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International audience; Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic‐based experimental comparisons is required. In long‐lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo‐response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress‐response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long‐lived trees.

International audience; A parallel study of the genetic structure of two oligophagous species associated with the same hosts was conducted to determine the main factors shaping the distribution of genetic diversity. The bark beetle Tomicus piniperda and the pine processionary moth (PPM) Thaumetopoea pityocampa are both associated with the genus Pinus and belong to different guilds (xylophagous vs defoliating species). The PPM is an ectophagous species that feeds on the needles of living trees, whereas T. piniperda is endophagous and bores galleries in the inner bark of weakened trees. Both species were sampled in the main regions of France, and their genetic structure was assessed after genotyping with five microsatellite markers. Populations of the PPM were significantly structured. A pattern of isolation by distance was found when distances were calculated as bypassing the Massif Central, whereas no such pattern could be found with raw geographic distances. On the contrary, most populations of T. piniperda were not differentiated. No effect of host species could be detected in either of the two species. We conclude that the two taxa have contrasting effective dispersal rates per generation, and we hypothesize that this reflects the different selection pressures acting on individual fitness via different strategies of host use.

International audience; Genetic variation in 23 populations of European chestnut (Castanea sativa L) to Ink Disease caused by Phytophthora cambivora (Petri) Buisman was studied in three labs. The populations represented three domestication levels (naturalized populations, coppice forests and orchards) and were sampled in 10 locations in five countries (Italy, France, Greece, Spain, and the UK). Adult chestnut susceptibility to Ink Disease was assessed by measuring lesion length following inoculation of excised shoots with P. cambivora. Half-sib families were harvested in most of these populations and the seedlings were root-inoculated. Provenance and family variance components were estimated. Significant variation in the extent of shoot colonization by P. cambivora was observed within and among adult tree populations, suggesting a large amount of genetic variation in resistance. No consistent ranking of the domestication levels for susceptibility was observed. Some results indicate selective pressure exerted by P. cambivora on local populations. Lesion measurements in a set of 48 trees inoculated in 2001 and 2002 were correlated (r = 0.58). One or more resistant trees (lesion length < 10 mm) were identified in 15 populations. Root inoculation of seedlings showed that only three families had a mean value for percentage of infected taproot = 15% or comparable to seedlings of the resistant control 'Marigoule'. Lesion lengths in parent trees and percentage of infection of the taproot of their seedlings were not highly correlated

International audience; The aim of this study was to assess the stimulatory effects of different low molecular weight organic compounds commonly present in root exudates on microbial activity and hydrolase activities, and the effects of high Cd concentrations in sandy soils collected from contaminated field plots on the stimulatory effects. Glucose, glutamic acid, citric acid, oxalic acid, or a mixture of all compounds were released by an artificial root surface in a simplified rhizosphere system. The effects were measured at 4 mm (bulk soil layer) distance from the root surface, 7 d after the root exudates release. Results showed that different root exudates were mineralized at different extent and had different stimulatory effects on microbial growth estimated by dsDNA content of soil, and on hydrolase activities, mostly localized in the rhizosphere soil layer. Mineralization of root exudates, microbial growth and stimulation of most of the measured hydrolase activities were drastically reduced by high Cd concentrations in soil

International audience; In order to determine the mechanical resistance of several forest tree species to rockfall, an inventory of the type of damage sustained in an active rockfall corridor was carried out in the French Alps. The diameter, spatial position and type of damage incurred were measured in 423 trees. Only 5% of trees had sustained damage above a height of 1.3 m and in damaged trees, 66% of broken or uprooted trees were conifers. Larger trees were more likely to be wounded or dead than smaller trees, although the size of the wounds was relatively smaller in larger trees. The species with the least proportion of damage through stem breakage, uprooting or wounding was European beech (Fagus sylvatica L.). Winching tests were carried out on two conifer species, Norway spruce (Picea abies L.) and Silver .r (Abies alba Mill.), as well as European beech, in order to verify the hypothesis that beech was highly resistant to rockfall and that conifers were more susceptible to uprooting or stem breakage. Nineteen trees were winched downhill and the force necessary to cause failure was measured. The energy (Efail) required to break or uproot a tree was then calculated. Most .r trees failed in the stem and spruce usually failed through uprooting. Beech was either uprooted or broke in the stem and was twice as resistant to failure as .r, and three times more resistant than spruce. Efail was strongly related to stem diameter in European beech only, and was signi.cantly higher in this species compared to Norway spruce. Results suggest that beech would be a better species to plant with regards to protection against rockfall. Nevertheless, all types of di.erent abiotic stresses on any particular alpine site should be considered by the forest manager, as planting only broadleaf species may compromise the protecting capacity of the forest e.g. in the case of snow avalanches. In order to determine the mechanical resistance of several forest tree species to rockfall, an inventory of the type of damage sustained in an active rockfall corridor was carried out in the French Alps. The diameter, spatial position and type of damage incurred were measured in 423 trees. Only 5% of trees had sustained damage above a height of 1.3 m and in damaged trees, 66% of broken or uprooted trees were conifers. Larger trees were more likely to be wounded or dead than smaller trees, although the size of the wounds was relatively smaller in larger trees. The species with the least proportion of damage through stem breakage, uprooting or wounding was European beech (Fagus sylvatica L.). Winching tests were carried out on two conifer species, Norway spruce (Picea abies L.) and Silver .r (Abies alba Mill.), as well as European beech, in order to verify the hypothesis that beech was highly resistant to rockfall and that conifers were more susceptible to uprooting or stem breakage. Nineteen trees were winched downhill and the force necessary to cause failure was measured. The energy (Efail) required to break or uproot a tree was then calculated. Most .r trees failed in the stem and spruce usually failed through uprooting. Beech was either uprooted or broke in the stem and was twice as resistant to failure as .r, and three times more resistant than spruce. Efail was strongly related to stem diameter in European beech only, and was signi.cantly higher in this species compared to Norway spruce. Results suggest that beech would be a better species to plant with regards to protection against rockfall. Nevertheless, all types of di.erent abiotic stresses on any particular alpine site should be considered by the forest manager, as planting only broadleaf species may compromise the protecting capacity of the forest e.g. in the case of snow avalanches.

