species and subspecies) present in the Mediterranean-European region (from Portugal to Cyprus). We identified some cases of woody species difficult to categorize as trees that we further called “cryptic trees”. We collected the occurrences of tree taxa by “administrative regions”, i.e. country or large island, and by biogeographical provinces. We studied the species-area relationship, and evaluated the conservation issues for threatened taxa following IUCN criteria. Results We identified 245 tree taxa that included 210 species and 35 subspecies, belonging to 33 families and 64 genera. It included 46 endemic tree taxa (30 species and 16 subspecies), mainly distributed within a single biogeographical unit. The countries with the highest tree richness are Greece (146 taxa), Italy (133), Albania (122), Spain (155), Macedonia (116), and Croatia (110). The species-area relationship clearly discriminated the richest central-eastern (Balkans) and northern (Alpine and Cevenno-Pyrenean) biogeographical provinces, against the five western provinces in the Iberian Peninsula. We identified 44 unrecognized “cryptic trees”, representing 21% of the total trees. Among the 245 taxa identified, 19 are considered to be threatened (15 CR + EN + VU) or near threatened (4 NT) by IUCN. Conclusions The Mediterranean-European region includes an unsuspectedly high number of tree taxa, almost 200 tree taxa more than in the central European region. This tree diversity is not distributed evenly and culminates in the central-eastern part of the Mediterranean region, whereas some large Tyrrhenian islands shelter several narrow endemic tree taxa. Few taxa are recognized as threatened in the IUCN Red list, and the vulnerability of these species is probably underestimated.
Published: 2019
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15. Valoriser et renforcer les mécanismes d’évolution génétique par la sylviculture, pour l’adaptation au changement climatique

Author: François Lefèvre, Thomas Boivin, Aurore Bontemps, François Courbet, Hendrik Davi, Marion Durand-Gillmann, Bruno Fady, Julie Gauzere, Cindy Gidoin, Marie-Joe Karam, Hadrien Lalagüe, Sylvie Oddou-Muratorio, and Christian Pichot
Subjects: Forestry, SD1-669.5
Abstract: L’adaptation est un enjeu majeur de la gestion forestière dans le contexte du changement climatique La diversité génétique qui caractérise les arbres forestiers leur confère un potentiel adaptatif très important mais pas illimité Prendre en compte les mécanismes de l’évolution dans les pratiques de gestion forestière adaptative renforcera la capacité des forêts gérées à répondre aux changements et aux aléas induits par le climat. En mettant l’accent sur le cas des forêts en régénération naturelle, nous proposons un cadre conceptuel général permettant d’intégrer la connaissance de ces mécanismes dans la prise de décision, dans une démarche de sylviculture par et pour l’évolution Ce cadre général pourra être décliné dans des situations locales diverses et complexes en s’appuyant sur la connaissance du contexte qu’ont les gestionnaires forestiers Nous développons une grille d’analyse simple, basée sur un petit nombre de paramètres caractérisant les mécanismes de l’évolution, pour comprendre l’impact des pratiques sylvicoles sur la dynamique de la diversité génétique et le maintien du potentiel d’évolution des populations d’arbres forestiers Après avoir rappelé l’état des connaissances sur les mécanismes de l’évolution chez les arbres forestiers, nous examinons les effets attendus de pratiques forestières actuelles ou innovantes sur ces mécanismes Pour illustrer la complexité des mécanismes en interaction, nous développons plus en détail les conséquences évolutives des interactions biotiques et celles d’un environnement fortement hétérogène La sylviculture par et pour l’évolution peut contribuer à l’adaptation des forêts au changement climatique Elle nécessite de combiner des objectifs à court et à long terme Nous proposons des pistes de recherche et d’expérimentation pour accompagner cette démarche.
Published: 2020
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16. Marginal/peripheral populations of forest tree species and their conservation status: report for Atlantic region

Author: Colin T. Kelleher, Brigitte Musch, and Bruno Fady
Subjects: Forest genetic resources, forest tree marginal populations, MaPs, marginality, Cost Action FP 1202 MaP FGR, Agriculture
Abstract: This report is a synthesis of information from the national reports, prepared as part of the COST Action FP1202 Strengthening conservation: a key issue for adaptation of marginal/peripheral populations of forest trees to climate change in Europe (MaPFGR). The individual national reports can be found as part of the supplemental data to the COST action. The data compiled in this report indicate that the Atlantic area has sufficient resources in terms of knowledge and capacity to assess the potential impact of climate change on marginal and peripheral (MaP) sites within the area. Maps of vegetation, soil, climate and climatic predictions are publicly available for most countries and often are of high quality and resolution. These can be utilized to help identify MaP sites and populations in the Atlantic area. In addition, some species have been characterized genetically and the genetic data can also be utilized to identify and characterize sites. However, genetic data is not universally available and in particular may be absent for peripheral sites. There are many data sources for phenotypic traits, such as data from provenance trials but these have not been assessed for MaP populations. There may not be sufficient legislative capacity for the conservation of MaP populations in comparison to, for example, annex habitats of the EU Habitats Directive. Although some of the MaP sites lie within Natura 2000 boundaries, many are not in protected areas. If MaP populations are not characterized and conserved there is a risk of losing traits that may be of potential in adaptation to climate change. A detailed spatial analysis incorporating all of the data is needed to give a comprehensive assessment of the potential threats to MaP populations in this area.
Published: 2018
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17. Author Correction: WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees

Author: Anne-Christine Monnet, Kévin Cilleros, Frédéric Médail, Marwan Cheikh Albassatneh, Juan Arroyo, Gianluigi Bacchetta, Francesca Bagnoli, Zoltán Barina, Manuel Cartereau, Nicolas Casajus, Panayotis Dimopoulos, Gianniantonio Domina, Aggeliki Doxa, Marcial Escudero, Bruno Fady, Arndt Hampe, Vlado Matevski, Stephen Misfud, Toni Nikolic, Daniel Pavon, Anne Roig, Estefania Santos Barea, Ilaria Spanu, Arne Strid, Giovanni Giuseppe Vendramin, and Agathe Leriche
Subjects: Science
Published: 2021
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18. Using socioeconomic system analysis to define scientific needs: a reverse engineering method applied to the conversion of a coal-fired to a wood biomass power plant

Author: Hendrik Davi, Laetitia Tuffery, Emmanuel Garbolino, Bernard Prévosto, and Bruno Fady
Subjects: forest, interdisciplinary, model, reverse-engineering, wood energy, Biology (General), QH301-705.5, Ecology, QH540-549.5
Abstract: One of the greatest challenges when addressing issues in complex social-ecological systems (SES), is the need for an efficient interdisciplinary framework when large-magnitude social and ecological disturbances occur. Teams comprising of scientists from different backgrounds and disciplines are frequently called upon to propose research methods and results that can be useful for policy and decision makers. However, most of the outcomes from these pluri-disciplinary teams appear extremely difficult to implement within a bigger picture because concepts, hypotheses, methods, and results are specific to each discipline. Here, we propose a reverse-engineering (RE) method to define the scientific needs that could help policy makers and citizens to assess the impacts of socioeconomic "disruptors" on social-ecological systems. We present this method using the example of an ongoing wood biomass energy plant (Gardanne) in the French Mediterranean region. In the Mediterranean region, species diversity is high, the forest cover is ample, but difficult access and low forest productivity make any biomass policy an ecological and social disruption. Our method is based on three complementary approaches to (1) describe the social-ecosystems, (2) draw up a map of interactions between actors and the impacts on the ecosystem, and (3) identify relevant questions needed for a global analysis of the impacts and potentialities of adaptation of actors and the ecosystems to the perturbation and the connections needed between the different disciplines. Our analysis showed that knowledge gaps have to be filled to assess forest resource vulnerability and better estimate how the different resource used (solid wood, biomass, landscape) competed together. Finally, we discuss how this method could be integrated into a broader transdisciplinary work allowing a coproduction of knowledge and solutions on a SES.
Published: 2020
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19. Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe.

Author: Louise Brousseau, Dragos Postolache, Martin Lascoux, Andreas D Drouzas, Thomas Källman, Cristina Leonarduzzi, Sascha Liepelt, Andrea Piotti, Flaviu Popescu, Anna M Roschanski, Peter Zhelev, Bruno Fady, and Giovanni Giuseppe Vendramin
Subjects: Medicine, Science
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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20. Genetic structure and diversity of the endangered fir tree of Lebanon (Abies cilicica Carr.): implications for conservation.

