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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.

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)

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.

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

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.

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

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

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.

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.

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.

International audience; No abstract available

International audience; Fragmentation acting over geological times confers wide, biogeographical scale and genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a widespread forest tree, Pinus nigra Arnold, the European black pine, and to resolve its demographic history, we described and modelled its spatial genetic structure and gene genealogy. We then tested which Pleistocene event, whether recent or ancient, could explain its widespread but patchy geographic distribution. We used a set of different genetic markers, both neutral and potentially adaptive, and either biparentally or paternally only inherited, and we sampled natural populations across the entire species range. We analysed the data using both frequentist population genetic and Bayesian inference methods to calibrate realistic, demographic timed scenarios. We also considered how habitat suitability might have affected demography by correlating climate variables at different recent Pleistocene ages with genetic diversity estimates. Species with geographically fragmented distribution areas are expected to display significant among-population genetic differentiation and low within-population genetic diversity. Contrary to these expectations, we show that the current diversity of Pinus nigra and its weak genetic spatial structure result from the Late Pleistocene or Early Holocene fragmentation of one ancestral population into six distinct genetic lineages. Gene flow among the different lineages is strong across forests and many current populations are admixed between lineages. We propose to modify the currently accepted international nomenclature made of five sub-species and name these six lineages using regionally accepted sub-species-level names.

This datapaper collects individual georeferenced tree height data from Pinus nigra Arn., P. pinaster Aiton, and P. pinea L. planted in common gardens in France, Germany, Morocco, and Spain. The data can be used to assess genetic variation and phenotypic plasticity with further applications in biogeography and forest management. The three datasets are available at (Vizcaino-Palomar et al. 2018a), (Vizcaino-Palomar et al. 2018b), and (Vizcaino-Palomar et al. 2018c), and the associated metadata are available at , and for P. nigra, P. pinaster and P. pinea, respectively.

International audience; Cedar is an emblematic Mediterranean forest tree. Genetic research activities on Mediterranean Cedrus species are progressively developed in relation to conservation, restoration, and exploitation plans of these forest tree species. However, currently available molecular biology tools supporting genetic research in these fields are still scarce and have a limited genetic resolution potential. We developed a new set of 12 nuclear microsatellite markers (nSSRs) on Cedrus atlantica that we combined with four previously developed ones in three multiplexes. We checked their monogenic inheritance in controlled crosses. We used a collection of 131 samples from six populations of C. atlantica to estimate null allele frequencies and probability of identity and to characterize the structure of genetic diversity in the fragmented distribution range of this species. We also tested the transferability of the markers to another set of 36 samples from the other Mediterranean Cedrus species and performed a phylogenetic analysis. The three multiplexes reached a high level of resolution potential that we used to evaluate sampling quality. Null allele frequency estimates showed no specific pattern across populations or across species and did not affect the results of biogeographic and phylogenic analyses. Our results reveal a very clear geographical genetic structure within C. atlantica, and the phylogenic tree matched previous analyses based on other markers. Our results confirm the potential interest of these nSSR multiplexes for genotyping in Cedrus.

Key message This review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology. Context A decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving genomics and bioinformatics toolbox has advanced our understanding of the structure, functioning, and evolution of forest tree genomes. Aims and methods This review highlights some of the discoveries and applications that “omics” technologies have made possible for forest trees over the past 10 years. Results In this review, we start by our current understanding of genome evolution and intricacies of gene regulation for reproduction, development, and responses to biotic and abiotic stresses. We then skim over advances in interactome analysis and epigenomics, the knowledge of the extent of genetic variation within and between species, revealing micro- and macro-evolutionary processes and species history, together with the complex architecture of quantitative traits. We finally end with applications in genetic resource conservation and breeding. Conclusion The knowledge gained through the use of these technologies has a huge potential impact for adapting forests to the main challenges they will have to face: changing demand from ecosystem services with potentially conflicting strategies in terms of conservation and use, as well as climate changes and associated threats. Genomics will undoubtedly play a major role over the next decade and beyond, not only to further understand the mechanisms underlying adaptation and evolution but also to develop and implement innovative management and policy actions to preserve the adaptability of natural forests and intensively managed plantations.