Vetiver grass (Vetiveria zizanioides), also known as Chrysopogon zizanioides, is a graminaceous plant native to tropical and subtropical India. The southern cultivar is sterile; it flowers but sets no seeds. It is a densely tufted, perennial grass that is considered sterile outside its natural habitat. It grows 0.5–1.5 m high, stiff stems in large clumps from a much branched root stock. The roots of vetiver grass are fibrous and reported to reach depths up to 3 m thus being able to stabilize the soil and its use for this purpose is promoted by the World Bank. Uprooting tests were carried out on vetiver grass in Spain in order to ascertain the resistance the root system can provide when torrential runoffs and sediments are trying to uproot the plant. Uprooting resistance of each plant was correlated to the shoot and root morphological characteristics. In order to investigate any differences between root morphology of vetiver grass in its native habitat reported in the literature, and the one planted in a sub-humid environment in Spain, excavation techniques were used to show root distribution in the soil. Results show that vetiver grass possesses the root strength to withstand torrential runoff. Planted in rows along the contours, it may act as a barrier to the movement of both water and soil. However, the establishment of the vetiver lags behind the reported rates in its native tropical environment due to adverse climatic conditions in the Mediterranean. This arrested development is the main limitation to the use of vetiver in these environments although its root strength is more than sufficient.

International audience; Two unigene datasets of Pinus taeda and Pinus pinaster were screened to detect di-, tri- and tetranucleotide repeated motifs using the SSRIT script. A total of 419 simple sequence repeats (SSRs) were identified, from which only 12.8% overlapped between the two sets. The position of the SSRs within their coding sequences were predicted using FrameD. Trinucleotides appeared to be the most abundant repeated motif (63 and 51% in P. taeda and P. pinaster, respectively) and tended to be found within translated regions (76% in both species), whereas dinucleotide repeats were preferentially found within the 5'- and 3'-untranslated regions (75 and 65%, respectively). Fifty-three primer pairs amplifying a single PCR fragment in the source species (mainly P. taeda), were tested for amplification in six other pine species. The amplification rate with other pine species was high and corresponded with the phylogenetic distance between species, varying from 64.6% in P. canariensis to 94.2% in P. radiata. Genomic SSRs were found to be less transferable; 58 of the 107 primer pairs (i.e., 54%) derived from P. radiata amplified a single fragment in P. pinaster. Nine cDNA-SSRs were located to their chromosomes in two P. pinaster linkage maps. The level of polymorphism of these cDNA-SSRs was compared to that of previously and newly developed genomic-SSRs. Overall, genomic SSRs tend to perform better in terms of heterozygosity and number of alleles. This study suggests that useful SSR markers can be developed from pine ESTs

International audience; Metapopulation dynamics and epidemiology of some diseases on sessile hosts (like pathogen fungi/tree interactions) can be modelled by contact processes on a graph. There exist several recent work on the structure of a graph, with classical notion like degree, diameter, small world property, etc., but quite fewer work on dynamics on graphs. Here, we model time discrete contact process on graphs with known degree distribution, with local mortality and spread along the edges with constant diffusion coefficient. We show that the knowledge of the degree distribution only leads to a mean field approximation only of the contact process. The fraction of infected hosts (or occupied patches) is modelled as a function of the degree of the vertex. As a consequence of mean field approximation, the stationary distribution at equilibrium belongs to a universal family of curves, which is independent of the degree distribution. An analytic description of this family is given. Each curve in the family is identified by one parameter only, which can be the mean infection rate (or occupancy rate) for the whole graph, obtained as a solution of an implicit equation containing the degree distribution. Finally, an exact equation relating the density of occupancy and the probability for types of edges is given, as a first step towards pair approximation on graphs

Summary We review here our own research and related work on hybridization between two widespread and largely sympatric European oak species (Quercus petraea and Q. robur). There is a near total lack of local differentiation in chloroplast DNA markers between them. A model is proposed to account for this lack of differentiation: invasion by one species of the range occupied by the other through pollen swamping. In support of this model, ecological, palaeoecological and population genetic studies indicate that one species (Q. robur) disperses its seeds better than the other one, that pollen flow is much more efficient than seed flow in oaks and that hybridization and introgression are asymmetric, hence reinforcing the ecological dynamics by facilitating the dispersal of Q. petraea in regions already colonized by Q. robur. ‘Resurrection’ of Q. petraea following this wave of hybridization appears to be rapid. More generally, available evidence indicates that hybridization could constitute an important mechanism of dispersal in both natural and human-induced plant invasions.

