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[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).

International audience

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

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.

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

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

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.

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.

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.

International audience; Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e., evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across 177 gene‐loci in a circum‐Mediterranean conifer (Pinus pinea L.) that represents one of the most extreme cases of genetic pauperization in widespread outbreeding taxa. We found very little genetic variation in both hypervariable nuclear microsatellites (SSRs) and gene‐loci, which translated into genetic diversity estimates one order of magnitude lower than those previously reported for pines. Such values were consistent with a strong population decline that began some ~1 Ma. Comparisons with the related and parapatric maritime pine (Pinus pinaster Ait.) revealed reduced rates of adaptive evolution (α and ωa) and a significant accumulation of genetic load. It is unlikely that these are the result from differences in mutation rate or linkage disequilibrium between the two species; instead they are the presumable outcome of contrasting demographic histories affecting both the speed at which these taxa accumulate genetic diversity, and the global efficacy of selection. Future studies, and programs for conservation and management, should thus start testing for the effects of genetic load on fitness, and integrating such effects into predictive models.

AimUnder rapid environmental change, phenotypic plasticity, if adaptive, could increase the odds for organisms to persist. Environmental variation over time is an important source of phenotypic plasticity. Likewise, phenotypic plasticity can vary with age in many organisms. However, little is known on phenotypic plasticity variation across species’ ranges. Our aims are: (i) to assess whether populations’ phenotypic plasticity is related to the inter-annual climate variation under which populations have evolved during the last century; (ii) to compare phenotypic plasticity among developmental classes; and (iii) to predict phenotypic plasticity across’ species ranges.LocationEurope and North-Africa.Time period1901-2014.Major taxa studiedPinus nigra, P. pinasterandP. pinea.MethodsWe used 372 646 individual tree height measurements at three developmental classes from a wide network of 38 common gardens in Europe and North Africa with provenances covering the distribution range of the species. With this data, we: i) build linear mixed-effect models of tree height as a function of tree age, population and climate; ii) estimate populations’ reaction norms from the fitted models; iii) calculate populations’ phenotypic plasticity indexes; iv) build models of populations’ phenotypic plasticity indexes as a function of inter-annual climate variation during the last century.ResultsWe found that i) most populations that have evolved under high inter-annual climate variation, in either maximum or minimum values in temperature or precipitation, exhibited high values of plasticity in tree height; ii) phenotypic plasticity for tree height was higher in young trees than in older ones, iii) phenotypic plasticity did not follow any particular geographical pattern across species’ ranges.Main conclusionsPhenotypic plasticity across the three Mediterranean pines’ ranges is related with the climate variation experienced over time and calls into question whether this plasticity could be adaptive and hence beneficial to cope with climate change in the short-term.

AimTo test whether adaptive and plastic trait responses to climate across species distribution ranges can be untangled using field observations, under the rationale that, in natural forest tree populations, long-term climate shapes local adaptation while recent climate change drives phenotypic plasticity.LocationEurope.Time period1901-2014.TaxaSilver fir (Abies alba Mill.) and sessile oak (Quercus petraea (Matt.) Liebl.).MethodsWe estimated the variation of individual tree height as a function of long-term and short-term climates to tease apart local adaptation, plasticity and their interaction, using mixed-effect models calibrated with National Forest Inventory data (in-situ models). To validate our approach, we tested the ability of in-situ models to predict independently tree height observations in common gardens where local adaptation to climate of populations and their plasticity can be measured and separated. In-situ model predictions of tree height variation among provenances (populations of different geographical origin) and among planting sites were compared to observations in common gardens and to predictions from a similar model calibrated using common garden data (ex-situ model).ResultsIn Q. petraea, we found high correlations between in-situ and ex-situ model predictions of provenance and plasticity effects and their interaction on tree height (r > 0.80). We showed that the in-situ models significantly predicted tree height variation among provenances and sites for Abies alba and Quercus petraea. Spatial predictions of phenotypic plasticity across species distribution ranges indicate decreasing tree height in populations of warmer climates in response to recent anthropogenic climate warming.Main conclusionsOur modelling approach using National Forest Inventory observations provides a new perspective for understanding patterns of intraspecific trait variation across species ranges. Its application is particularly interesting for species for which common garden experiments do not exist or do not cover the entire climatic range of the species.