Author: Lara Awad, Bruno Fady, Carla Khater, Anne Roig, and Rachid Cheddadi
Subjects: Medicine, Science
Abstract: The threatened conifer Abies cilicica currently persists in Lebanon in geographically isolated forest patches. The impact of demographic and evolutionary processes on population genetic diversity and structure were assessed using 10 nuclear microsatellite loci. All remnant 15 local populations revealed a low genetic variation but a high recent effective population size. FST -based measures of population genetic differentiation revealed a low spatial genetic structure, but Bayesian analysis of population structure identified a significant Northeast-Southwest population structure. Populations showed significant but weak isolation-by-distance, indicating non-equilibrium conditions between dispersal and genetic drift. Bayesian assignment tests detected an asymmetric Northeast-Southwest migration involving some long-distance dispersal events. We suggest that the persistence and Northeast-Southwest geographic structure of Abies cilicica in Lebanon is the result of at least two demographic processes during its recent evolutionary history: (1) recent migration to currently marginal populations and (2) local persistence through altitudinal shifts along a mountainous topography. These results might help us better understand the mechanisms involved in the species response to expected climate change.
Published: 2014
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21. Surviving in mountain climate refugia: new insights from the genetic diversity and structure of the relict shrub Myrtus nivellei (Myrtaceae) in the Sahara Desert.

Author: Jérémy Migliore, Alex Baumel, Marianick Juin, Bruno Fady, Anne Roig, Nathalie Duong, and Frédéric Médail
Subjects: Medicine, Science
Abstract: The identification of past glacial refugia has become a key topic for conservation under environmental change, since they contribute importantly to shaping current patterns of biodiversity. However, little attention has been paid so far to interglacial refugia despite their key role for the survival of relict species currently occurring in climate refugia. Here, we focus on the genetic consequences of range contraction on the relict populations of the evergreen shrub Myrtus nivellei, endemic in the Saharan mountains since at least the end of the last Green Sahara period, around 5.5 ka B.P. Multilocus genotypes (nuclear microsatellites and AFLP) were obtained from 215 individuals collected from 23 wadis (temporary rivers) in the three main mountain ranges in southern Algeria (the Hoggar, Tassili n'Ajjer and Tassili n'Immidir ranges). Identical genotypes were found in several plants growing far apart within the same wadis, a pattern taken as evidence of clonality. Multivariate analyses and Bayesian clustering revealed that genetic diversity was mainly structured among the mountain ranges, while low isolation by distance was observed within each mountain range. The range contraction induced by the last episode of aridification has likely increased the genetic isolation of the populations of M. nivellei, without greatly affecting the genetic diversity of the species as a whole. The pattern of genetic diversity observed here suggests that high connectivity may have prevailed during humid periods, which is consistent with recent paleoenvironmental reconstructions.
Published: 2013
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22. Annotation and Re-Sequencing of Genes from De Novo Transcriptome Assembly of Abies alba (Pinaceae)

Author: Anna M. Roschanski, Bruno Fady, Birgit Ziegenhagen, and Sascha Liepelt
Subjects: Abies alba, adaptation, annotation, candidate genes, de novo sequencing, Pinaceae, Biology (General), QH301-705.5, Botany, QK1-989
Abstract: Premise of the study: We present a protocol for the annotation of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer Abies alba. Methods and Results: A normalized cDNA library was built from an A. alba seedling. The sequencing on a 454 platform yielded more than 1.5 million reads that were de novo assembled into 25 149 contigs. Two complementary approaches were applied to annotate gene fragments that code for (1) well-known proteins and (2) proteins that are potentially adaptively relevant. Primer development and testing yielded 88 amplicons that could successfully be resequenced from genomic DNA. Conclusions: The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data. The primer set presented should be prioritized for single-nucleotide polymorphism detection in adaptively relevant genes in A. alba.
Published: 2013
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23. Common microgeographical selection patterns revealed in four European conifers

Author: Ivan Scotti, Hadrien Lalagüe, Sylvie Oddou‐Muratorio, Caroline Scotti‐Saintagne, Rose Ruiz Daniels, Delphine Grivet, François Lefevre, Philippe Cubry, Bruno Fady, Santiago C. González‐Martínez, Anne Roig, Isabelle Lesur‐Kupin, Francesca Bagnoli, Vanina Guerin, Christophe Plomion, Philippe Rozenberg, Giovanni G. Vendramin, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Edinburgh, Instituto Nacional de Investigación Agropecuaria (INIA), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), CREAF - Centre for Ecological Research and Applied Forestries, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Ministere de l'Ecologie, du Developpement Durable et de l'Energie10-MCGOT-GICC-8-CVS-139, ANR-12-ADAP-0007,FLAG,Génétique écologique des arbres forestiers : interactions entre flux de gènes et variabilité environnementale dans la détermination de l'adaptation locale et du potentiel d'adaptation(2012), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Agence Nationale de la Recherche (France), European Commission, Ministère de l'Écologie, du Développement durable et de l'Énergie (France), Scotti, Ivan, Oddou-Muratorio, Sylvie, Scotti-Saintagne, Caroline, Ruiz Daniels, Rose, Grivet, Delphine, Lefevre, François, Cubry, Philippe {0000-0003-1561-8949], Fady, Bruno, Lesur-Kupin, Isabelle, Bagnoli, Francesca {0000-0001-6909-0006], Plomion, Christophe, Rozenberg, Philippe, Vendramin, Giovanni G., and Hadrien Lalagüe
Subjects: forests, adaptive divergence, plants, [SDE]Environmental Sciences, Genetics, natural selection, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Ecology, Evolution, Behavior and Systematics, local adaptation
Abstract: 19 Pág., Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions., Agence Nationale de la Recherche, Grant/ Award Number: FLAG project (ANR-12- ADAP-0007-01); European Commission, Grant/Award Number: TOPWOOD project (MSCA-RISE-2014-645654- TOPWOOD) and grant agreement No. 676876 (GenTree); Ministère de l'Écologie, du Développement Durable et de l'Énergie, Grant/Award Number: GRAAL project (10-MCGOT-GICC-8-CVS-139)
Published: 2023
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24. Impact of a Change of Support on the Assessment of Biodiversity with Shannon Entropy.

Author: Didier Josselin, Ilène Mahfoud, and Bruno Fady
Published: 2008
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25. From genetic gain to economic gain: simulated growth and financial performance of genetically improved Pinus sylvestris and Pinus pinaster planted stands in France, Finland and Sweden

Author: Anssi Ahtikoski, Céline Meredieu, Thomas Perot, Bruno Fady, Annie Raffin, Sandrine Perret, Johan Sonesson, Christophe Orazio, Hernán Serrano-León, Marcus Lindner, European Forest Institute (EFI), EFI Planted Forests Facility, Partenaires INRAE, Natural Resources Institute Finland (LUKE), The Forestry Research Institute of Sweden, Skogforsk Uppsala Science Park, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale Forêt Pierroton (UEFP), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecosystèmes forestiers (UR EFNO), Institut Européen de la Forêt Cultivée, European Union's Horizon 2020 research and innovation programme (no. 676876 as part of the project GenTree, no 773383 as part of the project B4EST), he French Ministry of Agriculture and the Nouvelle Aquitaine region for the European Forest Institute, Planted Forest Facility., European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), and European Project: 773383,CORDIS
Subjects: 040101 forestry, Financial performance, 010504 meteorology & atmospheric sciences, biology, Economic gain, Pinus sylvestris, Pinus pinaster, Forestry, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, 01 natural sciences, Europe, %22">Pinus , Geography, Genetic gain, [SDE]Environmental Sciences, 0401 agriculture, forestry, and fisheries, Forest, 0105 earth and related environmental sciences
Abstract: A correction of this article has been published in: Forestry: An International Journal of Forest Research, Volume 94, Issue 3, July 2021, Page 477, https://doi.org/10.1093/forestry/cpab015; International audience; The translation of genetic gains into economic gains is important for evaluating the impact of using genetically improved forest reproductive material (FRM) in the forest sector. However, fewstudies based on European forests have been published to date. Here, we analyse the stand-level wood production and financial performance of planting genetically improved FRM in even-aged planted forests focusing on four European case studies with advanced breeding programme material and different management contexts: Scots pine (Pinus sylvestris L.) in southern Finland, central Sweden and central France, and maritime pine (Pinus pinaster Ait.) in southwestern France. The growth of improved stands was simulated using species-specific growth models by incorporating two levels of expected genetic gains (present and next generations of seed orchards, varying from 7 to 40 per cent depending on the breeding programme) into the estimated mean annual volume increment over a rotation (m3 ha(-1) yr(-1)). For each level of genetic gain, we tested the plantation of improved FRM managed with two silvicultural scenarios (maintaining the standard baseline rotation and thinning regime vs shorter rotation through the earlier achievement of the recommended felling criteria) in comparison with the plantation of the reference unimproved material (absence of genetic gain) managed according to the standard silvicultural regime. The use of improved FRM resulted in a larger financial performance in terms of soil expectation value (SEV (sic) ha(-1), discount rate 3 per cent) than planting unimproved reference material in all case studies and silvicultural scenarios for different wood price contexts (SEV gain from +20 to +190 per cent depending on the genetic and silvicultural context). The challenges associated with the economic assessment of realized gains fromgenetically improved FRM are discussed. We argue that silvicultural guidelines should be adapted to the use of improved FRM in order to gain better financial performance and flexible silvicultural response of planted forests to future environmental and socio-economic changes.
Published: 2021
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26. 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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27. Quelles gestions des forêts pour demain ?