International audience; Cedrus brevifolia is a narrowly distributed conifer species, currently limited to a single mountain in Cyprus, growing in restricted habitats on sites of different densities and sizes. This study assessed the influence of seed and pollen dispersal, as well as the effect of demographic and genetic features on the magnitude of fine-scale spatial genetic structure (SGS). Sampling was performed in 11 plots where 50 neighboring adult trees were sampled from each plot, while biparentally and paternally inherited genomes were used for analysis with microsatellites. Fine-scale SGS was significant but showed contrasting patterns among plots. Although the magnitude of SGS in C. brevifolia mainly results from restricted seed dispersal, short-distance pollen dispersal could also explain fine-scale SGS in some plots, which is rather uncommon in wind-pollinated conifer species. The lack of a general and consistent trend of SGS among plots and between genomes indicates that pollen and seed dispersal varies at plot level. The complex SGS patterns in C. brevifolia may result from the unequal ratio of male and female strobilies of trees within the same plots, at different reproductive periods. Demographic features such as habitat fragmentation did not influence the magnitude of SGS in C. brevifolia, whereas low tree aggregation reduced it. Further, the significant correlation observed between linkage disequilibrium (LD) and plots with significant SGS supports the assumption that under specific conditions, LD is likely to be caused by the magnitude of SGS.

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. Dataset access: https://doi.org/10.5281/zenodo.1308577. Associated metadata access: http://www.fao.org/geonetwork/srv/en/metadata.show?id=56996.

International audience; There is a general trend of biodiversity loss at global, regional, national and local levels. To monitor this trend, international policy processes have created a wealth of indicators over the last two decades. However, genetic diversity indicators are regrettably absent from comprehensive bin-monitoring schemes. Here, we provide a review and an assessment of the different attempts made to provide such indicators for tree genetic diversity from the global level down to the level of the management unit. So far, no generally accepted indicators have been provided as international standards, nor tested for their possible use in practice. We suggest that indicators for monitoring genetic diversity and dynamics should be based on ecological and demographic surrogates of adaptive diversity as well as genetic markers capable of identifying genetic erosion and gene flow. A comparison of past and present genecological distributions (patterns of genetic variation of key adaptive traits in the ecological space) of selected species is a realistic way of assessing the trend of intra-specific variation, and thus provides a state indicator of tree genetic diversity also able to reflect possible pressures threatening genetic diversity. Revealing benefits of genetic diversity related to ecosystem services is complex, but current trends in plantation performance offer the possibility of an indicator of benefit. Response indicators are generally much easier to define, because recognition and even quantification of, e.g., research, education, breeding, conservation, and regulation actions and programs are relatively straightforward. Only state indicators can reveal genetic patterns and processes, which are fundamental for maintaining genetic diversity. Indirect indicators of pressure, benefit, or response should therefore not be used independently of state indicators. A coherent set of indicators covering diversity-productivity-knowledge-management based on the genecological approach is proposed for application on appropriate groups of tree species in the wild and in cultivation worldwide. These indicators realistically reflect the state, trends and potentials of the world's tree genetic resources to support sustainable growth. The state of the genetic diversity will be based on trends in population distributions and diversity patterns for selected species. The productivity of the genetic resource of trees in current use will reflect the possible potential of mobilizing the resource further. Trends in knowledge will underpin the potential capacity for development of the resource and current management of the genetic resource itself will reveal how well we are actually doing and where improvements are required. (C) 2014 The Authors. Published by Elsevier B.V.

International audience; The current distribution of forest genetic resources on Earth is the result of a combination of natural processes and human actions. Over time, tree populations have become adapted to their habitats including the local ecological disturbances they face. As the planet enters a phase of human-induced climate change of unprecedented speed and magnitude, however, previously locally-adapted populations are rendered less suitable for new conditions, and 'natural' biotic and abiotic disturbances are taken outside their historic distribution, frequency and intensity ranges. Tree populations rely on phenotypic plasticity to survive in extant locations, on genetic adaptation to modify their local phenotypic optimum or on migration to new suitable environmental conditions. The rate of required change, however, may outpace the ability to respond, and tree species and populations may become locally extinct after specific, but as yet unknown and unquantified, tipping points are reached. Here, we review the importance of forest genetic resources as a source of evolutionary potential for adaptation to changes in climate and other ecological factors. We particularly consider climate-related responses in the context of linkages to disturbances such as pests, diseases and fire, and associated feedback loops. The importance of management strategies to conserve evolutionary potential is emphasised and recommendations for policy-makers are provided.