Raw data can be freely accessed online for French National Forest Inventories (http://inventaire-forestier.ign.fr), Quercus petraea (https://arachne.pierroton.inra.fr/QuercusPortal) and Abies alba common gardens (online repository, in progress). Climate data used for this study are available online (http://gentree.data.inra.fr/climate). R codes used for data analyses can be obtained from the corresponding author upon request.; International audience; Aim To test whether intraspecific trait responses to climate among populations across species distribution ranges can be untangled using field observations, under the rationale that, in natural forest tree populations, long-term climate shapes population responses while recent climate change drives phenotypic plasticity. Location Europe. Time period 1901-2014. Taxa Silver fir (Abies alba Mill.) and sessile oak [Quercus petraea (Matt.) Liebl.]. Methods We estimated the variation of individual tree height as a function of long-term and short-term climates to tease apart provenance effects (variation among populations of different geographical origin), plasticity and their interaction, using mixed-effect models calibrated with national forest inventory data (in-situ models). To validate our approach, we tested the ability of in-situ models to predict independently tree height observations in common gardens experiments where provenance and plastic effects can be measured and separated. In-situ model predictions of tree height variation among provenances and among planting sites were compared to observations in common gardens and to predictions from a similar model calibrated using common garden data (ex-situ model). Results In Q. petraea, we found high correlations between in-situ and ex-situ model predictions of provenance and plasticity effects and their interaction for tree height (r > .80). We showed that the in-situ models significantly predicted tree height variation among provenances and sites for A. alba and Q. petraea. Spatial predictions of phenotypic plasticity across species distribution ranges indicate decreasing tree height in populations of warmer climates in response to recent anthropogenic climate warming. Main conclusions Our modelling approach using national forest inventory observations provides a new perspective for understanding patterns of intraspecific trait variation across species ranges. Its application is particularly interesting for species for which common garden experiments do not exist or do not cover the entire climatic range of the species.

International audience; This study reinforces the argument that forest genetic resources for peripheral isolated plant populations (PIPP) need to come under rationalistic assessment, for developing and proposing conservation strategies of forest genetic resources. Cedrus brevifolia is a narrow endemic island tree occurring in a sole population. Using biparentally and paternally inherited microsatellites, the genetic contribution and genetic variation patterns within sites (subpopulations) and within plantations of this species were assessed. The C. brevifolia population recorded uneven partition of genetic diversity at the site and at local scales; mirroring the demography and genetic evolutionary factors that occurred in long-term at the intra-species level. Results from the plantations imply that screening and rejection of unsuitable seedlings before plantation establishment did not influence the genetic divergence of planted trees from the general genetic pool of natural population. Based on these outcomes, numerous conservation measures are proposed, towards maintaining the species’ genetic resources. These measures need to ensure the dynamic processes within stands. Thus, this study argues that for PIPP which recorded high genetic diversity and non-uniform distribution of genetic viability (complex genetic patterns), the several small conservation units seem to be the most rationalistic conservation units. In such case, forest genetic micro-reserves (GMR) can be enacted, where on-the-point dynamic in situ conservation activities can be adopted, while the GMR could be used for ex situ conservation purposes. In conclusion, in PIPP the maintenance of genetic diversity should be regarded as one of the main prerequisites for sustainable management and long-term survival of the species.

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

International audience; How populations of long-living species respond to climate change depends on phenotypic plasticity and local adaptation processes. Marginal populations are expected to have lags in adaptation (i.e. differences between the climatic optimum that maximizes population fitness and the local climate) because they receive pre-adapted alleles from core populations preventing them from reaching a local optimum in their climatically marginal habitat. Yet, whether adaptation lags in marginal populations are a common feature across phylogenetically and ecologically different species and how lags can change with climate change remain unexplored. To test for range-wide patterns of phenotypic variation and adaptation lags of populations to climate, we (a) built model ensembles of tree height accounting for the climate of population origin and the climate of the site for 706 populations monitored in 97 common garden experiments covering the range of six European forest tree species; (b) estimated populations' adaptation lags as the differences between the climatic optimum that maximizes tree height and the climate of the origin of each population; (c) identified adaptation lag patterns for populations coming from the warm/dry and cold/wet margins and from the distribution core of each species range. We found that (a) phenotypic variation is driven by either temperature or precipitation; (b) adaptation lags are consistently higher in climatic margin populations (cold/warm, dry/wet) than in core populations; (c) predictions for future warmer climates suggest adaptation lags would decrease in cold margin populations, slightly increasing tree height, while adaptation lags would increase in core and warm margin populations, sharply decreasing tree height. Our results suggest that warm margin populations are the most vulnerable to climate change, but understanding how these populations can cope with future climates depend on whether other fitness-related traits could show similar adaptation lag patterns.

