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Diversification of fruit tree species, cultivars, crops and companion plants is a way to reinforce ecosystem services towards productive and ‘pest suppressive’ fruit-tree based agroforestry systems (FT-AFS). We analyzed the approach and the outputs of three design processes that shared the same objectives of ecological intensification and diversification in FT-AFS. The approach targeted ‘pest suppressive’ processes but also resource use optimization within time and space between productive and associated plants. Basic and applied knowledge on ecological and biophysical processes, feedbacks and experiences of various stakeholders in the fruitchain permitted to make tradeoff between agronomic, ecological and organizational aspects. For genericity purpose, the functions of each plant species or assemblage (e.g. barrier, trap, production) were identified taking into account growth dynamics over time. The set-up of those FT-AFS prototypes implies changes in technics due to the spatial design (e.g. machinery adaptation, ergonomics) and changes in management of the agroecosystem, made ‘on the way’ considering the objectives and design principles as dynamic guidelines. The trajectory and performances of those systems are now assessed through multicriteria evaluation including organizational aspects and products’ valorization. All steps include an interdisciplinary and participative approach fostering exchanges, knowledge sharing and building, and providing innovative avenues in FT-AFS. Overall

International audience; Highlands, hydrographic systems and coastal areas have been hypothesised to form corridors across the hyperarid Sahara desert in North Africa, allowing dispersal and gene flow for non-xeric species. Here we aim to provide a genetic test for the trans-Saharan corridor model, and predict the location and stability of ecological-corridors, by combining phylogeography and palaeoclimatic modelling. The model was the Psammophis schokari (Schokari sand racer) group, fast-moving and widely distributed generalist colubrids occurring mostly in arid and semiarid scrublands. We combined dated phylogenies of mitochondrial and nuclear markers with palaeoclimatic modelling. For the phylogeographic analysis, we used 75 samples of P. schokari and P. aegyptius, and Bayesian and Maximum-Likelihood methods. For the ecological models, we used Maxent over the distribution of P. schokari and West African lineages. Models were projected to past conditions (mid Holocene, Last Glacial Maximum and Last Inter-Glacial) to infer climatic stable areas. Climatic stability was predicted to be mostly restricted to coastal areas and not spatially continuous. A putative temporary trans-Saharan corridor was identified in Eastern Sahara, with a more stable one along the Atlantic coast. Six parapatric lineages were identified within P. schokari, four occurring in North Africa. These likely diverged during the Pliocene. The Tamanraset River might have been a vicariant agent. African lineages may have experienced further subsequent diversification during the late Pleistocene. The main P. schokari refugia were probably located along the northern margins of the Sahara, allowing its North-to-South colonization. Trans-Saharan corridors seem to have played a role in P. schokari biogeography, allowing colonization of central Saharan mountains and Sahel. Some might have worked as refugia, and even the most stable corridors may have sections working as filters, depending on each climatic phase. We expect the use of trans-Saharan corridors to decrease for more mesic species or with less dispersal capabilities.

paper originating from a presentation made at the 13th International Plant Virus Epidemiology Symposium held at Avignon, France June 6-10, 2016; The “Papaya ringspot virus (PRSV) cluster” of cucurbit-infecting potyviruses contains five acknowledged species that have similar biological, serological and molecular properties. Additional data suggest there are other uncharacterized species from various locations in the world that likely belong to the PRSV cluster including a new PRSV-like virus reported from Sudan in 2003. Molecular and biological data indicated that the virus from Sudan belongs to a new species, tentatively named wild melon vein banding virus (WMVBV). The complete nucleotide sequence of a second virus from Sudan revealed it was a divergent relative of Moroccan watermelon mosaic virus (MWMV). Based on sequence similarity this virus was determined to be a distinct species and tentatively named Sudan watermelon mosaic virus (SuWMV). Molecular analyses indicate that SuWMV is a recombinant between WMVBV- and MWMV-related viruses. Based on surveys performed in Sudan between 1992 and 2012, SuWMV appeared 10 times more frequent than WMVBV in that country (14.6% vs. 1.5% of the samples tested). The geographic structure and molecular diversity patterns of the putative and acknowledged species suggest that the PRSV-like cluster originated in the Old World about 3600 years ago, with an important diversification in Africa.