International audience; This paper provides a review of theoretical and practical aspects related to genetic management of forest trees. The implementation of international commitments on forest genetic diversity has been slow and partly neglected. Conservation of forest genetic diversity is still riddled with problems, and complexities of national legal and administrative structures. Europe is an example of a complex region where the dis- tribution ranges of tree species extend across large geographical areas with profound environmental dif- ferences, and include many countries. Conservation of forest genetic diversity in Europe has been hampered by a lack of common understanding on the management requirements for genetic conserva- tion units of forest trees. The challenge resides in integrating scientific knowledge on conservation genet- ics into management of tree populations so that recommendations are feasible to implement across different countries. Here, we present pan-European minimum requirements for dynamic conservation units of forest genetic diversity. The units are natural or man-made tree populations which are managed for maintaining evolutionary processes and adaptive potential across generations. Each unit should have a designated status and a management plan, and one or more tree species recognized as target species for genetic conservation. The minimum sizes of the units are set at 500, 50 or 15 reproducing individuals depending on tree species and conservation objectives. Furthermore, silvicultural interventions should be allowed to enhance genetic processes, as needed, and field inventories carried out to monitor regen- eration and the population size. These minimum requirements are now used by 36 countries to improve management of forest genetic diversity.

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

The unambiguous identification of closely related species is useful for many practical purposes in forest tree species. For example, international laws require timber identification and the control of the origin of forest reproductive material. In this paper, we present a mitochondrial DNA marker which can be used to differentiate among groups of fir species (Abies spp.). Eight Mediterranean and one North American fir species (used as reference) were analysed at the fourth intron of the NAD subunit 5 gene. A total of six different haplotypes was identified, one in the American Abies concolor, the other five in Mediterranean species. Two different haplotypes were found each in the widespread A. alba and in A. cephalonica, one haplotype being shared among the two species. A single species specific haplotype was found in the near-eastern A. cilicica. The two southwestern species A. pinsapo and A. numidica shared one haplotype. The fifth haplotype was shared by all remaining eastern Mediterranean firs, A. cephalonica, A. bornmuelleriana, A. equi-troiani, and A. nordmanniana. Differences in haplotype sequences were mainly due to large insertions/deletions. Agarose gel electrophoresis thus provides a fast, cheap and reliable diagnosis method for species or species group identification.

Adaptive and wood quality trait data were collected and analyzed on commercially available Juglans regia and J. regia×J. nigra provenances and progenies planted across Europe in a multi-site network. A total of 19 seed sources, replicated 35 times per site, were planted at 13 sites from 5 European countries, encompassing the potential distribution area of timber production plantation sites. The following traits were evaluated: survival, height, diameter at breast height, stem form, apical dominance, vegetative budbreak, along with biotic and abiotic damage. Mean values were significantly different both among provenances/progenies and sites. Most common damage was late spring and early autumn frost. Bud break ranking was significantly correlated with provenance and progeny origin. Although J. regia is fast growing, southern European early budbreak plant material should not be planted under most middle European conditions where late spring frost can be expected, as it has a significant negative impact on architectural (and thus wood quality) traits. Hybrid J. regia×J. nigra progeny performed better than J. regia provenances/progenies for most traits measured. Differences were significantly in favor of hybrids at sites with medium to low fertility, although some locally selected seed sources tended to perform as well as hybrids on high fertility sites.