Author: Catherine Bastien, Thierry Caquet, Sarah-Louise Filleux, Catherine Foucaud-Scheunemann, Damien Bonal, Thomas Cordonnier, Christophe Plomion, Bruno Fady, Meriem Fournier, Erwin Dreyer, P, Wigneron J., Sylvain Delzon, Clement Stahl, Arnaud Sergent, Cochard, Hervé H., Oliver Brendel, Cyrille Rathgeber, Catherine Massonnet, Nicolas Bilot, Département écologie et biodiversité des milieux forestiers, prairiaux et aquatiques (ECODIV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction de la communication (DirCom), SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des Forêts Méditerranéennes (URFM), Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environnement, territoires en transition, infrastructures, sociétés (UR ETTIS), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: National audience; Production de bois, espace de loisirs, puits de carbone…Les forêts offrent de multiples services essentiels aux humains et à la Terre. Face à des aléas météorologiques qui s’intensifient avec le réchauffement climatique et des changements globaux menaçants (commerce international, déforestation), certains massifs dépérissent à un rythme inquiétant et nous invite à revoir la façon de gérer les forêts.
Published: 2022
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28. Modelling of spatial dynamics and biodiversity conservation on Lure mountain (France).

Author: Brice Anselme, François Bousquet, Arnaud Lyet, Michel Etienne, Bruno Fady, and Christophe Le Page
Published: 2010
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29. Forest Genetics Research in the Mediterranean Basin: Bibliometric Analysis, Knowledge Gaps, and Perspectives

Author: Bruno Fady, Edoardo Esposito, Khaled Abulaila, Jelena M. Aleksic, Ricardo Alia, Paraskevi Alizoti, Ecaterina-Nicoleta Apostol, Phil Aravanopoulos, Dalibor Ballian, Magda Bou Dagher Kharrat, Isabel Carrasquinho, Marwan Cheikh Albassatneh, Alexandru-Lucian Curtu, Rakefet David-Schwartz, Giovanbattista de Dato, Bouchra Douaihy, Nicolas-George Homer Eliades, Louis Fresta, Semir Bechir Suheil Gaouar, Malika Hachi Illoul, Vladan Ivetic, Mladen Ivankovic, Gaye Kandemir, Abdelhamid Khaldi, Mohamed Larbi Khouja, Hojka Kraigher, François Lefèvre, Ilène Mahfoud, Maurizio Marchi, Felipe Pérez Martín, Nicolas Picard, Maurizio Sabatti, Hassan Sbay, Caroline Scotti-Saintagne, Darrin T Stevens, Giovanni Giuseppe Vendramin, Barbara Vinceti, Marjana Westergren, European Commission, Fady, Bruno [0000-0003-2379-7617], Esposito, Edoardo [0000-0003-2414-6488], Abulaila, Khaled [0000-0001-6746-4342], Aleksic, Jelena M. [0000-0003-3457-905X], Alia, Ricardo [0000-0002-9426-0967], Alizoti, Paraskevi [0000-0002-5656-8434], Apostol, Ecaterina Nicoleta [0000-0001-6190-3869], Aravanopoulos, Phil [0000-0001-7194-2642], Ballian, Dalibor [0000-0002-0090-6617], Kharrat, Magda Bou Dagher [0000-0001-7969-1673], Carrasquinho, Isabel [0000-0003-1331-3236], Albassatneh, Marwan Cheikh [0000-0002-1466-8672], Curtu, Alexandru Lucian [0000-0001-8509-279X], David-Schwartz, Rakefet [0000-0001-5923-8636], de Dato, Giovanbattista [0000-0003-0289-1727], Douaihy, Bouchra [0000-0001-7600-3409], Eliades, Nicolas George Homer [0000-0002-8107-8584], Fresta, Louis [0000-0001-8645-7359], Gaouar, Semir Bechir Suheil [0000-0001-8691-7116], Ivetic, Vladan [0000-0003-0587-1422], Ivankovic, Mladen [0000-0003-1198-9902], Kandemir, Gaye [0000-0002-4503-5317], Khaldi, Abdelhamid [0000-0002-3258-8860], Kraigher, Hojka [0000-0001-5696-2178], Lefèvre, François [0000-0003-2242-7251], Mahfoud, Ilène [0000-0003-3900-5581], Marchi, Maurizio [0000-0002-6134-1744], Picard, Nicolas [0000-0001-5548-9171], Sabatti, Maurizio [0000-0001-7576-2112], Sbay, Hassan [0000-0002-2531-7982], Scotti-Saintagne, Caroline [0000-0001-6891-7315], Vendramin, Giovanni Giuseppe [0000-0001-9921-7872], Vinceti, Barbara [0000-0001-8908-2994], Westergren, Marjana [0000-0002-4204-0161], Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Identité Culturelle, Textes et Théâtralité (ICTT), Avignon Université (AU), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Aristotle University of Thessaloniki, Faculty of Forestry, University of Sarajevo, Université Saint-Joseph de Beyrouth (USJ), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Institute of Plant Sciences, Volcani Center, Institute of Plant Science, Frederick University, Univerité de Tlemcen, Groupement d'Interêt Public Ecosystèmes Forestiers GIP ECOFOR (GIP ECOFOR ), European Project: 1025645(2010), European Project: FP1202 ,COST Action MaP-FGR, 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, Ivetic, Vladan, Ivankovic, Mladen, Kandemir, Gaye, Khaldi, Abdelhamid, Kraigher, Hojka, Lefèvre, François, Mahfoud, Ilène, Marchi, Maurizio, Picard, Nicolas, Sabatti, Maurizio, Sbay, Hassan, Scotti-Saintagne, Caroline, Vendramin, Giovanni Giuseppe, Vinceti, Barbara, and Westergren, Marjana
Subjects: Ecology, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Forest genetic resources, Forestry, Conservation, Sustainable management, Mediterranean, Global change, Ecology, Evolution, Behavior and Systematics, Genetic diversity, Nature and Landscape Conservation
Abstract: 22 Pág. Centro de Investigación Forestal (CIFOR), Purpose of Review: Recognizing that in the context of global change, tree genetic diversity represents a crucial resource for future forest adaptation, we review and highlight the major forest genetics research achievements of the past decades in biodiversity-rich countries of the Mediterranean region. For this, we conducted a bibliometric analysis of the scientific literature spanning the past thirty years (1991–2020). Putting together the representative regionwide expertise of our co-authorship, we propose research perspectives for the next decade. Recent Findings: Forest genetics research in Mediterranean countries is organized into three different scientific domains of unequal importance. The domain “Population diversity and Differentiation” related to over 62% of all publications of the period, the domain “Environmental conditions, growth and stress response” to almost 23%, and the domain “Phylogeography” to almost 15%. Citation rate was trending the opposite way, indicating a strong and sustained interest in phylogeography and a rising interest for genetics research related to climate change and drought resistance. The share of publications from Asia and Africa to the total within the Mediterranean increased significantly during the 30-year period analyzed, reaching just below 30% during the last decade. Summary: Describing poorly known species and populations, including marginal populations, using the full potential of genomic methods, testing adaptation in common gardens, and modeling adaptive capacity to build reliable scenarios for forest management remain strategic research priorities. Delineating areas of high and low genetic diversity, for conservation and restoration, respectively, is needed. Joining forces between forest management and forest research, sharing data, experience, and knowledge within and among countries will have to progress significantly, e.g., to assess the potential of Mediterranean genetic resources as assisted migration material worldwide. Introductory quote:: Let us collect with care the facts we can observe, let us consult experience wherever we can, and when this experience is inaccessible to us, let us assemble all the inductions which observation of facts analogous to those which escape us can furnish and let us assert nothing categorically; in this way, we shall be able little by little to discover the causes of a multitude of natural phenomena, and, perhaps, even of phenomena which seem the most incomprehensible.. J.B. de Lamarck (Philosophie zoologique, 1809), cited by O. Langlet (1971)., European Union’s Horizon 2020 research and innovation program under grant agreement No. 676876 COST Action FP1202 “Strengthening conservation: a key issue for adaptation of marginal/peripheral populations of forest trees to climate change in Europe (MaP-FGR)
Published: 2022
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30. Correction to: Forest Genetics Research in the Mediterranean Basin: Bibliometric Analysis, Knowledge Gaps, and Perspectives

Author: Bruno Fady, Edoardo Esposito, Khaled Abulaila, Jelena M. Aleksic, Ricardo Alia, Paraskevi Alizoti, Ecaterina-Nicoleta Apostol, Phil Aravanopoulos, Dalibor Ballian, Magda Bou Dagher Kharrat, Isabel Carrasquinho, Marwan Cheikh Albassatneh, Alexandru-Lucian Curtu, Rakefet David-Schwartz, Giovanbattista de Dato, Bouchra Douaihy, Nicolas-George Homer Eliades, Louis Fresta, Semir Bechir Suheil Gaouar, Malika Hachi Illoul, Vladan Ivetic, Mladen Ivankovic, Gaye Kandemir, Abdelhamid Khaldi, Mohamed Larbi Khouja, Hojka Kraigher, François Lefèvre, Ilène Mahfoud, Maurizio Marchi, Felipe Pérez Martín, Nicolas Picard, Maurizio Sabatti, Hassan Sbay, Caroline Scotti-Saintagne, Darrin T. Stevens, Giovanni Giuseppe Vendramin, Barbara Vinceti, and Marjana Westergren
Subjects: Ecology, Forestry, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Published: 2022
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31. Sensibilité des indices de diversité à l'agrégation.