Increases in drought-induced tree mortality are being observedin tropical rain forests worldwide and are also likely to affectthe geographical distribution of tropical vegetation. However,the mechanisms underlying the drought vulnerability and environmental distribution of tropical species have been little studied. We measured vulnerability to xylem embolism (P50) of 13woody species endemic to New Caledonia and with differentxylem conduit morphologies. We examined the relation be-tween P50, along with other leaf and xylem functional traits,and a range of habitat variables. Selected species had P50values ranging between 4.03 and 2.00 MPa with most species falling in a narrow range of resistance to embolism above 2.7 MPa. Embolism vulnerability was significantly correlatedwith elevation, mean annual temperature and percentage ofspecies occurrences located in rain forest habitats. Xylem conduit type did not explain variation in P50. Commonly used functional traits such as wood density and leaf traits were notrelated to embolism vulnerability. Xylem embolism vulnerability stands out among other commonly used functional traits as amajor driver of species environmental distribution. Drought-induced xylem embolism vulnerability behaves as a physiological trait closely associated with the habitat occupation of rainforest woody species.

Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process. The molecular revolution and the possibility to integrate time into phylogenetic reconstructions have allowed studying extinction under different perspectives. Here, we review phylogenetic (temporal) and biogeographic (spatial) approaches to the inference of extinction and the challenges this process poses for reconstructing evolutionary history. Specifically, we focus on the problem of discriminating between alternative high extinction scenarios using time trees with only extant taxa, and on the confounding effect introduced by asymmetric spatial extinction – different rates of extinction across areas – in biogeographic inference. Finally, we identify the most promising avenues of research in both fields, which include the integration of additional sources of evidence such as the fossil record or environmental information in birth–death models and biogeographic reconstructions, the development of new models that tie extinction rates to phenotypic or environmental variation, or the implementation within a Bayesian framework of parametric non-stationary biogeographic models., Financial support came from MINECO, the Spanish Ministry of Economy and Competitiveness, project CGL2012-40129-C02-01 to IS, and from a Marie-Curie FP7–COFUND (AgreenSkills fellowship–26719) to AM.

Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders.

Understanding the mechanisms generating species distributions remains a challenge, especially in hyperdiverse tropical forests. We evaluated the role of rainfall variation, soil gradients and herbivory on seedling mortality, and how variation in seedling performance along these gradients contributes to habitat specialisation. In a 4-year experiment, replicated at the two extremes of the Amazon basin, we reciprocally transplanted 4638 tree seedlings of 41 habitat-specialist species from seven phylogenetic lineages among the three most important forest habitats of lowland Amazonia. Rainfall variation, flooding and soil gradients strongly influenced seedling mortality, whereas herbivory had negligible impact. Seedling mortality varied strongly among habitats, consistent with predictions for habitat specialists in most lineages. This suggests that seedling performance is a primary determinant of the habitat associations of adult trees across Amazonia. It further suggests that tree diversity, currently mostly harboured in terra firme forests, may be strongly impacted by the predicted climate changes in Amazonia.

International audience; Plant responses to natural enemies include formation of secondary metabolites acting as direct or indirect defenses. Volatile terpenes represent one of the most diverse groups of secondary metabolites. We aimed to explore evolutionary patterns of volatile terpene emission. We measured the composition of damage-induced volatile terpenes from 202 Amazonian tree species, spanning the angiosperm phylogeny. Volatile terpenes were extracted with solid-phase micro extraction and desorbed in a gas chromatography–mass spectrometry for compound identification. The chemical diversity of the terpene blend showed a strong phylogenetic signal as closely related species emitted a similar number of compounds. Closely related species also tended to have compositionally similar blends, although this relationship was weak. Meanwhile, the ability to emit a given compound showed no significant phylogenetic signal for 200 of 286 compounds, indicating a high rate of diversification in terpene synthesis and/or great variability in their expression. Three lineages (Magnoliales, Laurales, and Sapindales) showed exceptionally high rates of terpene diversification. Of the 70 compounds found in >10% of their species, 69 displayed significant correlated evolution with at least one other compound. These results provide insights into the complex evolutionary history of volatile terpenes in angiosperms, while highlighting the need for further research into this important class of compounds.