During the last decade, large data sets have been increasingly used to address key questions in the field of forest science, including: (1) the impact of climate change on productivity and species distribution; (2) the long-term course of carbon, water, and nutrient cycles; (3) the spread and virulence of pathogens; (4) the genetic basis of local adaptation; and (5) sustainable socio-economic strategies (Rehfeldt et al. 2001, 2002; Diaz-Balteiro and Romero 2008; Cappa et al. 2012; Benito-Garzon et al. 2013; Porth et al. 2013; Stephenson et al. 2014). Sound data are difficult to produce in forest science because trees are long lived, are elements of complex ecosystems, and are not easily amenable to simple experiments. Yet, foresters have observed, monitored, and measured trees and forest ecosystems for a very long time, producing impressive data sets. International provenance tests are carefully monitored since the early twentieth centrury (Rehfeldt et al. 2001, 2002); they compare in common gardens trees from seeds collected in different localities (provenances) in order to record the genetic diversity of traits of importance for forestry and adaptation. Similarly, long-term records are now available for the carbon budget, water use, and nutrient cycling of a large number of forest ecosystems in temperate, boreal, as well as tropical forests (Luyssaert et al. 2007). However, like in other fields of research, the fate of these data remains, in many cases, uncertain, which has certainly detrimental effects for the advancement of forest science and for the improvement of forest ecosystem management. In the best of cases, they were published (usually not in the form of raw data) along with companion articles discussing the results. In most cases, they are stored under heterogeneous formats in the personal files of researchers and risk disappearing when these researchers change interests or retire. Recent European and international projects have taken this concern very seriously and have initiated the construction of large metadata and databases (e.g., TreeBreedex and Evoltree for genetic data, European Fluxes Database Cluster like ICOS, CarboExtreme, GHG-Europe, InGOS, for long-term ecological monitoring). International networks that monitor functional and morphological changes in forests are pushing in this direction. Institutes and research departments simultaneously consolidate available data into standardized and interconnected databases. Such a wealth of data requires very specific database management and data sharing procedures (Michener and Jones 2012). In addition to producing increasingly large data sets from monitoring and automated machine collections, forest science also relies on a large number of short-term experiments whose main results are published in scientific journals, usually without providing the corresponding data that are sometimes lost after publication. There is a general feeling that such data are often under-analyzed by their authors and that they should be made available for re-use through synthesis and analysis to generate novel ideas and test theories at unprecedented scales. Handling Editor: Erwin Dreyer B. Fady : C. Pichot INRA, UR 629, Ecologie des Forets Mediterraneennes, Domaine St Paul, Site Agroparc, 84914 Avignon, France

European beech (Fagus sylvatica L.) is one of the most economically and ecologically important deciduous trees in Europe, yet little is known about its genomic diversity and its adaptive potential. Here, we detail the discovery and analysis of 573 single nucleotide polymorphisms (SNPs) from 58 candidate gene fragments that are potentially involved in abiotic stress response and budburst phenology using a panel of 96 individuals from southeastern France. The mean nucleotide diversity was low (θ π = 2.2 × 10-3) but extremely variable among gene fragments (range from 0.02 to 10), with genes carrying insertion/deletion mutations exhibiting significantly higher diversity. The decay of linkage disequilibrium (LD) measured at gene fragments >800 base pairs was moderate (the half distance of r 2 was 154 bp), consistent with the low average population-scaled recombination rate (ρ = 5.4 × 10-3). Overall, the population-scaled recombination rate estimated in F. sylvatica was lower than for other angiosperm tree genera (such as Quercus or Populus) and similar to conifers. As a methodological perspective, we explored the effect of minimum allele frequency (MAF) on LD and showed that higher MAF resulted in slower decay of LD. It is thus essential that the same MAF is used when comparing the decay of LD among different studies and species. Our results suggest that genome-wide association mapping can be a potentially efficient approach in F. sylvatica, which has a relatively small genome size. © 2013 Springer-Verlag Berlin Heidelberg.

International audience; & Context Managing forests under climate change requires adaptation. The adaptive capacity of forest tree populations is huge but not limitless. Integrating evolutionary consider-ations into adaptive forestry practice will enhance the ca-pacity of managed forests to respond to climate-driven changes. & Aims Focusing on natural regeneration systems, we pro-pose a general framework that can be used in various and complex local situations by forest managers, in combination with their own expertise, to integrate evolutionary consid-erations into decision making for the emergence of an evolution-oriented forestry. & Methods We develop a simple process-based analytical grid, using few processes and parameters, to analyse the impact of forestry practice on the evolution and evolvability of tree populations. & Results We review qualitative and, whenever possible, quantitative expectations on the intensity of evolutionary drivers in forest trees. Then, we review the effects of actual and potential forestry practice on the evolutionary processes. We illustrate the complexity of interactions in two study cases: the evolutionary consequences for forest trees of biotic in-teractions and of highly heterogeneous environment. & Conclusion Evolution-oriented forestry may contribute adapting forests to climate change. It requires combining short-term and long-term objectives. We propose future lines of research and experimentation.