Author: Ilène Mahfoud, Didier Josselin, and Bruno Fady
Published: 2007
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32. Author Correction: WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees

Author: Arne Strid, Gianluigi Bacchetta, Estefania Santos Barea, Panayotis Dimopoulos, Nicolas Casajus, Anne-Christine Monnet, Zoltán Barina, Juan Arroyo, Manuel Cartereau, Toni Nikolić, Kévin Cilleros, Giovanni G. Vendramin, Arndt Hampe, Stephen Misfud, Daniel Pavon, Francesca Bagnoli, Gianniantonio Domina, Aggeliki Doxa, Marwan Cheikh Albassatneh, Bruno Fady, Frédéric Médail, Anne Roig, Vlado Matevski, Ilaria Spanu, Marcial Escudero, Agathe Leriche, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Musée National d'Histoire Naturelle de Luxembourg (MNHN), Department of Plant Biology and Ecology, University of Seville, Istituto Nazionale di Fisica Nucleare, Sezione di Cagliari (INFN, Sezione di Cagliari), Istituto Nazionale di Fisica Nucleare (INFN), University of Fiorentino, Hungarian Natural History Museum (Magyar Természettudományi Múzeum), Centre de Synthèse et d’Analyse sur la Biodiversité (CESAB), Fondation pour la recherche sur la Biodiversité (FRB), University of Patras, School of Medicine, Università degli studi di Palermo - University of Palermo, University of Sevilla, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Macedonian Academy of Sciences and Arts [Skopje, North Macedonia] (MASA), EcoGozo, Regional Development Directorate - Ministry for Gozo, Faculty of Textile Technology, Department of Applied Chemistry, University of Zagreb, University of Zagreb, Bakkevej 6, 5853, Ørbæk, Denmark, University of Seville, IFAC SESTO FIORENTINO ITA, Partenaires IRSTEA, and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)
Subjects: Statistics and Probability, Mediterranean climate, Databases, Factual, 010504 meteorology & atmospheric sciences, Science, MEDLINE, Forests, Library and Information Sciences, 01 natural sciences, Trees, Education, 03 medical and health sciences, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Community ecology, Author Correction, Ecosystem, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, Phylogenetic tree, Conservation biology, Mediterranean Region, Published Erratum, Biodiversity, Computer Science Applications, Geography, Biogeography, Forest ecology, Statistics, Probability and Uncertainty, Cartography, Information Systems
Abstract: Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.
Published: 2021
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33. Caution needed with the EU forest plantation strategy for offsetting carbon emissions

Author: Bruno Fady, Julien Ruffault, Nicolas Martin-StPaul, Hendrik Davi, Ecologie des Forêts Méditerranéennes (URFM), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Mitigation, [SDV]Life Sciences [q-bio], Tree planting, 01 natural sciences, Genetic diversity, Adaptation, Seed market, Plantation, 2. Zero hunger, Agroforestry, Forest plantation, Sowing, Forestry, 04 agricultural and veterinary sciences, 15. Life on land, Forest nursery market, Tree (data structure), Geography, Habitat, 13. Climate action, Greenhouse gas, 040103 agronomy & agriculture, Carbon footprint, 0401 agriculture, forestry, and fisheries, 010606 plant biology & botany
Abstract: International audience; As part of the 2015 Paris climate agreement and under its Green Deal, the EU proposes to strongly rely on forests for offsetting its carbon footprint. However, planting trees should be avoided in wildfire prone and drought prone habitats, which are expanding significantly as climate warms across Europe. In favorable habitats, tree planting remains a controversial solution and the risk of using inappropriate material is high in the absence of long-term planning, unfortunately typical of the forest seed and nursery sector. The EU forest tree planting strategy should pay close attention to local land-use issues, to within- and among-species genetic diversity and should adopt relevant, pluri-annual funding schemes and planting contracts rather than letting market opportunities govern the future of forest tree plantations.
Published: 2021
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34. What is a tree in the Mediterranean Basin hotspot? A critical analysis

Author: Panayotis Dimopoulos, Gianluigi Bacchetta, Zoltán Barina, Juan Arroyo, Vlado Matevski, Gianniantonio Domina, Anne-Christine Monnet, Frédéric Médail, Daniel Pavon, Bruno Fady, Toni Nikolić, Marwan Cheikh Albassatneh, Stephen Mifsud, Agathe Leriche, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Faculty of Science [Zagreb], University of Zagreb, University of Patras, Università degli Studi di Cagliari = University of Cagliari (UniCa), Dept. de Biologia Vegetal y Ecologia, Universidad de Sevilla / University of Sevilla, Department of Botany, Hungarian Natural History Museum (Magyar Természettudományi Múzeum), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Palermo - University of Palermo, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Macedonian Academy of Sciences and Arts [Skopje, North Macedonia] (MASA), EcoGozo, Regional Development Directorate - Ministry for Gozo, ANR-11-LABX-0061, ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Department of Biology, Division of Plant Biology, Laboratory of Botany, University of Patras, Centro Conservazione Biodiversità, Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, University of Sevilla, Department of Agriculture, Food and Forest Sciences, University of Palermo, Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Faculty of Science, University of Zagreb, Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Macedonian Academy of Sciences and Arts, ANR-11-IDEX-0001-02/11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Médail, Frédéric, Monnet, Anne-Christine, Pavon, Daniel, Nikolic, Toni, Dimopoulos, Panayoti, Bacchetta, Gianluigi, Arroyo, Juan, Barina, Zoltán, Albassatneh, Marwan Cheikh, Domina, Gianniantonio, Fady, Bruno, Matevski, Vlado, Mifsud, Stephen, Leriche, Agathe, and University of Patras [Patras]
Subjects: Tree distributions, 010504 meteorology & atmospheric sciences, Plant biogeography, Mediterranean region, Threatened trees, Tree definition, Tree distributions, Biodiversity, Threatened tree, Functional diversity, Plant biogeography, 01 natural sciences, Mediterranean Basin, bassin méditerranéen, biogeographie historique, Trait values, Mediterranean region, Threatened trees, Tree definition, lcsh:QH540-549.5, IUCN Red List, Endemism, Milieux et Changements globaux, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Nature and Landscape Conservation, écosystème forestier, taxon, Near-threatened species, Ecology, Tree distribution, Forestry, 04 agricultural and veterinary sciences, 15. Life on land, système vasculaire des plantes, Traits, Ecology, Evolution, Behavior and Systematic, Biodiversity hotspot, Geography, Threatened species, Settore BIO/03 - Botanica Ambientale E Applicata, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Species richness, lcsh:Ecology
Abstract: Background: Tree species represent 20% of the vascular plant species worldwide and they play a crucial role in the global functioning of the biosphere. The Mediterranean Basin is one of the 36 world biodiversity hotspots, and it is estimated that forests covered 82% of the landscape before the first human impacts, thousands of years ago. However, the spatial distribution of the Mediterranean biodiversity is still imperfectly known, and a focus on tree species constitutes a key issue for understanding forest functioning and develop conservation strategies. Methods: We provide the first comprehensive checklist of all native tree taxa (species and subspecies) present in the Mediterranean-European region (from Portugal to Cyprus). We identified some cases of woody species difficult to categorize as trees that we further called “cryptic trees”. We collected the occurrences of tree taxa by “administrative regions”, i.e. country or large island, and by biogeographical provinces. We studied the species-area relationship, and evaluated the conservation issues for threatened taxa following IUCN criteria. Results: We identified 245 tree taxa that included 210 species and 35 subspecies, belonging to 33 families and 64 genera. It included 46 endemic tree taxa (30 species and 16 subspecies), mainly distributed within a single biogeographical unit. The countries with the highest tree richness are Greece (146 taxa), Italy (133), Albania (122), Spain (155), Macedonia (116), and Croatia (110). The species-area relationship clearly discriminated the richest central-eastern (Balkans) and northern (Alpine and Cevenno-Pyrenean) biogeographical provinces, against the five western provinces in the Iberian Peninsula. We identified 44 unrecognized “cryptic trees”, representing 21% of the total trees. Among the 245 taxa identified, 19 are considered to be threatened (15 CR + EN + VU) or near threatened (4 NT) by IUCN. Conclusions: The Mediterranean-European region includes an unsuspectedly high number of tree taxa, almost 200 tree taxa more than in the central European region. This tree diversity is not distributed evenly and culminates in the central-eastern part of the Mediterranean region, whereas some large Tyrrhenian islands shelter several narrow endemic tree taxa. Few taxa are recognized as threatened in the IUCN Red list, and the vulnerability of these species is probably underestimated. French Foundation for Research on Biodiversity (FRB). Centre for Synthesis and Analysis of Biodiversity data ANR-11-LABX-0061
Published: 2019
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35. Effective population size does not make a practical indicator of genetic diversity in forest trees