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; The adaptation of social-ecological systems such as managed forests depends largely on decisions taken by forest managers who must choose among a wide range of possible futures to spread risks. We used robust decision theory to guide management decisions on the translocation of tree populations to compensate for climate change.We calibrated machine learning correlational models using tree height data collected from five common garden tests in France where Abies alba provenances from 11 European countries are planted. Resulting models were used to simulate tree height in the planting sites under current and 2050 climates (regional concentration pathway scenarios (RCPs) 2.6, 4.5, 6.0 and 8.5). Our results suggest an overall increase in tree height by 2050, but with large variation among the predictions depending on the provenance and the RCPs. We applied maximin, maximax and minimax decision rules to address outcomes under five uncertain states of the world represented by the four RCPs and the present climate (baseline). The maximin rule indicated that for 2050, the best translocation option for maximising tree height would be the use of provenances from Northwest France into all target zones. The maximax and minimax regret rules pointed out the same result for all target zones except for the ‘Les Chauvets’ trial, where the East provenance was selected. Our results show that decision theory can help management by reducing the number of options if most decision rules converge. Interestingly, the commonly suggested recommendation of using multiple provenances to mitigate long-term maladaptation risks or from ‘pre-adapted’ populations from the south was not supported by our approach.

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.

Mediterranean forests are found in the Mediterranean basin, California, the South African Cape Province, South and southwestern Australia and parts of Central Chile. They represent 1.8 % of the world forest areas of which the vast majority is found in the Mediterranean basin, where historical and paleogeographic episodes, long-term human influence and geographical and climatic contrasts have created ecosystemic diversity and heterogeneity. Even if evergreen is dominant, deciduous trees are also represented, with different forest types including dense stands with a closed canopy (forests sensu stricto) and pre-forestal or pre-steppic structures with lower trees density and height. The Mediterranean basin is also a hot spot of forest species and genetic diversity, with 290 woody species versus only 135 for non-Mediterranean Europe. However, the characteristics of the Mediterranean area (long-standing anthropogenic pressure, significant current human activity and broad biodiversity) make it one of the world’s regions most threatened by current changes. Four examples of Mediterranean forest types, present in south and north of the Mediterranean basin and more or less threatened, are developed in order to show that linking “hard sciences” and humanities and social sciences is necessary to understand these complex ecosystems. We show also that these forests, in spite of specific climatic constraints, can also be healthy and productive and play a major ecological and social role. Furthermore, even if the current human activity and global change constitute a risk for these exceptional ecosystems, Mediterranean forests represent a great asset and opportunities for the future of the Mediterranean basin.

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; The conservation and sustainable use of forests in the twenty-first century pose huge challenges for forest management and policy. Society demands that forests provide a wide range of ecosystem services, from timber products, raw materials and renewable energy to sociocultural amenities and habitats for nature conservation. Innovative management and policy approaches need to be developed to meet these often-conflicting demands in a context of environmental change of uncertain magnitude and scale. Genetic diversity is a key component of resilience and adaptability. Overall, forest tree populations are genetically very diverse, conferring them an enormous potential for genetic adaptation via the processes of gene flow and natural selection. Here, we review the main challenges facing our forests in the coming century and focus on how recent progress in genetics can contribute to the development of appropriate practical actions that forest managers and policy makers can adopt to promote forest resilience to climate change. Emerging knowledge will inform and clarify current controversies relating to the choice of appropriate genetic resources for planting, the effect of silvicultural systems and stand tending on adaptive potential and the best ways to harness genetic diversity in breeding and conservation programs. Gaps in our knowledge remain, and we identify where additional information is needed (e.g., the adaptive value of peripheral populations or the genetic determinism of key adaptive traits) and the types of studies that are required to provide this key understanding.