International audience; The Salzmann pine (Pinus nigra ssp. salzmannii) is an endemic subspecies of black pine native to the Western Mediterranean basin. In Spain, Salzmann pine covers extensive areas (approx. 350 000 ha), while in France where few scattered populations subsist, its distribution area is estimated at approx. 3 000 ha. We used a dendroecological approach to understand the impact of climate fluctuations on Salzmann pine from France. Spatial and temporal variability of radial growth response was compared in three ecologically different populations (Conflent, Gorges du Tarn, Saint-Guilhem-le-D,sert). The Conflent population showed a strong sensitivity to spring precipitation deficits (March to June), while at Gorges du Tarn and Saint-Guilhem sites, autumn (October) of the previous year and winter (February) temperatures explained more variance than precipitations and were, respectively, negatively and positively correlated to radial growth. Although covering a limited distribution range in France, Salzmann pine demonstrated large differences in radial growth response to climate and soil variations.

International audience; Mediterranean pines share many common life-history traits. They are found at almost all altitudinal levels around the Mediterranean Basin, from sea level to high-elevation mountains, and from hot and dry to wet and cold bioclimates. Their distribution ranges from widespread to regional and narrow, and from dense extensive populations to small populations of scattered individuals. They have been extensively used by human civilizations for millennia. I show which are the main phylogenetic, ecological, and climatic factors explaining the patterns of within and among-population genetic diversity in Mediterranean pines. I use a narrative synthesis approach and multiple examples from the literature on pine species from the Mediterranean Basin and California. While Mediterranean pines have the highest levels of differentiation worldwide, their genetic diversity increases from west to east and is significantly reduced in low-elevation species. Factors such as ancestral adaptation to wildfire, reduction of effective population size during the Last Glacial Maximum, long distance dispersal during the Holocene, and more recent adaptation to patchy environmental conditions could explain these patterns. Because of contrasted ecological, demographic, historical, and geographical processes, and despite their common biological attributes, pines of the Mediterranean Basin display complex biogeographic patterns at neutral gene level that can help retrace their evolutionary history. Although individual species often represent unique case studies that make generalizations risky, locating habitats of significantly high and low genetic diversity is key for detecting and understanding the major factors affecting gene diversity and may prove useful for profiling areas of high conservation value in the Mediterranean.

International audience; Dispersal and recruitment play a critical role in determining the abundance and the spatial structure of regeneration. In this study, we estimated landscape scale seed dispersal using the inverse modeling method by fitting seedling counts to seed tree location and fertility in the European silver fir Abies alba Miller. Seed trees and seedlings from three age cohorts were counted in 30 plots on Mont Ventoux (southeastern France) at elevations from 995 to 1,605 m, where the following ecological variables were measured: elevation, slope, aspect, light availability, and tree density. We developed and fitted a dispersal model, including a new parameter, recruitment rate, which depended both on the ecological characteristics of the plots and on seed production. Elevation was the factor that affected seedling recruitment the most, with an optimum value at around 1,200 m. Estimated A. alba seed dispersal distances were short (median values for the three cohorts, respectively, 16.4-13.2-19.6 m). We demonstrated that including the ecological characteristics of plots and post-dispersal recruitment processes realistically reduced estimates of seed dispersal distances which are otherwise grossly over-estimated using inverse modeling procedures.