Author: Michele Bozzano, Bruno Fady, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and European Forest Institute (EFI)
Subjects: 0106 biological sciences, 0303 health sciences, Genetic diversity, Ecology, [SDV]Life Sciences [q-bio], Conservation, 15. Life on land, Biology, Forest trees, 010603 evolutionary biology, 01 natural sciences, Europe, 03 medical and health sciences, Effective population size, Indicator, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Nature and Landscape Conservation
Abstract: International audience
Published: 2021
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36. Spatial patterns of genus-level phylogenetic endemism in the tree flora of Mediterranean Europe

Author: Anne-Christine Monnet, Francesca Bagnoli, Arndt Hampe, Frédéric Médail, Panayotis Dimopoulos, Giovanni G. Vendramin, Toni Nikolić, Gianni Baccheta, Agathe Leriche, Marwan Cheikh Albassatneh, Bruno Fady, Juan Arroyo, Loic Ponger, Marcial Escudero, Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Aix-Marseille University, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology and Ecology, University of Seville, Università degli Studi di Cagliari = University of Cagliari (UniCa), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), University of Patras [Patras], Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Division of Botany [Zagreb], Department of Biology [Zagreb], Faculty of Science [Zagreb], University of Zagreb-University of Zagreb-Faculty of Science [Zagreb], University of Zagreb-University of Zagreb, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Life and Environmental Sciences, Botany Division, University of Cagliari, Cagliari, Italy, Department of Biology, Laboratory of Botany, University of Patras, Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), and University of Patras
Subjects: 0106 biological sciences, Mediterranean climate, Nonmetric Multidimensional Scaling, Biodiversity, Context (language use), Conservation, Relative environmental turnover, 010603 evolutionary biology, 01 natural sciences, Mediterranean Basin, Phylogenetic diversity, relative environmental turnover, phylogenetic endemism, Phylogenetic endemism, Endemism, Ecology, Evolution, Behavior and Systematics, Phylogenetic tree, Ecology, 010604 marine biology & hydrobiology, conservation, Euro-Mediterranean vascular flora, 15. Life on land, Geography, 13. Climate action, [SDE]Environmental Sciences, Spatial ecology, phylogenetic diversity
Abstract: Aim: The Mediterranean Basin is a major hotspot of plant biodiversity, including forest trees. Over the past centuries, Mediterranean forests have been fragmented and over-exploited, to which the threats of climate change are now added. Our aim is to better understand patterns and processes of tree biodiversity in the Mediterranean and to provide indicators complementing the traditional approaches to biodiversity conservation based on species counts and occurrences, using georeferenced phylogenetic diversity and endemism analyses in a spatial ecological context. Location: Mediterranean Europe. Methods: Using a dated phylogeny of the 64 Euro-Mediterranean tree genera, we calculated phylogenetic diversity for all 50 × 50 km2 grid cells spanning Mediterranean Europe (n = 643) and compared values with those obtained for genus-level taxonomic diversity. Then, we tested the relative influence of geography, past and present climate, and soil on tree diversity (phylogenetic or taxonomic) and its geographical turnover. Geographical patterns of phylogenetic endemism were inferred using the Categorical Analyses of Neo- and Paleo-Endemism (CANAPE) methodology. Results: We showed that phylogenetic and taxonomic diversity within and among cells are correlated and influenced by soil parameters as well as current, Holocene and Late Glacial Maximum climate. Southern Spain, Cyprus and some Aegean islands contained areas of disproportionately high phylogenetic diversity and a concentration of phylogenetic paleo-endemics, while phylogenetic neo-endemism was high in eastern Sicily. Mixed phylogenetic endemism regions were detected in southern Spain and Portugal, in the Balkans and in Crete. Main conclusions: Our phylogenetic approach provides relevant indicators for better protecting forests of the Mediterranean, encompassing past and present evolutionary processes and factors. We consider areas that show a concentration of evolutionary history manifested by high phylogenetic endemism as high priority targets for the conservation of the European tree flora. Aix-Marseille University ANR-11-LABX-0061
Published: 2021
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37. Conservation and Breeding of Mediterranean Pines

Author: Isabel Rodríguez-Quilón, Yusuf Kurt, Bruno Fady, Ricardo Alía, Fulvio Ducci, José Climent, and Paraskevi Alizoti
Subjects: Mediterranean climate, Geography, business.industry, Range (biology), Environmental resource management, Forest management, Species distribution, Sustainability, Reforestation, National forest, business, Forest genetic resources
Abstract: Sustainable use of forest genetic resources in Mediterranean pines should consider different aspects such as the conservation of genetic resources, the actions derived from the breeding programs, and the transfer and use of forest reproductive material (FRM) in forestry. These three aspects should all be integrated into forest management at different spatial scales (from stand, to landscape to the entire species distribution range), and should also be integrated into different national and regional policies (biodiversity conservation, reforestation, national forest inventories, research), which should be based on the most precise information available to enable decision making. This chapter reviews the state of the art of the conservation and improvement of genetic resources in Mediterranean pines. Firstly, we analyze the different evolutionary factors affecting the conservation of genetic resources in Mediterranean pines, the threats to these genetic resources and the strategies and actions implemented for their conservation. We stress the lack of a general framework for the conservation of genetic resources, due to some limiting factors derived both from socio-economic differences of the countries, and from differences in the actual knowledge on the genetic resources of the different species. In the second step, we review the breeding activities for Mediterranean pines, their strategies and main achievements. Most of these activities are of low intensity, and should take advantage of breeding without breeding approaches to be cost-effective. We then analyze some aspects related to the transfer and use of FRM in these species, the basis for decision making and the implications for sustainable conservation and use of forest genetic resources.
Published: 2021
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38. Using socioeconomic system analysis to define scientific needs: a reverse engineering method applied to the conversion of a coal-fired to a wood biomass power plant

Author: Laetitia Tuffery, Bruno Fady, Hendrik Davi, Bernard Prévosto, Emmanuel Garbolino, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Economie de l'Environnement - Montpellier - UMR 5211 (CEE-M), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Climpact Data Science, Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work is a contribution to the Labex OT-Med (ANR-11-LABX-0061) and was funded by the Labex DRIIHM, Réseau des Observatoires Hommes - Milieux - Centre National de la Recherche Scientifique (ROHM-CNRS), ANR-11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011), Centre d'Economie de l'Environnement - Montpellier (CEE-M), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Resource (biology), QH301-705.5, Computer science, Vulnerability, 01 natural sciences, [SHS]Humanities and Social Sciences, 03 medical and health sciences, forest, 0302 clinical medicine, 11. Sustainability, Biology (General), Adaptation (computer science), Productivity, Social disruption, QH540-549.5, reverse-engineering, Biomass (ecology), model, Ecology, business.industry, Environmental resource management, 15. Life on land, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, wood energy, 010601 ecology, Coproduction, Work (electrical), 13. Climate action, interdisciplinary, business, 030217 neurology & neurosurgery
Abstract: International audience; One of the greatest challenges when addressing issues in complex social-ecological systems (SES), is the need for an efficient interdisciplinary framework when large-magnitude social and ecological disturbances occur. Teams comprising of scientists from different backgrounds and disciplines are frequently called upon to propose research methods and results that can be useful for policy and decision makers. However, most of the outcomes from these pluri-disciplinary teams appear extremely difficult to implement within a bigger picture because concepts, hypotheses, methods, and results are specific to each discipline. Here, we propose a reverse-engineering (RE) method to define the scientific needs that could help policy makers and citizens to assess the impacts of socioeconomic “disruptors” on social-ecological systems. We present this method using the example of an ongoing wood biomass energy plant (Gardanne) in the French Mediterranean region. In the Mediterranean region, species diversity is high, the forest cover is ample, but difficult access and low forest productivity make any biomass policy an ecological and social disruption. Our method is based on three complementary approaches to (1) describe the social-ecosystems, (2) draw up a map of interactions between actors and the impacts on the ecosystem, and (3) identify relevant questions needed for a global analysis of the impacts and potentialities of adaptation of actors and the ecosystems to the perturbation and the connections needed between the different disciplines. Our analysis showed that knowledge gaps have to be filled to assess forest resource vulnerability and better estimate how the different resource used (solid wood, biomass, landscape) competed together. Finally, we discuss how this method could be integrated into a broader transdisciplinary work allowing a coproduction of knowledge and solutions on a SES.
Published: 2020
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39. Genetics to the rescue: managing forests sustainably in a changing world