The European black pine (Pinus nigra Arn.) is an ecologically and economically important conifer discontinuously and often patchily distributed across different ecological environments and climatic conditions around the Mediterranean Basin. Many studies aiming at understanding the evolutionary history of the species have been carried out, particularly in the hope of resolving the taxonomy of this collective species where many subspecies have been described. So far, neither morphology, enzyme, and metabolite polymorphism nor DNA marker studies have been able to converge on a single taxonomy, and the evolutionary history of the European black pine remains unclear. To date, nuclear microsatellites (nSSRs) are not available for P. nigra. In this work we designed two multiplexes of eight and six nSSRs each, both characterized by high amplification quality and polymorphism. Nine nSSRs were specifically developed for the European black pine starting from six transcriptomes sequenced using Next Generation Sequencing (NGS) techniques following the Illumina method, while five previously developed for other pines were successfully transferred to P. nigra. The mean number of alleles per locus was 5.9, and the observed heterozygosity ranged between 0.341 and 0.875. F ST was statistically significant for all loci, and Bayesian clustering approaches revealed a geographically meaningful population structure. We thus show this set of 14 nSSRs to be highly informative for population genetic studies and of significant interest to resolve the taxonomy of the European black pine.

Genetic association studies in forest tress would greatly benefit from information on tree response to environmental stressors over time. Dendroecology can close this gap by providing such time series measurements. Here, we jointly analyzed dendroecological and genetic data to explore the genetic basis of resistance, recovery and resilience to episodic stress in silver fir. We used individual level tree-ring data to characterize the growth patterns of surviving silver fir (Abies alba) during the forest dieback in the 1970s and 1980s in Central Europe and associated them with SNPs in candidate genes. Most trees at our study sites in the Bavarian Forest experienced severe growth decline from 1974 until the mid-1980s, which peaked during the drought year of 1976. Using the machine learning algorithm random forest, we identified 15 candidate genes that were associated with the variance in resistance, resilience and recovery among trees in this period. With our study we show that the unique possibility of phenotypic time series archived in tree-rings are a powerful resource in genetic association studies. We call for a closer collaboration of dendroceologists and forest geneticists to focus on integrating individual tree level signals in genetic association studies in long lived trees.

Finding outlier loci underlying local adaptation is challenging and is best approached by suitable sampling design and rigorous method selection. In this study, we aimed to detect outlier loci (single nucleotide polymorphisms, SNPs) at the local scale by using Aleppo pine (Pinus halepensis), a drought resistant conifer that has colonized many habitats in the Mediterranean Basin, as the model species. We used a nested sampling approach that considered replicated altitudinal gradients for three contrasting sites. We genotyped samples at 294 SNPs located in genomic regions selected to maximize outlier detection. We then applied three different statistical methodologies&mdash, Two Bayesian outlier methods and one latent factor principal component method&mdash, To identify outlier loci. No SNP was an outlier for all three methods, while eight SNPs were detected by at least two methods and 17 were detected only by one method. From the intersection of outlier SNPs, only one presented an allelic frequency pattern associated with the elevational gradient across the three sites. In a context of multiple populations under similar selective pressures, our results underline the need for careful examination of outliers detected in genomic scans before considering them as candidates for convergent adaptation.

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.