We studied the phylogeography of alder buckthorn (Frangula alnus), a bird-dispersed shrub or small tree distributed over most of Europe and West Asia and present in three of the four main refugia of West Palaearctic temperate woody plants: the Iberian Peninsula, the Balkans and Anatolia. A total of 78 populations from 21 countries were analysed for chloroplast DNA variation using polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP), and 21 different haplotypes were distinguished. We found a very strong overall population differentiation (GST = 0.81) and phylogeographical struc- ture, and a sharp contrast between the haplotype-rich refugia and the almost completely uniform area of postglacial colonization. The haplotype network comprises three lineages made up of haplotypes from the Iberian Peninsula, Anatolia with the Caucasus, and tem- perate Europe. The Iberian and the Anatolian branches represent parts of a major lineage that spans over the whole northern Mediterranean Basin and some neighbouring areas and probably dates back to the Tertiary. Many haplotypes of this lineage are distributed locally and most populations are fixed for a single haplotype; these populations have apparently been very stable since their establishment, experiencing negligible gene flow and few mutations. The temperate European lineage consists of one very widespread and abundant plus six locally distributed haplotypes. Four of them are located in Southeast Europe, the putative refugium of all extant temperate European populations. Contrary to populations from Iberia and Anatolia, F. alnus populations from the southeastern European refugium have most genetic variation within populations. Bird-mediated seed dispersal has apparently allowed not only a very rapid postglacial expansion of F. alnus but also subsequent regular seed exchanges between populations of the largely continuous species range in temperate Europe. In contrast, the disjunct F. alnus populations persisting in Mediterranean mountain ranges seem to have experienced little gene flow and have therefore accumulated a high degree of differentiation, even at short distances. Populations from the southern parts of the glacial refugia have contributed little to the postglacial recolonization of Europe, but their long- term historical continuity has allowed them to maintain a unique store of genetic variation

The proliferation of genetically modified crops has created a need for methods to predict the likelihood of gene introgression into related species in situ. We present a model of a modified crop and an associated unmodified plant population removed spatially from the modified crop but not completely isolated from it, reflecting standard practices for isolation of field trials. We develop models for two kinds of life histories, broadly based on Brassica and Gossypium, taxa that are targets for genetic modification. We find that current prescriptions for field trials are likely to lead to escape of transgenes into wild populations when outcrossing rates are moderate and hybrids are fertile. The results are sensitive to pollen rain within plausible bounds for model parameters, suggesting buffer widths are an important aspect of the design of field trials. When gene introgression requires the spontaneous development of a polyploid, the likelihood of gene introgression is lower but still appreciable in realistic circumstances. Events that are unlikely over periods of a few years become almost certain within scales of a few decades, emphasising the need for gene risk assessments to be set in specified time frames. The models serve to identify the parts of the system that are poorly known and that are important in determining outcomes, providing a focus for future research. There is a need for research on the consequences of changes in fitness due to the transgenes, competitive interactions between related species, and the broader ecological consequences of changes in agricultural practice resulting from the use of genetically modified crops.

International audience; The bast scale Matsucoccus feytaudi is a specific pest of maritime pine that is endemic in the Iberian Peninsula and southwestern France, and invasive in southeastern France, Italy and Corsica where it causes heavy damages. We developed eight microsatellite polymorphic markers using an enrichment protocol in order to study the invasion pathways and infer the genetic diversity of the populations. All loci could be successfully amplified with no evidence of null alleles. Cross-species amplifications failed to amplify the congeneric Matsucoccus josephi

Association studies aim to discover the genetic basis of genetic diseases or drug responses through the comparison of unrelated affected and nonaffected individuals in large populations assumed to be at Hardy–Weinberg equilibrium (HWE). The HWE principle and the main causes of departures are first described with a focus on population stratification (Wahlund effect), which is one of the major problems in association studies. Recent statistical methods developed to detect and control for it are briefly reviewed. Keywords: Hardy–Weinberg equilibrium; Wahlund effect; population stratification; linkage disequilibrium; association studies

I. SYNTHÈSE DES ACTIVITÉS SCIENTIFIQUES........................................................41. Introduction...................................................................................... 41.1. Génétique de la qualité de la graine du soja......................................... 41.2. Méta-analyse de locus à effet quantitatif (QTL)......................................52. Flux de gènes et arbres forestiers............................................................ 62.1. Contexte.................................................................................... 62.1.1. Les flux de gènes pourquoi, comment............................................ 62.1.2. Une brève histoire de la recherche de paternité............................... 72.1.3. Arbres et flux de gènes............................................................. 82.2. Développements méthodologiques......................................................92.2.1. Mesurer la qualité d'un système de marquage : les probabilités d'exclusion ..92.2.1.1. Principe.......................................................................... 92.2.1.2. Comparaison des marqueurs microsatellites et AFLP................... 102.2.2. Recherche de paternité et de parenté..........................................112.3. Populations naturelles et flux de gènes.............................................. 122.3.1. Structure génétique fine, flux de graines et fratries......................... 122.3.2. Nombre de pères....................................................................132.4. Populations améliorées et flux de gènes............................................. 152.4.1. Test variétal et marqueurs chez le pin maritime............................. 152.4.2. Fonctionnement des vergers à graines.......................................... 162.4.3. Apparentement chez les vignes cultivées...................................... 192.5. Paternité et parenté chez les chênes européens : le projet OAKFLOW......... 192.5.1. Principe.............................................................................. 202.5.2. Premiers résultats.................................................................. 202.5.3. Perspectives......................................................................... 212.6. Génétique, chênes et paysages........................................................ 213. Perspectives : flux de gènes intra- et interspécifiques.................................. 233.1. Flux de gènes dans le complexe d'espèces des chênes blancs.................... 233.2. Approches méthodologiques............................................................263.2.1. Flux de gènes instantanés intra- et inter-population......................... 263.2.2. Méthodes de reconstitution des apparentements sans pedigree........... 273.3. Interactions biotiques et biodiversité.................................................283.3.1. Dispersion des chênes sous l'effet des geais....................................283.3.2. Dispersion des graines : génétique et pathologie............................. 293.4. Une école-chercheur "philosophie et histoire des sciences biologiques"........ 304. En guise de conclusion........................................................................ 325. Références...................................................................................... 33