Author: Filippos A. Aravanopoulos, Barbara Vinceti, Marcus Lindner, Raquel Benavides, Fernando Valladares, Bruno Fady, Christian Rellstab, Santiago C. González-Martínez, Delphine Grivet, Martin Lascoux, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aristotle University of Thessaloniki, Spanish National Research Council [Madrid] (CSIC), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INIA MADRID ESPAGNE, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Uppsala Universitet [Uppsala], European Forest Institute (EFI), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance), and This publication is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 676876 (GenTree).
Subjects: 0106 biological sciences, phenotype, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Biodiversity, Climate change, policy, Horticulture, Biology, Diversification (marketing strategy), 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetics, Lagging, Molecular Biology, 030304 developmental biology, media_common, 0303 health sciences, Genetic diversity, Natural selection, Genomic diversity, conservation, Forestry, 15. Life on land, 13. Climate action, breeding, Sustainability, [SDE]Environmental Sciences, environment, Diversity (politics)
Abstract: International audience; There is growing concern that the implementation of political agreements on climate change and biodiversity will not be enough to protect forests in the short run and up to the end of the 21st century. As mitigation efforts are lagging behind self-imposed, reasonable targets, genetic diversity will have a large and significant part to play in the process of adapting forests to climate change. Genetic diversity, the raw material of evolution, can be used for adaptation by natural selection and artificial breeding, in naturally regenerated and plantation forests alike. The two-day scientific conference: “#rescueforests: Genetics to the rescue - Managing forests sustainably in a changing world”, addressed the genetic diversity of forests. More specifically, the conference was about natural as well as assisted adaptive processes, their spatial scale, from fine grain to landscape and ecoregions, and how much of the genome it involves. It also dealt with phenotypes and how much of their variation is determined by underlying genetic diversity. And finally, and perhaps most importantly, the conference emphasized the importance of conservation and sustainable use of this genetic diversity as a nature-based solution to adapt under the fast pace of climate change. The conference demonstrated how improved knowledge on genomic diversity and evolutionary mechanisms can help to rescue forests, either naturally or by means of management.
Published: 2020
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40. Adaptation to drought is coupled with slow growth, but independent from phenology in marginal silver fir ( Abies alba Mill.) populations

Author: Bruno Fady, Nina Buchmann, Katalin Csilléry, Universität Zürich [Zürich] = University of Zurich (UZH), Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Marie Sklodowska-Curie Individual Fellowship 705972
Subjects: 0106 biological sciences, 0301 basic medicine, demography, quantitative genetics, Population, Drought tolerance, lcsh:Evolution, drought tolerance, Growing season, Context (language use), Biology, Adaptive divergence, Assisted migration, Climate change, Demography, Phenology, Quantitative genetics, δ13C, 010603 evolutionary biology, 01 natural sciences, phenology, 03 medical and health sciences, Genetics, lcsh:QH359-425, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, assisted migration, Water-use efficiency, education, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Ecology, Evolution, Behavior and Systematics, education.field_of_study, adaptive divergence, Ecology, 15. Life on land, biology.organism_classification, Abies alba, 030104 developmental biology, climate change, 13. Climate action, delta C-13, Adaptation, General Agricultural and Biological Sciences
Abstract: Drought is one of the most important selection pressures for forest trees in the con-text of climate change. Yet, the different evolutionary mechanisms, and their envi-ronmental drivers, by which certain populations become more drought tolerant than others is still little understood. We studied adaptation to drought in 16 silver fir (Abies alba Mill.) populations from the French Mediterranean Alps by combining observa-tions on seedlings from a greenhouse experiment (N = 8,199) and on adult tress in situ (N = 315). In the greenhouse, we followed half-sib families for four growing seasons for growth and phenology traits, and tested their water stress response in a "drought until death" experiment. Adult trees in the field were assessed for δ13C, a proxy for water use efficiency, and genotyped at 357 SNP loci. SNP data was used to gen-erate a null expectation for seedling trait divergence between populations in order to detect the signature of selection, and 31 environmental variables were used to identify the selective environment. We found that seedlings originating from popula-tions with low soil water capacity grew more slowly, attained a smaller stature, and resisted water stress for a longer period of time in the greenhouse. Additionally, adult trees of these populations exhibited a higher water use efficiency as evidenced by their δ13C. These results suggest a correlated evolution of the growth-drought toler-ance trait complex. Population divergence in bud break phenology was adaptive only in the second growing season, and evolved independently from the growth-drought tolerance trait complex. Adaptive divergence in bud break phenology was principally driven by the inter- and intra-annual variation in temperature at the geographic origin of the population. Our results illustrate the different evolutionary strategies used by populations to cope with drought stress at the range limits across a highly heteroge-neous landscape, and can be used to inform assisted migration programs. ISSN:1752-4571 ISSN:1752-4563
Published: 2020
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41. The legacy of climate variability over the last century on populations' phenotypic variation in tree height

Author: Natalia Vizcaíno-Palomar, Sven Mutke, Bruno Fady, Ricardo Alía, Annie Raffin, Marta Benito Garzón, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Unité expérimentale Forêt Pierroton (UEFP), and ANR-10-IDEX-0003,IDEX BORDEAUX,Initiative d'excellence de l'Université de Bordeaux(2010)
Subjects: Environmental Engineering, 010504 meteorology & atmospheric sciences, Population level, Environmental change, Climate, Climate Change, Population, Climate change, Mixed-effect models, 010501 environmental sciences, Biology, Maritime pine, 01 natural sciences, Trees, Africa, Northern, Environmental Chemistry, Stone pine, education, Waste Management and Disposal, 0105 earth and related environmental sciences, Local adaptation, education.field_of_study, Genetic diversity, Phenotypic plasticity, Ecology, Developmental stage, Black pine, 15. Life on land, Pinus, Pollution, Europe, Biological Variation, Population, [SDE]Environmental Sciences, Trait
Abstract: International audience; Phenotypic plasticity and local adaptation are the two main processes underlying trait variability. Under rapid environmental change, phenotypic plasticity, if adaptive, could increase the odds for organisms to persist. However, little is known on how environmental variation has shaped plasticity across species ranges over time. Here, we assess whether the portion of phenotypic variation of tree populations linked to the environment is related to the interannual climate variability of the last century and how it varies among populations across species ranges and age. To this aim, we used 372,647 individual tree height measurements of three pine species found in low elevation forests in Europe: Pinus nigra Arnold, P. pinaster Aiton and P. pinea L Measurements were taken in a network of 38 common gardens established in Europe and North Africa with 315 populations covering the distribution range of the species. We fitted linear mixed-effect models of tree height as a function of age, population, climate and competition effects. Models allowed us to estimate tree height response curves at the population level and indexes of populations' phenotypic variation, as a proxy of phenotypic plasticity, at 4,8 and 16 years old, and relate these indexes to the interannual climate variability of the last century. We found that phenotypic variation in tree height was higher in young trees than in older ones. We also found that P pinea showed the highest phenotypic variation in tree height compared with P pinasfer anti P nigra. Finally, phenotypic variation in tree height may be partly adaptive, and differently across species, as climate variability during the last century at the origin of the populations explained between 51 and 69% of the current phenotypic variation of P. nigra and P. pinea, almost twice of the levels of P. pinaster. Main conclusions: Populations' phenotypic variation in tree height is largely explained by the climate variability that the populations experienced during the last century, which we attribute to the genetic diversity among populations.
Published: 2020
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42. 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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43. The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author: Marlène Lefebvre, Ermioni Malliarou, Silvia Matesanz, Benjamin Dauphin, Marc Villar, Giovanni G. Vendramin, Jean Thevenet, Guillaume Bodineau, Johan Westin, José Alberto Ramírez-Valiente, Katrin Heer, Juan J. Robledo-Arnuncio, Elisabet Martínez-Sancho, Mirko Liesebach, Olivier Gilg, Pascal Milesi, Dominique Veisse, Frédéric Bernier, Eduardo Notivol, Sonja T. Kujala, Cristina C. Bastias, Vincent Lejeune, Bruno Fady, Célia Michotey, Felix Gugerli, Annie Raffin, Claudio Grefen, José M. García del Barrio, Marianne Correard, Florian Knutzen, Norbert Turion, Tanja Pyhäjärvi, Tor Myking, Mariaceleste Labriola, Silvio Schueler, Camilla Avanzi, Bárbara Carvalho, Lenka Slámová, Christophe Plomion, Anna-Maria Farsakoglou, Fernando Valladares, Andrea Piotti, Evangelos Barbas, José Climent, Florence Courdier, Ilaria Spanu, Patrick Fonti, Jean-Paul Charpentier, Birte Pakull, Nicolas Mariotte, Ricardo Alía, Vladimir L. Semerikov, Sandro Morganti, Outi Savolainen, Stephen Cavers, Georg von Arx, Francesca Bagnoli, Arnaud Jouineau, Mari Mette Tollefsrud, Kurt Ramskogler, Catherine Bastien, Filippos A. Aravanopoulos, Katri Kärkkäinen, Grégoire Le-Provost, Christian Rellstab, Darius Danusevičius, Lars Opgenoorth, Martin Lascoux, Santiago C. González-Martínez, Christoph Hartleitner, Agathe Hurel, Raquel Benavides, Mehdi Pringarbe, Alan Gray, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Philipps University, 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), Centre for Ecology and Hydrology, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Aristotle University of Thessaloniki, Institute of the Science of Food Production. CNR., Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BioForA), Institut National de la Recherche Agronomique (INRA)-Office National des Forêts (ONF), Unité expérimentale Forêt Pierroton (UEFP), Génétique et Biomasse Forestières Orléans (GBFOR), Institut National de la Recherche Agronomique (INRA), Vytautas Magnus Univ, 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, University of Oulu, Uppsala University, Thünen Institute of Forest Genetics, Universidad Rey Juan Carlos [Madrid] (URJC), Norwegian Institute of Bioeconomy Research (NIBIO), Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), 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: Statistics and Probability, 010504 meteorology & atmospheric sciences, Skogsvetenskap, [SDV]Life Sciences [q-bio], Library and Information Sciences, tree-ring and wood density, 01 natural sciences, Black poplar, Ecology and Environment, Education, 03 medical and health sciences, Fagus sylvatica, Recursos genéticos forestales, lcsh:Science, Beech, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, biology, Forest Science, Scots pine, Botany, VDP::Landbruks- og Fiskerifag: 900::Landbruksfag: 910::Skogbruk: 915, Forestry, Picea abies, Botanik, 15. Life on land, biology.organism_classification, Bases de datos, Computer Science Applications, Geography, Betula pendula, Pinus pinaster, lcsh:Q, Quercus petraea, Forest ecology, Statistics, Probability and Uncertainty, Europa, 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 density Technology Type(s) measuring table • calculation Factor Type(s) tree species Sample Characteristic - Organism Betula pendula • Fagus sylvatica • Picea abies • Populus nigra • Pinus pinaster • Pinus sylvestris • Quercus petraea Sample Characteristic - Location Europe Published
Published: 2020
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44. Evolutionary relevance of lineages in the European black pine (Pinus nigra) in the transcriptomic era