Seed production is a strong indicator of plant fitness and plays a major role in population dynamics. However, the environmental and Seed production is a strong indicator of plant fitness and plays a major role in population dynamics. However, the environmental and endogenous factors driving seed production are still poorly described and are often hard to disentangle. Consequently, we combined principal components analysis and mixed-effects linear models that can consider the multicollinearity of the explanatory variables and quantify their respective influence on the spatio-temporal variability in reproduction. We applied this method to analyze the relationships between cone production in Abies alba Mill. trees (6829 individual reports of cone production). We estimated the relationships between cone production and climate, elevation, tree size (diameter and height), age, crown defoliation rate, and past radial growth. We found that the distribution of annual cone production was highly skewed; 21% of the trees did not produce any cones, whereas 3.7% produced more than 100 cones in a single year. Among the endogenous factors, tree size explained 57% of the variation in cone production with large trees being the most productive. Low radial growth rates in previous years were mostly associated with higher cone production (14% of the variation), while elevation and crown defoliation had non-monotonic effects on reproduction. Finally, years of high cone production were strongly correlated with the difference between the April temperatures of the two previous years and were also associated with a dry spring 2 yr prior to cone production followed by a humid spring the previous year. These results highlight the complexity of the abiotic and biotic factors involved in reproduction and their respective and interactive influence on the interannual and interindividual variability in cone production.endogenous factors driving seed production are still poorly described and are often hard to disentangle. Consequently, we combined principal components analysis and mixed-effects linear models that can consider the multicollinearity of the explanatory variables and quantify their respective influence on the spatio-temporal variability in reproduction. We applied this method to analyze the relationships between cone production in Abies alba Mill. trees (6829 individual reports of cone production). We estimated the relationships between cone production and climate, elevation, tree size (diameter and height), age, crown defoliation rate, and past radial growth. We found that the distribution of annual cone production was highly skewed; 21% of the trees did not produce any cones, whereas 3.7% produced more than 100 cones in a single year. Among the endogenous factors, tree size explained 57% of the variation in cone production with large trees being the most productive. Low radial growth rates in previous years were mostly associated with higher cone production (14% of the variation), while elevation and crown defoliation had non-monotonic effects on reproduction. Finally, years of high cone production were strongly correlated with the difference between the April temperatures of the two previous years and were also associated with a dry spring 2 yr prior to cone production followed by a humid spring the previous year. These results highlight the complexity of the abiotic and biotic factors involved in reproduction and their respective and interactive influence on the interannual and interindividual variability in cone production.

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.

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.

Chapitre 2; All around the Mediterranean, forest systems have been shaped by long-term anthropogenic impacts. Today, they provide multiple goods and services. We show how the social-ecological system approach offers a good framework to understand their biodiversity, functioning and dynamics. Mediterranean forests have a huge biodiversity, not only in terms of the number of species but also in terms of within-species genetic diversity (at least tree species). We present a tentative typology of Mediterranean forests regarding this biodiversity. Then, we explain how the dynamics of Mediterranean forests is driven in particular by a combination of three characteristics: specific environmental constraints (mainly summer water deficit), a marked spatial heterogeneity of the environment at all scales, disturbance regime (e.g. fire, droughts, pest attacks, human pressure) of variable intensity and frequency. The future challenges for the Mediterranean forests will be to respond simultaneously to: (i) increased threats related to climate change and human pressure, (ii) new demand for multiple ecosystem services locally, (iii) emerging interest for Mediterranean resources to support adaptive strategies in other regions.

International audience; Biodiversity is the diversity of life at all scales, from genes to ecosystems. Predicting its patterns of variation across the globe is a fundamental issue in ecology and evolution. Diversity within species, that is, genetic diversity, is of prime importance for understanding past and present evolutionary patterns, and highlighting areas where conservation might be a priority. Using published data on the genetic diversity of species whose populations occur in the Mediterranean basin, we calculated a coefficient of correlation between within-population genetic diversity indices and longitude. Using a meta-analysis framework, we estimated the role of biological, ecological, biogeographic, and marker type factors on the strength and magnitude of this correlation in six phylla. Overall, genetic diversity increases from west to east in the Mediterranean basin. This correlation is significant for both animals and plants, but is not uniformly expressed for all groups. It is stronger in the southern than in the northern Mediterranean, in true Mediterranean plants than in plants found at higher elevations, in trees than in other plants, and in bi-parentally and paternally than in maternally inherited DNA makers. Overall, this correlation between genetic diversity and longitude, and its patterns across biological and ecological traits, suggests the role of two non-mutually exclusive major processes that shaped the genetic diversity in the Mediterranean during and after the cold periods of the Pleistocene: east-west recolonization during the Holocene and population size contraction under local Last Glacial Maximum climate in resident western and low elevation Mediterranean populations.