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The spatial distribution of soil invertebrates is aggregated with high-density patches alternating with low-density zones. A high degree of spatio-temporal organization generally exists with identified patches of specific species assemblages, in which species coexist according to assembly rules related to competitive mechanisms for spatial and trophic resources occur. However, these issues have seldom been addressed. The spatio-temporal structure of a native earthworm community in a natural savanna and a grass–legume pasture in the Colombian “Llanos” was studied during a 2-year-period. A spatially explicit sampling design (regular grid) was used to discern the distribution pattern of species assemblages in both systems. Earthworms were collected from small soil pits at three different sampling dates. Data collected from 1 m2 soil monoliths were also used in the present study. Data were analyzed with the partial triadic analysis (PTA) and correlograms, while niche overlap was computed with the Pianka index. The PTA and correlogram analysis revealed that earthworm communities displayed a similar stable spatial structure in both systems during the 2-year study period. An alternation of population patches where different species' assemblages dominated was common to all sampling dates. The medium-sized Andiodrilus sp. and Glossodrilus sp. exhibited a clear spatial opposition in natural savanna and the grass–legume pasture for the duration of the study. The Pianka index showed a high degree of niche overlapping in several dimensions (vertical distribution, seasonality of population density) between both species. The inclusion of space-time data analysis tools as the PTA and the use of classical ecological indices (Pianka) in soil ecology studies may improve our knowledge of earthworm assemblages' dynamics., The study was supported by a grant within the Macrofauna project (EC-STD2). We wish to thank Richard Thomas, Dennis Friesen, Edgar Amézquita (CIAT), and to Jaime Triana and Darío Cárdenas (CORPOICA) for their technical and scientific assistance. The first author is deeply grateful to technicians who helped in the field during sampling campaign, Jaime Soto, José García, Guillermo Murcia and Salvador Rojas. Partial financial support was provided by the Managing Acid Soils (MAS) Consortium of the Soil, Water and Nutrient Management (SWNM) Systemwide Program. Our most sincere thanks to Patrick Lavelle (IRD), and Christien Ettema (Wageningen University) for their inputs and constructive discussions, and two anonymous referees for their useful comments on an earlier version of this paper.

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International audience; With non domesticated species, like most forest trees, the assessment of heritability for traits of adaptive relevance represents one of the first steps granting future conservation and breeding programs. This essential step, however, is lengthy to conduct on long-lived species, implying mostly ex situ experiments and little environmental resemblance to the original populations. A major obstacle for in situ genetic studies has been the difficulty in grasping the extent of family interrelations in natural populations. Recent developments in molecular biology, however, are making genetic markers readily available and more efficient for measurement of relatedness. Theoretical improvements have also been proposed to infer the heritability and the evolution of genetic variance from the joint analysis of natural relatedness and the in situ quantitative trait variation. Here we propose one of the first evaluations with forest tree species of this in situ approach. The studied population comprised 280 trees of two interbreeding species: Quercus petraea and Quercus robur. This study considered as many as 60 different traits: foliar morphology, growth, phenology, wood properties, wood defects and wood biochemical compounds, some of which with no published records of heritability estimations. A total of 17 highly polymorphic microsatellite markers were studied in the sample. The genetic markers revealed low levels of relatedness and variance of relatedness, which are in principle unfavourable conditions for the detection of heritability. We proceeded by ranking the estimates among traits, and carried out randomization test to setup confidence intervals. We found that those traits known to be highly heritable in the species or at least in related taxons (i.e. phenology, wood physical and biochemical properties) appeared at the top of the trait ranking for the two species, with highly significant associations between the genetic distance revealed by the genetic markers and the phenotypic resemblance. On the opposite, other traits known to have mode rate heritabilities, like growth, showed positive but no significant associations. Moreover, the two species exhibited different heritability patterns for leaf morphology traits, known to discriminate Quercus species. Although this in situ methodology cannot substitute its more precise ex situ counterpart, it could become an excellent exploratory tool of the natural occurring variation, and the detection of valuable populations for conservation purposes. We discuss the role of some useful add-ons that might further improve this in situ approach, like spatial statistics and simulation studies.

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Genetic diversity is a prerequisite for species adaptation to a changing world. We studied chloroplast and nuclear genetic diversity of oaks in two fragmented woodlands in south-western France. The chloroplast DNA polymorphism shows that oaks have a common population history, that is an Iberian postglacial maternal origin. However haplotype structures are totally different between the two studied areas due to contrasted landscape dynamics. Intense haplotype sharing between species in the Aurignac area shows that unidirectional hybridization and introgression may have lead to migration by pollen swap for at least pubescent oak. The comparison of nuclear diversity between two stands, one with an even-aged management in a continuous habitat and the other with a coppice with standard management in a fragmented landscape, shows that management does not affect nuclear diversity. The overlapping generations and the frequent partial harvest in the case of coppice with standard can explain the maintenance of high diversity level. We also show that isolation by distance have no effect on the genetic diversity of the studied oaks, characterized by long generation time and high pollen flow. The ecological background seems to have a great effect on interspecific diversity in the Aurignac region, where four species of oaks are sometimes co-occuring in the same stand. Interspecific gene flow likely increases intraspecific genetic diversity, as must be the case for pubescent oaks, Nous avons étudié la diversité génétique chloroplastique et nucléaire des chênes appartenant à deux paysages forestiers fragmentés du sud-ouest de la France. L'histoire de ces populations a été retracée grâce au polymorphisme de l'ADN chloroplastique. Alors que ce marqueur démontre que les chênes ont une origine maternelle ibérique, sa structuration géographique contrastée entre les deux sites témoigne de dynamiques paysagères différentes. Les diversités nucléaires des chênes d'une forêt gérée en futaie régulière en peuplement continu et de ceux d'une forêt gérée en taillis sous futaie en peuplement fragmenté sont équivalentes, le mode de gestion n'a pas ici de conséquence détectable sur la diversité intraspécifique. Le contexte écologique semble jouer un rôle prédominant dans la diversité interspécifique ce qui pourrait influencer, par l'hybridation, la diversité intraspécifique. Le chêne pubescent semble en effet avoir recolonisé les milieux par introgression récurrente, ce qui expliquerait l'importante diversité nucléaire de cette espèce