Author: Sanna Olsson, Delphine Grivet, Caroline Scotti-Saintagne, Vera Vendramin, Guia Giovannelli, Bruno Fady, Federica Cattonaro, Giovanni G. Vendramin, INIA-CIFOR, Universidad de Valladolid [Valladolid] (UVa), IGA Technol Serv Srl, Via J Linussio 51, I-33100 Udine, Italy, Partenaires INRAE, IGA Technology Services (IGATS), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Research Council (CNR), INIA-MAPAMA EG17-048 1305/2013, PTA2015-10836-I, and European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDE.MCG]Environmental Sciences/Global Changes, SNP, Geographical population, European Black Pine, Orthologous gene, Horticulture, Subspecies, Biology, 01 natural sciences, Mediterranean Basin, Transcriptome, 03 medical and health sciences, Genetics, Evolutionary dynamics, Molecular Biology, Phylogeny, fungi, Forestry, 15. Life on land, biology.organism_classification, 030104 developmental biology, Habitat, Evolutionary biology, Taxonomy (biology), Nuclear genetic marker, 010606 plant biology & botany
Abstract: International audience; European black pine (Pinus nigra J.F.Arnold) is an ecologically and economically important conifer growing across southern Europe and the Mediterranean Basin in a variety of habitats. Its morphological and ecological variabilities as well as geographic origin are the basis for subspecies level taxonomic identification and forestry practice recommendations. Yet, no true consensus exists and genomic resources are lacking for resolving the taxonomy of P. nigra and assessing its adaptive potential. To provide genetic tools for further research, we generated novel genomic resources using six de novo transcriptomic assemblies representing major biogeographic regions where the species is growing naturally. Using two closely related species, Pinus sylvestris and Pinus halepensis, as outgroups, we identified a set of 2200 nuclear, putatively orthologous, single-copy genes. In addition, we identified a set of 405,624 polymorphic SNPs for P. nigra. Based on these resources, we were able to confirm the division of P. nigra into two wide geographical population groups and to provide new insights into evolutionary dynamics of the species.
Published: 2020
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45. Nutzung und Verstärkung der Mechanismen genetischer Evolution durch waldbauliches Handeln, im Hinblick auf eine Anpassung an den Klimawandel

Author: François Lefèvre, Thomas Boivin, Aurore Bontemps, Francois Courbet, Hendrik Davi, Marion Durand-Gillmann, Bruno Fady, Julie Gauzere, Cindy Gidoin, Marie-Joe Karam, Hadrien Lalagüe, Sylvie Oddou-Muratorio, Christian Pichot, Ecologie des Forêts Méditerranéennes (URFM), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDE]Environmental Sciences
Abstract: International audience; Adaptation is a major stake of forest management in the climate change context The genetic diversity of forest trees confers them a huge – yet not boundless – adaptive potential Taking evolutionary mechanisms into account in adaptive forest management practices will reinforce the capacity of managed forests to respond to climate-induced changes and hazards By laying the emphasis on forests under natural regeneration conditions,we propose a general conceptual framework that includes knowledge on these mechanisms in decision- making processes, in a silvicultural approach through and for evolution This general framework will encompass diverse and complex local situations by relying on knowledge of local contexts from forest managers. We developed a simple analysis grid based on a small number of parameters characterising evolutionary mechanisms to understand the impact of silvicultural practices on the genetic diversity dynamics and the maintenance of the evolutionary potential of forest tree populations After recalling the current state of knowledge on the evolutionary mechanisms of forest trees, we examined the expected effects of current or innovative silvicultural practices on these mechanisms To illustrate the complexity of these interacting mechanisms, we further studied the evolutionary consequences of biotic interactions and of interactions in a highly heterogeneous environment Silviculture through and for evolution can contribute to the adaptation of forests to climate change This will require combining short-term and long-term objectives We further propose lines ofresearch and experimentation to support this approach.; L’adaptation est un enjeu majeur de la gestion forestière dans le contexte du changement climatique La diversité génétique qui caractérise les arbres forestiers leur confère un potentiel adaptatif très important mais pas illimité Prendre en compte les mécanismes de l’évolution dans les pratiques de gestion forestière adaptative renforcera la capacité des forêts gérées à répondre aux changements et aux aléas induits par le climat. En mettant l’accent sur le cas des forêts en régénération naturelle, nous proposons un cadre conceptuel général permettant d’intégrer la connaissance de ces mécanismes dans la prise de décision, dans une démarche de sylviculture par et pour l’évolution Ce cadre général pourra être décliné dans des situations locales diverses et complexes en s’appuyant sur la connaissance du contexte qu’ont les gestionnaires forestiers Nous développonsune grille d’analyse simple, basée sur un petit nombre de paramètres caractérisant les mécanismes de l’évolution, pour comprendre l’impact des pratiques sylvicoles sur la dynamique de la diversité génétique et le maintien du potentiel d’évolution des populations d’arbres forestiers Après avoir rappelé l’état des connaissances sur les mécanismes de l’évolution chez les arbres forestiers, nous examinons les effets attendus de pratiques forestières actuelles ou innovantes sur ces mécanismes Pour illustrer la complexité des mécanismes en interaction, nous développons plus en détail les conséquences évolutives des interactions biotiques et celles d’un environnement fortement hétérogène La sylviculture par et pour l’évolution peut contribuer à l’adaptation des forêts au changement climatique Elle nécessite de combiner des objectifs à court et à long terme Nous proposons des pistes de recherche et d’expérimentation pour accompagner cette démarche.
Published: 2020