Trees' long lifespan, long-distance dispersal abilities and high year-to-year variability in fecundity are thought to have pervasive consequences for the demographic and genetic structure of recruited seedlings. However, we still lack experimental studies quantifying the respective roles of spatial processes such as restricted seed and pollen dispersal and temporal processes such as mast seeding on patterns of regeneration. Dynamics of European beech (Fagus sylvatica) seedling recruitment was monitored in three plots from 2004 to 2006. Six polymorphic microsatellite genetic markers were used to characterize seedlings and their potential parents in a 7.2-ha stand. These seedlings were shown to result from 12 years of recruitment, with one predominant year of seedling recruitment in 2002 and several years without significant recruitment. Using a spatially explicit mating model based on parentage assignment, short average dispersal distances for seed (δ(s) = 10.9 m) and pollen (43.7 m < δ(p)

Aim We address the question of whether broad scale biogeographical structure of species diversity (SD) matches that of genetic diversity (GD) of vascular plants. Location The Mediterranean basin. Methods We normalized vascular plant species richness (SD) estimates per country using the Med-Checklist taxonomic database. We used a linear regression analysis to correlate normalized country estimates with country longitudinal position. We also compiled published and geo-referenced within-population GD data for tree species, which had populations in the Mediterranean. We normalized GD estimates for each population across species. Again, we used a linear regression analysis to correlate GD with population longitudinal position. We then compared the populations’ geographical and bioclimatic trends for GD with Last Glacial Maximum (LGM) palaeo-climate data and the species current ecological requirements. Results The eastern Mediterranean and the coast of former Yugoslavia had higher SD than other regions. There was no overall spatial structure of SD in the Mediterranean, whereas there was an east–west trend of decreasing GD. This trend for GD tended to covary with an east–west warm/wet–cold/dry trend detected during the LGM. Low elevation xerothermic pine species displayed significantly less GD than higher elevation mesothermic or mountain pine species. Main conclusions We suggest that LGM climate may have significantly shaped the current longitudinal and altitudinal patterns of GD we observed in woody taxa across the Mediterranean, although it did not affect comparable SD patterns. In particular, colder LGM summer temperatures in the western Mediterranean may have reduced population sizes significantly more than in the eastern Mediterranean. As plant species richness and GD did not covary, SD and GD may not be used as surrogates of one another in the Mediterranean basin. As they contain comparatively less GD, conservation priorities in the Mediterranean should focus on hot spots of endemism and Western Mediterranean populations and species.

Understanding local adaptation in forest trees is currently a key research and societal priority. Geographically and ecologically marginal populations provide ideal case studies, because environmental stress along with reduced gene flow can facilitate the establishment of locally adapted populations. We sampled European silver fir (Abies alba Mill.) trees in the French Mediterranean Alps, along the margin of its distribution range, from pairs of high- and low-elevation plots on four different mountains situated along a 170-km east-west transect. The analysis of 267 SNP loci from 175 candidate genes suggested a neutral pattern of east-west isolation by distance among mountain sites. F(ST) outlier tests revealed 16 SNPs that showed patterns of divergent selection. Plot climate was characterized using both in situ measurements and gridded data that revealed marked differences between and within mountains with different trends depending on the season. Association between allelic frequencies and bioclimatic variables revealed eight genes that contained candidate SNPs, of which two were also detected using F(ST) outlier methods. All SNPs were associated with winter drought, and one of them showed strong evidence of selection with respect to elevation. Q(ST)-F(ST) tests for fitness-related traits measured in a common garden suggested adaptive divergence for the date of bud flush and for growth rate. Overall, our results suggest a complex adaptive picture for A. alba in the southern French Alps where, during the east-to-west Holocene recolonization, locally advantageous genetic variants established at both the landscape and local scales.

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.

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

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.

We developed primers for the amplification of six polymorphic nuclear microsatellites in Mediterranean Cedrus taxa. Microsatellites originated from two Cedrus atlantica genomic libraries enriched for TC (four markers) and TG (two markers) motifs. No distortion from Mendelian segregation was observed. There were up to eight alleles per locus and mean expected heterozygosity was 0.75. Four microsatellites also amplified in the Himalayan cedar. These markers should be helpful for species identification, diversity studies, parentage analysis and genome mapping and to monitor biodiversity in endangered Mediterranean Cedrus forests.

International audience; 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.

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.