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International audience; This landscape study was based on the sampling of 20 replicated landscape sites (1 km2 each) that were located within the floodplain of the river Seine. For each site, 13 landscape variables were measured at three dates (1963–1985–2000). The aim of this study was to investigate the overall landscape variability through its different dimensions (space vs. time) and to assess the relative importance of each dimension. We used a new statistical method, i.e., partial triadic analysis (PTA), which allowed us to assess both (1) the spatial variability of the floodplain landscape and its dynamics in time and (2) the dynamic trajectories of the landscape variables for each site. The results showed, at the floodplain scale, the same landscape pattern has emerged since 1963, although a major trend was observed which consisted in a decrease in meadows resulting from an increase in arable crops. At the site scale, landscape sites, even if they were all influenced by this general trend during the 40-year period, showed contrasting trajectories. These results suggest that similar sites in 2000 do not necessarily share common histories and that contrasting sites in 2000 may have originated from similar patterns in 1963. The issue of biodiversity surrogates is then discussed, suggesting that new landscape metrics should be developed, emphasising spatial variability and (or) temporal dynamics

International audience; A humped-back relationship between species richness and community biomass has frequently been observed in plant communities, at both local and regional scales, although often improperly called a productivity–diversity relationship. Explanations for this relationship have emphasized the role of competitive exclusion, probably because at the time when the relationship was first examined, competition was considered to be the significant biotic filter structuring plant communities. However, over the last 15 years there has been a renewed interest in facilitation and this research has shown a clear link between the role of facilitation in structuring communities and both community biomass and the severity of the environment. Although facilitation may enlarge the realized niche of species and increase community richness in stressful environments, there has only been one previous attempt to revisit the humped-back model of species richness and to include facilitative processes. However, to date, no model has explored whether biotic interactions can potentially shape both sides of the humped-back model for species richness commonly detected in plant communities. Here, we propose a revision of Grime's original model that incorporates a new understanding of the role of facilitative interactions in plant communities. In this revised model, facilitation promotes diversity at medium to high environmental severity levels, by expanding the realized niche of stress-intolerant competitive species into harsh physical conditions. However, when environmental conditions become extremely severe the positive effects of the benefactors wane (as supported by recent research on facilitative interactions in extremely severe environments) and diversity is reduced. Conversely, with decreasing stress along the biomass gradient, facilitation decreases because stress-intolerant species become able to exist away from the canopy of the stress-tolerant species (as proposed by facilitation theory). At the same time competition increases for stress-tolerant species, reducing diversity in the most benign conditions (as proposed by models of competition theory). In this way our inclusion of facilitation into the classic model of plant species diversity and community biomass generates a more powerful and richer predictive framework for understanding the role of plant interactions in changing diversity. We then use our revised model to explain both the observed discrepancies between natural patterns of species richness and community biomass and the results of experimental studies of the impact of biodiversity on the productivity of herbaceous communities. It is clear that explicit consideration of concurrent changes in stress-tolerant and competitive species enhances our capacity to explain and interpret patterns in plant community diversity with respect to environmental severity

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Among abiotic stresses, water deficit is probably the most severe limiting factor of plantgrowth and development. In South-Western France climatologists predict a significantincrease of temperature combined with lower rainfall during the growing period for the nextcentury. Such modifications will place forest trees in the presence of new and suddenenvironmental constraints. It is therefore essential to know if these organisms will be able toface such climatic changes. In other words, if plantation of improved varieties will maintainthe present level of productivity with lower water availability as well as sustain severedrought episodes. The capacity of these organisms to adapt to such perturbations will dependon both their phenotypic plasticity and their genetic diversity. In the frame of this thesis, westudied molecular plasticity of maritime pine seedlings grown in hydroponics and exposed toosmotic stress using polyethylene glycol as osmoticum. A factorial design crossing twoecotypes (France & Morocco) by different levels of stress (short & long term) was used tostudy the transcriptomic and proteomic responses of the root system. Our investigationsfocused on accumulation of 7,000 transcripts and 1,200 proteins. Statistical analysis revealeddifferentially expressed genes according to ecotype and condition effects. More interestingwas genes whose molecular plasticity was genetically controlled, revealing ecotype dependentstrategy to response to the imposed stresses. The adaptive significance of these genes could beconfirmed by analysing their patterns of nucleotidic diversity with the main objective ofdetecting molecular signature of natural selection., L'alimentation en eau constitue le principal facteur limitant la croissance, voire la survie desplantes. Les modèles climatiques prévoient pour les 50 à 100 années à venir une baisse desprécipitations et des températures estivales accrues dans la moitié sud de la France. La duréede vie d'une forêt de pin maritime, de sa plantation jusqu'à la coupe d'exploitation estjustement de 50 ans. Il est donc important de savoir si ces organismes pourront faire face à cesbrusques changements climatiques ; en d'autres termes si les variétés améliorées plantéesaujourd'hui pourront maintenir le niveau actuel de productivité dans un milieu plus pauvre eneau, et tolérer des épisodes de sécheresse intense. La capacité de ces organismes à faire face àces perturbations brutales dépendra à la fois de leur plasticité phénotypique et de leur diversitégénétique. Dans le cadre de cette thèse, nous avons étudié la plasticité moléculaire du systèmeracinaire de jeunes plants de pin maritime élevés en milieu hydroponique et soumis à un stressosmotique par ajout de polyéthylène glycol. Un plan factoriel croisant deux écotypes (Franceet Maroc) par cinq niveaux de stress a permis d'analyser les réponses du transcriptome et duprotéome à court et long terme. Nos investigations ont porté sur l'accumulation des transcritsde 7000 gènes et de 1200 protéines. L'analyse statistique des données a permis d'identifierdes gènes dont la plasticité moléculaire est génétiquement contrôlée, révélant des stratégies deréponse différentes de chaque écotype. La valeur adaptative de ces gènes pourra alors êtreconfirmée par l'interprétation des patrons de diversité nucléotidique de ces gènes candidats.