Leaf unfolding is a key ecosystem parameter controlling carbon and water fluxes and affecting forest dynamics. This parameter is highly sensitive to temperature and, consequently, often used as an indicator of global change. In this paper, we analyzed weekly leaf unfolding dynamics for seven temperate species ( Fagus sylvatica L., Acer opalus Mill., Sorbus aria L., Quercus pubescens Willd. Abies alba Mill., Pinus sylvestris L., Pinus nigra Arnold). The effects of temperature on leaf unfolding were studied in situ using several methods and proxies. First, in a spatial approach, leaf unfolding dates were measured along two altitudinal gradients situated on the north and south face of the Mont Ventoux to test altitudinal and slope effects. Second, in a temporal approach, the year effect was analyzed on the north face by comparing two contrasted years (2006 and 2007). Finally, the role of temperature was investigated directly by linking leaf unfolding patterns and temperatures recorded during the leaf unfolding process itself. Two major conclusions were obtained. First, three distinct leaf unfolding patterns were revealed: a rapid sigmoid pattern for the deciduous species group, a slow kinetic pattern for the pines and an intermediate pattern for A. alba . Second, we found an unexpected pattern of variation in the response to spatial or temporal variation of temperature. The more sensitive a species was to temperature variations between years, the less sensitive it was to temperature variations due to altitude. Finally, we discuss that these results can be correlated to two major life history traits: evergreen vs. deciduous and shade tolerant vs. shade intolerant.

International audience; Several demographic factors can produce family structured patches within natural plant populations, particularly limited seed and pollen dispersal and small effective density. In this paper, we used computer simulations to examine how seed dispersal, density, and spatial distribution of adult trees and seedlings can explain the spatial genetic structure (SGS) of natural regeneration after a single reproductive event in a small population. We then illustrated the results of our simulations using genetic (isozymes and chloroplast microsatellites) and demographic experimental data from an Abies alba (silver fir) intensive study plot located in the Southern French Alps (Mont Ventoux). Simulations showed that the structuring effect of limited dispersal on seedling SGS can largely be counterbalanced by high effective density or a clumped spatial distribution of adult trees. In addition, the clumping of natural regeneration far from adult trees, which is common in temperate forest communities where gap dynamics are predominant, further decreases SGS intensity. Contrary to our simulation results, low adult tree density, aggregated spatial distribution of seedlings, and limited seed dispersal did not generate a significant SGS in our A. alba experimental plot. Although some level of long distance pollen and seed flow could explain this lack of SGS, our experimental data confirm the role of spatial aggregation (both in adult trees and in seedlings far from adult trees) in reducing SGS in natural populations

The annual height increment of the shoot can be divided into two morphogenetic components: the number of stem units initiated in the bud prior to bud break and their mean length. Observations were made on the lateral shoots of 43 Abiescephalonica open-pollinated families from three provenances located in an experimental site in southern France. Genetic parameters of the two components were evaluated with an analysis of variance. Correlations both between components and with annual height increment were examined at the phenotypic, genotypic, and individual levels. Differences between provenances were the result of number of stem units and annual height increment. Number of stem units presented a very high heritability and was strongly correlated to annual height increment at all variance levels. Mean stem unit length appeared to be more dependent on environmental variations and was less closely correlated to annual height increment, especially when genotypic data were considered. This particular growth strategy could be the consequence of A. cephalonica's adaptation to a Mediterranean-type climate. Of the two components studied, number of stem units was a better genetic predictor of annual height increment. A negative correlation between number of stem units and mean stem unit length was made apparent at the phenotypic and individual levels and should be considered when using number of stem units as a selection criterium.

Genetic diversity was described in 17 cedar populations covering the geographical range of the four species of the genus Cedrus. The study was conducted using amplified fragment length polymorphism (AFLP) on haploid tissues (megagametophytes). Eleven selective AFLP primer pairs generated a total of 107 polymorphic amplification products. Correspondence and genetic distance analyses indicated that Cedrus deodara constitutes a separate gene pool from the Mediterranean cedars. Within Mediterranean cedars, we distinguished two groups: the first one is made of Cedrus atlantica, while the second one is made of Cedrus libani and Cedrus brevifolia, these latter two species being genetically similar despite important divergence previously observed for morphological and physiological traits. The lowest intrapopulation variability was found in the two C. deodara populations analyzed. Surprisingly, C. brevifolia, the endemic taxon from the island of Cyprus that is found in small and fragmented populations, showed one of the highest levels of diversity. This unexpected pattern of diversity and differentiation observed for C. brevifolia suggests a recent divergence rather than a relictual, declining population. Patterns of diversity within- and among-populations were used to test divergence and fragmentation hypotheses and to draw conclusions for the conservation of Cedrus gene pools.