• Premise of the study Pinus pinea is one of the few widespread plant species that are also genetically depauperate. It is also an important commercial species with high market value seeds. A deeper knowledge of the existing population genetic variation was needed. • Methods and Results Twelve nuclear microsatellites were isolated from genomic and cDNA sequences and screened for variability in 729 individuals from 33 natural populations. Low level of genetic variability was confirmed with average expected heterozygosity of 0.11. Hardy-Weinberg equilibrium expectations were not met in only ~10% of the possible locus/population combinations. All loci were in linkage equilibrium, and the frequency of null alleles was very low (≤ 1% in 332 out of 396 locus/ population combinations). Nine out of the 12 microsatellites were successfully transferred to P. halepensis. • Conclusions Despite low polymorphism, these new markers will be useful to resolve population structure and hold potential for seed origin identification and traceability. © 2012 Botanical Society of America.

International audience; Inbreeding depression is a key factor affecting the persistence of natural populations, particularly when they are fragmented. In species with mixed mating systems, inbreeding depression can be estimated at the population level by regressing the average progeny fitness by the selfing rate of their mothers. We applied this method using simulated populations to investigate how population genetic parameters can affect the detection power of inbreeding depression. We simulated individual selfing rates and genetic loads from which we computed fitness values. The regression method yielded high statistical power, inbreeding depression being detected as significant (5 % level) in 92 % of the simulations. High individual variation in selfing rate and high mean genetic load led to better detection of inbreeding depression while high among-individual variation in genetic load made it more difficult to detect inbreeding depression. For a constant sampling effort, increasing the number of progenies while decreasing the number of individuals per progeny enhanced the detection power of inbreeding depression. We discuss the implication of among-mother variability of genetic load and selfing rate on inbreeding depression studies.

Endemic island plant species with a narrow distribution are often, but not always, linked to low genetic variation within populations and a lack of differentiation among populations. Cedrus brevifolia is a narrow endemic island tree species of Cyprus. Its range is restricted to a single forest, divided into five neighbouring sites. This study, using biparentally inherited nuclear microsatellites and paternally inherited plastid (chloroplast) microsatellites, assessed the genetic variation of C. brevifolia within its sole population and the level of genetic differentiation among formed sites. The results from both markers showed high diversity (nuclear HT = 0.70; plastid HT = 0.93), strongly suggesting that the species did not experience severe bottleneck events or extensive genetic drift. Besides, the maintenance of a high genetic diversity in C. brevifolia may suggest that it originates from a widespread congener species. Significant genetic differentiation at nuclear (GST = 0.052) and plastid (GST = 0.119) markers was found among the formed sites. Remarkably, the relatively high genetic differentiation found at plastid markers was comparable to values observed in two widespread congener cedar species. The genetic differentiation probably occurred due to fragmentation of a previously uniform population. This would lead to the shaping of different genetic groups (Bayesian analysis) and to significant population substructure. Furthermore, significant values observed for both isolation by distance and large-scale spatial genetic structure could indicate ineffective gene flow among sites and the early geographical isolation of the more isolated sites from the core population. peerReviewed

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; Diffusion is one of the most frequently used assumptions to explain dispersal. Diffusion models and in particular reaction–diffusion equations usually lead to solutions moving at constant speeds, too slow compared to observations. As early as 1899, Reid had found that the rate of spread of tree species migrating to northern environments at the beginning of the Holocene was too fast to be explained by diffusive dispersal. Rapid spreading is generally explained using long distance dispersal events, modelled through integro-differential equations (IDEs) with exponentially unbounded (EU) kernels, i.e. decaying slower than any exponential. We show here that classical reaction–diffusion models of the Fisher–Kolmogorov–Petrovsky–Piskunov type can produce patterns of colonisation very similar to those of IDEs, if the initial population is EU at the beginning of the considered colonisation event. Many similarities between reaction–diffusion models with EU initial data and IDEs with EU kernels are found; in particular comparable accelerating rates of spread and flattening of the solutions. There was previously no systematic mathematical theory for such reaction–diffusion models with EU initial data. Yet, EU initial data can easily be understood as consequences of colonisation–retraction events and lead to fast spreading and accelerating rates of spread without the long distance hypothesis.