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Diplôme : Master 1 Professionnel; DEUG

International audience

Diplôme : DES

International audience; With non domesticated species, like most forest trees, the assessment of heritability for traits of adaptive relevance represents one of the first steps granting future conservation and breeding programs. This essential step, however, is lengthy to conduct on long-lived species, implying mostly ex situ experiments and little environmental resemblance to the original populations. A major obstacle for in situ genetic studies has been the difficulty in grasping the extent of family interrelations in natural populations. Recent developments in molecular biology, however, are making genetic markers readily available and more efficient for measurement of relatedness. Theoretical improvements have also been proposed to infer the heritability and the evolution of genetic variance from the joint analysis of natural relatedness and the in situ quantitative trait variation. Here we propose one of the first evaluations with forest tree species of this in situ approach. The studied population comprised 280 trees of Iwo interbreeding species: Quercus petraea and Quercus robur. This study considered as many as 60 different traits: foliar morphology, growth, phenology, wood properties, wood defects and wood biochemical compounds, some of which with no published records of heritability estimations. A total of 17 highly polymorphic microsatellite markers were studied in the sam pie. The genetic markers revealed low levers of relatedness and variance of relatedness, which are in principle unfavourable conditions for the detection of heritability. We proceeded by ranking the estimates among traits, and carried out randomization test to setup confidence intervals. We found that those traits known to be highly heritable in the species or at least in related taxons (i.e. phenology, wood physical and biochemical properties) appeared at the top of the trait ranking for the two species, with highly significant associations between the genetic distance revealed by the genetic markers and the phenotypic resemblance. On the opposite, other traits known to have moderate heritabilities, like growth, showed positive but no significant associations. Moreover, the Iwo species exhibited different heritability patterns for leaf morphology traits, known to discriminate Quercus species. Although this in situ methodology cannot substitute its more precise ex situ counterpart, it could become an excellent exploratory tool of the natural occurring variation, and the detection of valuable populations for conservation purposes. We discuss the role of some useful add-ons that might further improve this in situ approach, like spatial statistics and simulation studies.

International audience; In a lysimeter set-up, compost addition to an industrial contaminated soil slightly reduced phytotoxicity to bean seedlings. The "Phytotoxicity Index" (on a scale from 1 to 4) decreased from 3.5 to 2.8. The same treatment also reduced metal accumulation in grasses: mean Zn, Cd and Pb concentrations decreased respectively from 623 to 135, from 6.2 to 1.3 and from 10.7 to < 6 mg kg(-1) dry weight. When combined with inorganic metal immobilizing amendments, compost had a beneficial effect on plant responses additional to the inorganic amendments alone. Best results were obtained when using compost (C) + cyclonic ashes (CA) + steel shots (SS). The "Phytotoxicity Index" decreased to 1.7, highest diversity of spontaneously colonizing plants occurred, and metal accumulation in grasses reduced to values for uncontaminated soils. Based on the first year evaluation, C + CA + SS showed to be an efficient treatment for amendment assisted phytostabilization of the contaminated Overpelt soil

Trees do not form a natural group but share attributes such as great size, longevity, and high reproductive output that affect their mode and tempo of evolution. In particular, trees are unique in that they maintain high levels of diversity while accumulating new mutations only slowly. They are also capable of rapid local adaptation and can evolve quickly from nontree ancestors, but most existing tree lineages typically experience low speciation and extinction rates. We discuss why the tree growth habit should lead to these seemingly paradoxical features. Copyright © 2006 by Annual Reviews. All rights reserved.

International audience; A total of 51 ancient oak wood samples originating from various European archaeological sites, dating from the Neolithic period to the 18th century, were assayed for the presence of reproducible chloroplast (cp) DNA sequences. Five polymorphic chloroplast fragments were targeted. Only five of the samples could be fully genetically characterised, revealing four different oak cpDNA haplotypes. In all cases, the haplotypes detected on ancient woods and the haplotypes characterised from fresh samples from the same localities matched. Overall, this congruence is consistent with a genetic continuity between ancient and modern European oaks, confirming the hypothesis that the mapped genetic patterns largely reflect the original structure that established during the post-glacial. This stability of the genetic structure implies that, in the future, the technique could be used to infer or confirm the transport of wood by man, providing interesting perspectives for the genetic analysis of ancient woods.