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

Author: Ilaria Spanu, Marcial Escudero, Anne Roig, Marwan Cheikh Albassatneh, Anne-Christine Monnet, Francesca Bagnoli, Agathe Leriche, Arndt Hampe, Frédéric Médail, Juan Arroyo, Giovanni G. Vendramin, Panayotis Dimopoulos, Gianluigi Bacchetta, Loic Ponger, Toni Nikolić, Bruno Fady, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology and Ecology, University of Seville, Structure et Instabilité des Génomes (STRING), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Faculty of Science [Zagreb], University of Zagreb, Centro Conservazione Biodiversità, Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Institute of Biosciences and Bioressources (IBBR), Department of Biology, Division of Plant Biology, Laboratory of Botany, University of Patras, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Erasmus Mundus ASSUR, Programme national PAUSE - Collège de France, ANR-11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università degli Studi di Cagliari = University of Cagliari (UniCa), University of Patras [Patras], Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Institute of Ecology and Environmental Sciences, Sorbonne University, Musée National d'Histoire Naturelle de Luxembourg (MNHN), Faculty of Science, University of Zagreb, UMR BioGeCo, INRA & Université Bordeaux, Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Biodiversité, Gènes et Communautés, ANR: 11-LABX-0061,Labex OT- Med,ANR-11-LABEX-0061, and University of Patras
Subjects: 0106 biological sciences, Mediterranean climate, Flora, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Mediterranean Basin, Bayesian, DNA sequencing, 03 medical and health sciences, Tree (descriptive set theory), Genus, Molecular evolution, Phylogenetics, mating system, 030304 developmental biology, 0303 health sciences, Ecology, molecular evolution, Woody plants, conservation, plastid DNA, Maximum likelihood, 15. Life on land, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Geography, [SDE]Environmental Sciences
Abstract: International audience; We produced the first time-calibrated phylogeny of all 64 native tree genera occurring on the European side of the Mediterranean Basin. This phylogeny is based on 3 plastid DNA sequences (rbcL matK and trnH-psbA), 4 recognized fossil dates and 10 secondary calibrations. Based on the inferred topology, we then tested whether the investigated tree flora exhibits phylogenetic clustering in both life-history traits known to influence reproduction and species' vulnerability to extinction. Our topology and the estimated dates mostly conform to published partial phylogenies and are highly congruent with the Angiosperm Phylogeny Group classification except for some minor incongruences including the still debated phylogenetic position of Magnoliids. The four strictly endemic genera of the Mediterranean Basin (Chamaerops, Phillyrea, Spartium and Tetraclinis) all showed emergence dates (11-72 Ma) long before the onset of the Mediterranean climate. We did not find any imprints of phylogenetic sorting processes on the life-history traits we studied, except for the mode of seed dispersal, which showed a clustered distribution across our topology. The presence of species at risk of potential extinction within a given genus was randomly distributed along the phylogenetic tree. Species with deficient data were significantly nested within a few of the most recently evolved angiosperm genera. Our analysis closes knowledge gaps and provides a valuable basis for studying the biogeo-graphical and ecological processes that have generated the Mediterranean tree flora. It can also inform conservation planning strategies that aim at broadening traditional taxonomy-focused perspectives with components of evolutionary history and phylogenetic singularity.
Published: 2020
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47. Managing forest genetic resources as a strategy to adapt forests to climate change: perceptions of European forest owners and managers

Author: Marcus Lindner, Mattia Manica, Barbara Vinceti, Bruno Fady, Pieter Johannes Verkerk, Nina Lauridsen, Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), European Forest Institute (EFI), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance), Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, and This research was part of the GenTree project which has received funding from the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No. 676876.
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Settore AGR/05 - ASSESTAMENTO FORESTALE E SELVICOLTURA, media_common.quotation_subject, Climate change, Plant Science, 010603 evolutionary biology, 01 natural sciences, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Effects of global warming, Order (exchange), Perception, Forest genetic resources, Forest ecology, Quality (business), Adaptation, 0105 earth and related environmental sciences, media_common, Forest management, business.industry, Environmental resource management, Forestry, 15. Life on land, Forest reproductive material, 13. Climate action, Psychological resilience, Business
Abstract: Managing genetic diversity is of key importance in fostering resilience of forest ecosystems to climate change. We carried out a survey reaching over 200 forest owners and managers from 15 European countries to understand their perceptions of the main threats to forest ecosystems, their knowledge of forest genetic resources (FGR) and their attitude toward actively managing these resources to strengthen the resilience of forest ecosystems to climate change. Respondents perceived pests and diseases to be the top-ranking threats to forests, followed by windstorms and drought, with differences across countries. They stated to be aware of the potential offered by managing FGR and indicated that they paid attention to origin and quality in their choice of planting material. Generally, respondents showed a positive attitude in using forest reproductive material foreign to the planting site, to better match the projected future climate conditions, introducing either a new native tree species or a new non-local genotype of a species already planted (keeping the same species but changing the source of planting material). However, forest reproductive material from local sources was largely preferred over non-local material (both genetically improved and not improved). Forest managers and owners may need to be exposed to more evidence of the potential benefits deriving from active adaptation and mitigation management of FGR before implementing adaptive measures. Also, more efforts should be invested in understanding perceptions and motivations of European forest owners and managers, in order to better tailor advice on optimal measures to counteract the detrimental effects of climate change.
Published: 2020
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48. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding

Author: Margaret Staton, Jason A. Holliday, Santiago C. González-Martínez, Bruno Fady, Christophe Plomion, Christian Lexer, Ross W. Whetten, Myriam Heuertz, Sally N. Aitken, Janice E. K. Cooke, J. P. Jaramillo-Correa, Department of Forest Resources and Environmental Conservation [Blacksburg], Virginia Tech [Blacksburg], Department of Forest and Conservation Sciences, University of British Columbia (UBC), Department of Biological Sciences, University of Alberta, Ecologie des Forêts Méditerranéennes [Avignon] (URFM 629), Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes et Communautés, Institute of Ecology, Universidad Nacional Autónoma de México (UNAM), Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Department of Entomology and Plant Pathology, The University of Tennessee [Knoxville], Department of Forestry and Environmental Resources, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), LabEx Arbre (ANR-11-LABX-0002-01), the Equipex Xyloforest (ANR-10-EQPX-16)/ IdEx Bordeaux (ANR No.-10-IDEX-03-02), European Project: 676876, Ecologie des Forêts Méditerranéennes (URFM), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), University of Vienna [Vienna], and Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM)
Subjects: 0301 basic medicine, Conservation genetics, arbre forestier, Range (biology), Population, Climate change, Genomics, adaptation, phylogeography, Biology, forest tree, 03 medical and health sciences, genomics/proteomics, évolution moléculaire, genomics, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, génomique végétale, Ecology, Evolution, Behavior and Systematics, education.field_of_study, Land use, molecular evolution, Ecology, forestry, phylogéographie, 15. Life on land, Forest genetic resources, Phylogeography, 030104 developmental biology, conservation genetics, 13. Climate action, conservation des ressources génétiques
Abstract: Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled ‘Genomics and Forest Tree Genetics’ was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.
Published: 2017
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49. Molecular and quantitative genetics of stone pine (Pinus pinea)

Author: Francesca Bagnoli, Bruno Fady, Sven Mutke, Giovanni G. Vendramin, Santiago C. González-Martínez, Instituto Nacional de Investigación Agropecuaria (INIA), Sustainable Forest Management Res Inst IuFOR, Universitad de Valladolid, Consiglio Nazionale delle Ricerche (CNR), Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), and Nandwani D.
Subjects: 0106 biological sciences, Mediterranean climate, Marsh, geography.geographical_feature_category, Pine nuts, Range (biology), Ecology, Woodland, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Domestication, Population bottleneck, Geography, Mediterranean stone pine, Refugium (population biology), Genetic depletion, [SDE]Environmental Sciences, Orchard, 010606 plant biology & botany
Abstract: The Mediterranean stone pine is currently on its way to domestication. Its genuine Mediterranean pine nuts are among the most expensive nuts in the world because they are mainly wild-collected from pine forests and woodlands. Despite the wide current distribution of stone pine over the whole Mediterranean biome, old-growth forests are scarce, often associated locally with dynamics on lose sands, coastal dunes or former estuary marshes. The species has been found to be genetically depauperate, putatively due to a population bottleneck in a local refugium during the Last Glacial Maximum confirmed in southern Iberia, and a possibly anthropic range expansion during Holocene. Only recently, cone harvesting and processing mechanisation have allowed for profitable pine nut production from orchard plantations. In Spain and Portugal, first elite clones have been registered for their use as grafted orchard crop.
Published: 2019
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50. Ecological gradients as an evolutionary opportunity for Mediterranean biodiversity

Author: Bruno Fady, Marc Bally, Alberte Bondeau, Francois Carlotti, Anne Chenuil, Wolfgang Cramer, Jean-Pierre Féral, Thierry Gauquelin, Anne-Christine Monnet, Séverine Thomas, France Van Wambeke, Aurelle, D., Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), 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), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), and Carlotti, François
Subjects: [SDE] Environmental Sciences, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDU] Sciences of the Universe [physics], [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU]Sciences of the Universe [physics], [SDE]Environmental Sciences, [SDE.ES] Environmental Sciences/Environmental and Society, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, [SDE.ES]Environmental Sciences/Environmental and Society, [SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

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