Abies alba is one of the major European mountain forest species for which a gene resource conservation network exists in France. However, scattered populations from southwestern Alps (southeastern France) are poorly represented in this network. Using a sample of 16 populations, two of which are already included in the network, the structural pattern of genetic diversity was investigated to help decide whether additional populations should be included in the conservation network. Traits were analyzed using both seeds and progenies of selected trees from natural stands (19–43 per stand) grown 4 years in nursery. The southwestern Alpine regional resource was structured into three ecological groups: Sub-Mediterranean Alps, Intermediate Alps and Ligurian Alps. Multivariate analyses were used to compare phytoecological distribution and variability of adaptive and non-adaptive traits. The following traits were analyzed: (i) isozyme diversity of open-pollinated seeds harvested from the stands (seven variables), (ii) mean monoterpene composition of original stands using nursery test progenies (seven variables) and (iii) growth, bud phenology and drought resistance traits using nursery test progenies (nine variables). The 3-group ecological diversity can be relatively well-explained by terpene data but not by isozyme or adaptive trait data. Synthetic variables generated from grouped original data concur with the ecological pattern. Most adaptive trait variability was found within populations, which indicates that selective forces operate at the micro-geographical level. This study suggests a lack of representative populations for the Abies alba genetic conservation network both in Ligurian and Sub-Mediterranean Alpine ecological group. It also suggests that due to isolation, the scattered Sub-Mediterranean ecological group has less non-adaptive genetic diversity and may require additional conservation focus.

International audience; 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.

International audience; Unexpected ploidy levels observed in a previous flow cytometric analysis of Cupressus dupreziana endosperm, led us to hypothesize an asexual seed production in this endangered species. We tested here this possible apomixis, studying isozyme variability of endosperms, embryos and seed coats extracted from open pollinated seeds. Electrophoretic bands observed in zymograms of PGI2 and LAP, the only two polymorphic systems, were in agreement with bands observed in C. sempervirens zymograms. Zymograms of C. dupreziana endosperms were identical to those of the diploid maternal tissue, as observed in C. sempervirens. Hypothesizing a codominant nuclear DNA control for both PGI2 and LAP, a similar electrophoretic expression of these systems in endosperm and embryo, and the absence of modifier genes, the lack of endosperm bands in most embryo zymograms was interpreted as the result of a strictly paternal origin of embryo nuclear DNA in C. dupreziana seeds.; Absence d'allèles maternels dans les zymogrammes des embryons de Cupressus dupreziana A. Camus. De précédents travaux portant sur les niveaux de ploïdie de l'endosperme des graines de Cupressus dupreziana, nous avaient conduit à émettre l'hypothèse d'une reproduction apomictique chez cette espèce menacée. Cette hypothèse a été ici testée par l'étude de la variabilité enzymatique d'endospermes, d'embryons et de téguments de graines issues de pollinisation libre. Les zymogrammes observés pour les deux systèmes polymorphes, PGI2 et LAP, sont conformes à ceux observés chez C. sempervirens. Les zymogrammes des endospermes de C. dupreziana sont identiques à celui de l'arbre mère, comme précédemment observé chez C. sempervirens. La plupart des zymogrammes produits par les embryons des graines de C. dupreziana ne contiennent pas les bandes électrophorétiques des endospermes correspondants. Chez tous les gymnospermes étudiés, PGI2 et LAP sont des marqueurs codominants, sous contrôle génétique nucléaire. Chez C. sempervirens l'expression de ces systèmes est indépendante des tissus (endosperme ou embryon) et aucun gène modificateur n'est connu. Dans ce contexte, nous formulons l'hypothèse d'une origine strictement paternelle de l'ADN nucléaire des embryons.