Species effects and ecological conditions on ten heartwood ellagitannins (vescalin, castalin, roburins A-E, grandinin, vescalagin and castalagin)and ellagic acid were investigated in a 100 years old stand of 5 ha located in western France (La Petite Charnie State Forest, Sarthe). The sample included a total of 286 trees (118 sessile oaks, 158 pedunculate oaks and 10 individuals with an intermediate morphology) located in three ecological zones (plateau, slope, small valley). The main factor influencing oak extractives level was botanical species. The ecological zone effect appears negligible. Pedunculate oak is generally richer in ellagitannins (48.4 mg/g against 34.4 for sessile oak), although a clear boundary between the two species cannot be established. Ellagitannin content was found to be correlated with ring width for pedunculate oak and not for sessile oak. The vescalagin/castalagin ratios differed between the two species (0.69 for Quercus robur against 0.53 for Quercus petraea). The distribution of ellagitannin contents is not strongly structured spatially, Les effets de l’espèce et des conditions écologiques sur le contenu du duramen externe de dix ellagitanins (vescaline, castaline, roburines A à E, grandinine, vescalagine, castalagine) et de l’acide ellagique ont été étudiés dans un peuplement équien (100 ans) de chêne d’une surface de 5 ha située dans l’ouest de la France (forêt domaniale de La Petite Charnie, Sarthe). L’échantillon total se composait de 286 arbres (118 chênes sessiles, 158 chênes pédonculés et 10 chênes intermédiaires) répartis en mélange dans trois zones écologiques du peuplement (plateau, pente et fond de vallon). Le facteur principal qui influence la teneur en ellagitanin est l’espèce botanique, alors que le facteur « zone » est négligeable dans les conditions expérimentales considérées. Le bois de chêne pédonculé est plus riche en ellagitanins que celui du chêne sessile (48,4 mg/g pour le chêne pédonculé ; 34,4 mg/g pour le chêne sessile), mais une distinction claire entre les deux espèces ne peut être établie. Une corrélation entre la teneur en ellagitanin et la largeur de cerne est observée pour le chêne pédonculé à la différence du cas du chêne sessile. Le rapport vescalagine/castalagine est plus élevé pour le chêne pédonculé que pour le chêne sessile (0,69 et 0,53). La structuration spatiale est faible

International audience; Microsatellites are widely used markers for multiple purposes in oaks. We describe a complete procedure for cheap DNA extraction and fast microsatellites genotyping by multiplex PCR. 10 loci were selected to form two multiplex kits including three loci that show a high differentiation between Quercus robur and Q. petraea. The loci were tested in three oak species and show a high mean genetic diversity of 0.84. The cumulative exclusion probability for parentage analysis was 0.999977 for single parent and 1.0 for paternity. Finally, the relatively high differentiation coefficient (Gst = 0.04) will facilitate species assignment based on genotypes in oaks

The D2.0.2 Progress report Module 2 contains an overview of the work conducted and activities carried out by the Module partners during the first year. It presents a description of progress toward the objectives of the project and the milestones and deliverables foreseen. The identification of the problems encountered and corrective actions taken or proposed are also presented. Appendix 1 provides detailed annual report from each Work-Package

International audience

International audience; Earthworms often form spatially structured populations characterised by alternate clusters of either low or high density. This study compared various soil properties and herbaceous plant biomass between areas of high and low earthworm density (i.e. patches and gaps) in a tropical grassland (la Mancha, Veracruz, Mexico). We aimed at identifying those variables that might explain the observed spatial distribution or, conversely be explained by the community pattern. We examined the spatial aggregation by means of the Spatial Analysis by Distance IndicEs (SADIE) system and showed the presence of significant patches and gaps. Only a few variables significantly differed between patches and gaps. Areas corresponding to earthworm patches and gaps had more silt and clay, respectively, in the 10–30 cm soil layer. There was no difference in the C content in the different particle-size classes expressed in absolute values (mg C g−1 soil) but the proportion of C associated to > 200 μm particles was larger in the patches (0–10 cm layer) while there was more C associated to the fine particle (< 50 μm) in the gaps (10–30 cm soil layer). Patches and gaps did not differ significantly in terms of cation concentrations (K, Mg and Ca), pH, soil bulk density or herbaceous plant dry mass. The lack of clear relationships between earthworm distribution and soil parameters in this study suggest that earthworm populations and soil properties may occur at different spatial scales

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; A comparative study of the spatial distributions and the quantity of biogenic structures produced by earthworms and termites (Odontotermes nilensis and Ancistrotermes guineensis) has been conducted in a mango orchard at Thiès (Senegal).This study showed that surface biogenic structures may represent a large amount of modified soil (up to 536.5 g m−2) which vary depending upon the seasons and the species. Whilst the quantity of casts was independent on the season (178.6 g m−2), O. nilensis sheetings fluctuated with the seasons. In addition, we show that the spatial organisation of surface biogenic structures fluctuates with seasons. It displays patches ranging from 5 to 15 m. There is a link between the distribution of earthworm casts and the vegetation. In addition, spatial distribution was also linked to the biology of constructing species. We observed that the A. guineensis’ filling structures were mainly located under the mango trees during the dry season where the stems and the brushwoods were abundant. It appears that the spatio-temporal distribution of the biogenic structures under study depended upon two main factors: season and vegetation. However, depending upon the biology of the engineer, these two factors influenced the spatial distribution of structures in different ways

FR2116; International audience; This landscape study was based on the sampling of 20 replicated landscape sites (1 km2 each) that were located within the floodplain of the river Seine. For each site, 13 landscape variables were measured at three dates (1963–1985–2000). The aim of this study was to investigate the overall landscape variability through its different dimensions (space vs. time) and to assess the relative importance of each dimension.We used a new statistical method, i.e., partial triadic analysis (PTA), which allowed us to assess both (1) the spatial variability of the floodplain landscape and its dynamics in time and (2) the dynamic trajectories of the landscape variables for each site. The results showed, at the floodplain scale, the same landscape pattern has emerged since 1963, although a major trend was observed which consisted in a decrease in meadows resulting from an increase in arable crops. At the site scale, landscape sites, even if they were all influenced by this general trend during the 40-year period, showed contrasting trajectories. These results suggest that similar sites in 2000 do not necessarily share common histories and that contrasting sites in 2000 may have originated from similar patterns in 1963. The issue of biodiversity surrogates is then discussed, suggesting that new landscape metrics should be developed, emphasising spatial variability and (or) temporal dynamics.