Aim Our aims were to test whether morphological species of mountain pines were genetically supported in the western part of the distribution range of the Pinus mugo species complex (Pinus mugo Turra sensu lato), to resolve genetically homogeneous clusters of populations, to determine historical demographic processes, and to assess the potential hybridization of mountain pines with Scots pine, Pinus sylvestris L. Location Populations were sampled in the Iberian System, the Pyrenees, the French Mont Ventoux, Vosges and Jura mountains, the German Black Forest and throughout the Alps. This corresponded to a range-wide sampling for mountain pine sensu stricto (Pinus uncinata Ram.) and to a sampling of the western parts of the ranges of dwarf mountain pine (Pinus mugo Turra sensu stricto) and bog pine/peatbog pine [Pinus rotundata Link/Pinus × pseudopumilio (Willk.) Beck]. Methods In total, 786 individuals of P. mugo sensu lato from 29 natural populations, and 85 individuals of P. sylvestris from four natural populations were genotyped at three chloroplast microsatellites (cpSSRs). Populations were characterized for standard genetic diversity statistics and signs of demographic expansion. Genetic structure was explored using analysis of molecular variance, differentiation statistics and Bayesian analysis of population structure (BAPS). Results One hundred haplotypes were identified in P. mugo sensu lato. There was a stronger differentiation between geographical regions than between morphologically identified taxa (P. mugo sensu stricto, P. uncinata and P. rotundata/P. ×pseudopumilio). Overall genetic differentiation was weak (GST = 0.070) and displayed a clear phylogeographic structure [NST = 0.263, NST > N ST (permuted), P < 0.001]. BAPS identified a Pyrenean and an Alpine gene pool, along with several smaller genetic clusters corresponding to peripheral populations. Main conclusions The core regions of the Pyrenees and Alps were probably recolonized, respectively by P. uncinata and P. uncinata/P. mugo sensu stricto, from multiple glacial refugia that were well connected by pollen flow within the mountain chains. Pinus rotundata/P. × pseudopumilio populations from the Black Forest, Vosges and Jura mountains were probably recolonized from various glacial populations that kept their genetic distinctiveness despite late glacial and early Holocene expansion. Marginal P. uncinata populations from the Iberian System are compatible with elevational shifts and long-term isolation. The causes of haplotype sharing between P. mugo sensu lato and P. sylvestris require further research. © 2009 Blackwell Publishing Ltd.

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

Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite markers in three French Fagus sylvatica populations: (1) maximum likelihood methods that compare observed and expected homozygote frequencies in the population under the assumption of Hardy-Weinberg equilibrium and (2) direct null allele frequency estimates from progeny where parent genotypes are known. We show that null allele frequencies are high in F. sylvatica (7.0% on average with the population method, 5.1% with the progeny method), and that estimates are consistent between the two approaches, especially when the number of sampled maternal half-sib progeny arrays is large. With null allele frequencies ranging between 5% and 8% on average across loci, population genetic parameters such as genetic differentiation (F ST) may be mostly unbiased. However, using markers with such average prevalence of null alleles (up to 15% for some loci) can be seriously misleading in fine scale population studies and parentage analysis.

International audience; We present a range-wide synthesis of our own research and related work on the complex postglacial history of Abies alba Mill. It is based on macroremains, fossil pollen records as well as on different genetic markers. The geographic distribution of genetic lineages and allele frequencies together with the fossil records confirm multiple refugia with at least three of them being sources for the Holocene range expansion into Central Europe, representing so-called effective refugia. One is located in the northern Apennines. A long-term refugium in the southern Balkans contributes to northward expansion with a branch along the Carpathians in the East and the Dinaric Alps in the West. Furthermore, new allozyme data indicate a third effective refugium in the northern or western Balkans, respectively. Using different genetic marker categories the differentiation of A. alba populations could be attributed to different time scales. A separation of maternal lineages took place in previous glacial cycles of the Quaternary, while a second pattern of genetic differentiation is the result of isolation processes during the last glaciation and subsequent gene flow after range expansion. Suture and introgression zones of refugial gene pools were clearly recognised. The patterns of genetic variation and genetic diversity spanning between rear and leading edges of the present range are discussed for evolutionary implications and conservation strategies.