Cortical oleoresin composition of lateral shoots (mono- and sesquiterpenes) was analysed by gas chromatography on 18 Mediterranean fir populations grown in experimental fields in southern France: 13 Abies cephalonica Loudon provenances and one A. borisii regis Mattfeld provenance from Greece, 2 A. alba Miller provenances from Romania and Bulgaria, 1 Abies bornmuelleriana Mattfeld provenance and 1 A. equi trojani Ascherson and Sintenis provenances from Turkey. Terpenes with the highest between-provenance variability were limonene, β-pinene, longifolene, δ-cadinene and α-humulene. Both similarity in terpene composition of all the firs studied and paleogeographical data demonstrated the possible existence of a unique Eastern Mediterranean tertiary ancestor for present-day Aegean species. The Pliocene marine transgression of the Aegean basin could have caused this geographical disjunction. According to this hypothesis, A. alba would have appeared in the Northern part of the Aegean and then colonized all of Europe while A. bornmuelleriana would have appeared in its Eastern part. Frequent Pleistocene contacts between the two species could have contributed to the individualization of A. equi trojani and given rise to the particular morphology of the south-eastern ecotypes of A. alba. In the western part of the basin, A. cephalonica populations would have appeared. Southern migrations of A. alba during the Ice Age and contact with A. cephalonica in refugia probably led to the development of A. borisii regis hybrid populations. Evidence for an A. alba gene flow can be found in the southernmost A. cephalonica populations.

Although they most probably contain original genetic combinations, rear-edge, xeric limit populations are poorly known and have received limited interest from scientists and forest managers alike. Much effort is needed to better understand and manage these populations which will prove critical for the benefits of economically and ecologically important forest species under climate change.

The ecological potentials of Abies cephalonica are interesting for reforestation in Mediterranean France. They were at the origin of studies currently performed on 20 of its provenances in an experimental network in southern France. The following characteristics were studied : morphology of above-ground vegetative structure (needles and stems), composition and yield in monoterpenes and sesquiterpenes from cortical tissues, isozyme variation in seed tissues, height growth and morphogenetic components of height growth, vegetative bud flushing phenology and resistance of seeds and seedlings to water stress. Results from each study were reviewed and discussed in this paper. Conclusions were developed concerning potential phylogeny of the Greek fir since the Tertiary, geographic variability of height growth and adaptation traits and genetic parameter estimates of these traits. A multi-criteria picture of Abies cephalonica's variability in its natural range could thus be drawn., Abies cephalonica a des potentialités écologiques intéressantes pour le reboisement en France méditerranéenne. Celles ci ont motivé l’étude de divers caractères de vingt de ses provenances dans un réseau de plantations comparatives dans le sud de la France : morphologie de l’appareil végétatif aérien (aiguilles et rameaux), composition et rendement en monoterpènes et sesquiterpènes de tissus corticaux, polymorphisme isoenzymatique de gamétophytes et embryons, croissance en hauteur et composantes morphogénétiques de cette croissance, phénologie du débourrement végétatif de l’axe principal et résistance au stress hydrique aux stades graine et plantule. Les résultats acquis pour chacune de ces études ont été synthétisés et discutés dans ce travail. Les conclusions développées ont trait à la phylogénie potentielle du sapin de Grèce depuis la fin du Tertiaire, à la variabilité géographique de ses caractères de croissance et d’adaptation et à l’estimation des paramètres génétiques de ces mêmes caractères. Il en découle un panorama multi-critère de la variabilité d'Abies cephalonica dans son aire d’origine., Fady Bruno, Arbez Michel. Amplitude et structuration de la variabilité génétique du sapin de Céphalonie (Abies cephalonica Loudon). In: Ecologia mediterranea, tome 16,1990. pp. 59-72.

Species with fragmented populations and low population size often display low within-population genetic diversity and strong among-population differentiation. Laurus nobilis L. (Lauraceae), common laurel, has a scattered distribution throughout the Mediterranean, with only few autochthonous populations. Our goal was to elucidate if this species has range-wide genetic structure and if planted material can be traced back to its origin. Genetic diversity was investigated using 4 polymorphic nuclear microsatellites (nSSR) transferred from two species of Lauraceae. Sixty-six laurel trees were selected from 7 widely separated populations within the Mediterranean distribution area of the species. A total of 34 alleles (9 alleles per locus on average) were found. Mean genetic diversity within-population (Hs), was 0.558. Genetic differentiation among populations (GST = 0.243) was high compared to that of other angiosperms. Laurus nobilis can be separated into two main gene pools, one from western (Tunisia, Algeria and France) and the other from eastern Mediterranean (Turkey). The Algerian, Tunisian and French populations presented a strong genetic similarity, compatible with the fact that North African laurel populations could be recently introduced from north-western Mediterranean stock.