National audience

This review synthesizes the available knowledge on drought-disease interactions in forest trees with a focus on (1) evidence and patterns of drought-disease interactions, (2) current understanding of processes and mechanisms, and (3) three well documented cases studies. The first part is based on the analysis of a database of slightly more than one hundred studies, obtained by keyword searches combining drought, diseases or pathogens, and forest trees. A large majority of published studies referred to a positive association between drought and disease, i.e. disease favoured by drought or drought and disease acting synergistically on tree health status, with a predominance of canker/dieback diseases, caused by pathogens like Botryosphaeria, Sphaeropsis, Cytospora and Biscognauxia (Hypoxylon). The type of disease-related variables (incidence vs. severity) and the intensity and timing of water stress were shown to be significant factors affecting the drought- infection interaction. Interactions with other abiotic stresses and species-specific and genetic effects, related to host or pathogen, have also been reported. Direct effects of drought on pathogens are generally negative, although most fungal pathogens exhibit an important plasticity and can grow at water potentials well below the minimum for growth of their host plants. Studies on indirect effects of drought on pathogens through other community interactions are still relatively scarce. Positive drought-infection effects can mostly be explained by indirect effects of drought on host physiology. The predisposition and the multiple stress hypotheses are presented, as well as recent developments in the study of the molecular basis of abiotic and biotic stress, and their interactions. Sphaeropsis sapinea on pines, Biscognauxia mediterranea on oaks and root pathogens in declines associated with drought provide illustrative examples, treated as case studies, of pathogens of current significance associated with drought. The conclusion highlights some knowledge gaps, e.g. the role of latent parasites and the shift to a pathogenic stage, or t, Cette revue synthétise les connaissances actuelles sur les interactions entre sécheresse et maladies chez les arbres forestiers, avec trois grandes parties : (1) description des types d’interaction ; (2) connaissances acquises sur les mécanismes impliqués ; (3) trois études de cas bien étudiées. La première partie est basée sur l’analyse d’une base de données d’une centaine d’études, sélectionnées par recherche sur mots clés. La plupart de ces études se rapportent à des maladies favorisées par la sécheresse ou à un effet synergique entre sécheresse et maladie sur l’état sanitaire des arbres, avec une prédominance de maladies à chancres ou de rameaux, causées par des espèces des genres Botryosphaeria, Sphaeropsis, Cytospora et Biscognauxia (Hypoxylon). Un effet significatif de l’intensité et de la durée du stress est montré dans certains cas sur le développement des maladies. Les effets de la sécheresse peuvent être différents selon qu’il s’agit de variables liées à l’incidence ou à la sévérité de la maladie. Des interactions avec d’autres stress abiotiques ou en relation avec des effets génétiques ou spécifiques ont également été décrits. Les effets directs de la sécheresse sur les pathogènes sont généralement négatifs, mais les champignons montrent une grande plasticité et peuvent généralement se développer à des potentiels hydriques inférieurs à ceux inhibant la croissance de leurs hôtes. Les effets positifs entre sécheresse et infection s’expliquent principalement par des effets indirects sur la physiologie des hôtes. Les hypothèses sur la prédisposition et les stress multiples sont présentées, ainsi que les développements récents sur les bases moléculaires des stress et de leurs interactions. Les trois études de cas concernent Sphaeropsis sapinea sur pins, Biscognauxia mediterranea sur chênes et l’interaction entre pathogènes racinaires et sécheresse dans les dépérissements. Dans la conclusion, quelques perspectives de recherche à privilégier sont mentionnées, comme le rôle et la biologie des parasites latents, ou la génétique de quelques groupes fongiques. Sur un plan pratique, la nécessité de limiter la dissémination des parasites, particulièrement cruciale dans le cas des parasites latents, est soulignée

International audience; Here, palaeobotanical and genetic data for common beech (Fagus sylvatica) in Europe are used to evaluate the genetic consequences of long-term survival in refuge areas and postglacial spread. Four large datasets are presented, including over 400 fossil-pollen sites, 80 plant-macrofossil sites, and 450 and 600 modern beech populations for chloroplast and nuclear markers, respectively. The largely complementary palaeobotanical and genetic data indicate that: (i) beech survived the last glacial period in multiple refuge areas; (ii) the central European refugia were separated from the Mediterranean refugia; (iii) the Mediterranean refuges did not contribute to the colonization of central and northern Europe; (iv) some populations expanded considerably during the postglacial period, while others experienced only a limited expansion; (v) the mountain chains were not geographical barriers for beech but rather facilitated its diffusion; and (vi) the modern genetic diversity was shaped over multiple glacial-interglacial cycles. This scenario differs from many recent treatments of tree phylogeography in Europe that largely focus on the last ice age and the postglacial period to interpret genetic structure and argue that the southern peninsulas (Iberian, Italian and Balkan) were the main source areas for trees in central and northern Europe