Présenté devant un groupe coopératif d'industriels forestiers et d'universitaires brésiliens, à l'invitation du CIRAD et de l'Ambassade de France au Brésil, l'exposé donne un point de vue européen sur les forêts et le changement climatique, le situant en particulier vis-à-vis de la diversité des forêts françaises à objectif de production et de leurs contrastes avec les sylviculture de plantation brésiliennes. La communication cherche, au-delà des différences de contexte biogéographique, social et industriel, à montrer l'importance de l'itinéraire technique plantation dans la mise en œuvre des différentes options de changement de gestion.

Dans un objectif de contribuer à la diversification la production de la banane aux Antilles françaises, les équipes de recherche du CIRAD et de l’INRA ont entrepris d’explorer la variabilité qualitative des bananes dessert et à cuire et les potentialités d’élaboration de produits transformés. La mise en évidence de liens entre les conditions de production (sol, climat) et les caractéristiques sensorielles et nutritionnelles ont conduit à l’identification de la dénomination « banane de Montagne ». Celle-ci se caractérise par une texture plus ferme, une pulpe plus jaune et présente des teneurs minérales plus faibles. L’évaluation de la qualité au sein de la biodiversité variétale a montré que les variétés locales et les hybrides, issus du programme de création variétale du CIRAD, présentaient des caractéristiques organoleptiques et physico-chimiques leur permettant de se différencier de la variété standard, laCavendish. Parmi les hybrides étudiés, certains ont présenté des aptitudes à la conservation similaires à celle de la Cavendish, leur conférant un potentiel de développement. Des pistes de recherche et développement ont été proposées dans la perspective d’une diversification à travers la fabrication de produits transformés., With the aim to contribute to the diversification of banana production in the French West Indies, research teams from CIRAD and INRA have begun to explore variability in quality of dessert and cooking bananas and potentialities of processed products development. The identification of relationship between production conditions (soil, climate) and the sensory and nutritional characteristics led to the designation "Banane Montagne" as a quality sign for a specific production. It is characterized by a firmer texture, more yellow pulp and provides lower mineral content. Quality assessment of diversity among varieties showed that local varieties and the hybrids from the breeding program of CIRAD have specific taste and chemical characteristics that markedly differentiate themselves from the standard variety, the Cavendish. Among the hybrids studied some showed a storability similar toCavendish, giving them a potential for development. Research projects are being developed on bananas as raw material in agrofood processes aiming to offer new processed and innovative products.

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High-throughput sequencing technologies have the potential to decipher genomic diversity at a moderate cost. Propionibacterium freudenreichii is an Actinobacterium used in cheese technology (responsible for aroma and holes in Swiss cheese) and that has probiotic properties (bifidogenic and with anti-inflammatory properties in human and animal). 23 strains of Propionibacterium freudenreichii covering 18 different sequence types out of 46 (Dalmasso et al. AEM 2010) were (i) sequenced by Solexa-Illumina paired-end sequencing and (ii) de novo assembled using Velvet software. Depending on strain, 63 to 166 scaffolds were obtained. These scaffolds were arranged along the reference genome CIRM-BIA1, previously obtained from traditional Sanger sequencing (Falentin et al. PlosOne 2010). For each strain, single nucleotide polymorphism and insertion deletion events were plotted against reference genome. Sequences were automatically annotated (by blastp and pattern matching) on the INRA AGMIAL platform. By bidirectional best-hit, each gene was attributed either to core genome or accessory genome. In some strains, some genes belonging to the accessory genome corresponded with genomic islands and confered peculiar phenotypes (ability to lactose degradation for exemple). In the future, screening of P. freudenreichii (~500 strains) collection on genetic basis at CIRM-BIA biological resource center (Rennes) will help in strain choice for cheese starter and probiotic market.

Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. This study investigates the molecular diversity and the population structure of this bacterium via multilocus sequence typing (MLST). Internal fragments of seven genes sequenced for 113 strains of different subspecies and origins allowed the resolution of 46 sequence types (STs) with occurrence frequencies ranging from 1 to 11. The core genome of the species harbours a low level of nucleotide polymorphism. In our data, single nucleotide polymorphisms account for only 2.28% of the concatenated sequences, and the average polymorphism rate in pairwise comparisons is 0.46%. The analyses reveal quantitatively comparable contributions of recombination and mutation in nucleotide changes at core genome loci along cell lineages. Remarkably, the STs exhibit little if any dairy biotope specialization. Phenotypic characterisation of the strains, based on their aptitude to use lactose and nitrate, shows that the two previously identified subspecies (freudenreichii and shermani) do notreflect the ancestral relationships in the P. freudenreichii population. The considerable phenotypic heterogeneity, found even at the ST level, suggests instead a history of recurrent switches between phenotypes.

International audience

Background Cyprinids display the most abundant and widespread species among the European freshwater Teleostei and are known to hybridize quite commonly. Nevertheless, a limited number of markers for conducting comparative differentiation, evolutionary and hybridization dynamics studies are available to date. Findings Five multiplex PCR sets were optimized in order to assay 41 cyprinid-specific polymorphic microsatellite loci (including 10 novel loci isolated from Chondrostoma nasus nasus, Chondrostoma toxostoma toxostoma and Leuciscus leuciscus) for 503 individuals (440 purebred specimens and 63 hybrids) from 15 European cyprinid species. The level of genetic diversity was assessed in Alburnus alburnus, Alburnoides bipunctatus, C. genei, C. n. nasus, C. soetta, C. t. toxostoma, L. idus, L. leuciscus, Pachychilon pictum, Rutilus rutilus, Squalius cephalus and Telestes souffia. The applicability of the markers was also tested on Abramis brama, Blicca bjoerkna and Scardinius erythrophtalmus specimens. Overall, between 24 and 37 of these markers revealed polymorphic for the investigated species and 23 markers amplified for all the 15 European cyprinid species. Conclusions The developed set of markers demonstrated its performance in discriminating European cyprinid species. Furthermore, it allowed detecting and characterizing hybrid individuals. These microsatellites will therefore be useful to perform comparative evolutionary and population genetics studies dealing with European cyprinids, what is of particular interest in conservation issues and constitutes a tool of choice to conduct hybridization studies.

Background Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. Results A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69). The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. Conclusions In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.

National audience

Staphylococcus aureus causes disease in humans and a wide array of animals. Of note, S. aureus mastitis of ruminants, including cows, sheep, and goats, results in major economic losses worldwide. Extensive variation in genome content exists among S. aureus pathogenic clones. However, the genomic variation among S. aureus strains infecting different animal species has not been well examined. To investigate variation in the genome content of human and ruminant S. aureus , we carried out whole-genome PCR scanning (WGPS), comparative genomic hybridizations (CGH), and the directed DNA sequence analysis of strains of human, bovine, ovine, and caprine origin. Extensive variation in genome content was discovered, including host- and ruminant-specific genetic loci. Ovine and caprine strains were genetically allied, whereas bovine strains were heterogeneous in gene content. As expected, mobile genetic elements such as pathogenicity islands and bacteriophages contributed to the variation in genome content between strains. However, differences specific for ruminant strains were restricted to regions of the conserved core genome, which contained allelic variation in genes encoding proteins of known and unknown function. Many of these proteins are predicted to be exported and could play a role in host-pathogen interactions. The genomic regions of difference identified by the whole-genome approaches adopted in the current study represent excellent targets for studies of the molecular basis of S. aureus host adaptation.

International audience; Background: Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions. Methology/Principal Findings: Based on a long-term (1972–2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns. Conclusion/Significance: Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependant on recent ecological processes.

On étudie l’impact de l’utilisation gallo-romaine ancienne sur la diversité des espèces d’arthropodes dans la forêt de Thuilley-aux-Groseilles. Dans 6 sites (3 proches des habitats gallo-romains et 3 en zone non perturbée), les arthropodes ont été piégés dans 4 types de piège pendant une saison de végétation. Sur les 8914 individus identifiés, 433 espèces ont été déterminées. La diversité de Shannon moyenne par site est élevée (5,5 binons). Il n’apparaît pas de différences importantes entre types d’utilisation ancienne pour les paramètres classiques de diversité (richesse spécifique, diversité de Shannon, nombre total d’individus observés). Par contre, les cortèges d’espèces présents sur les sites perturbés ou non perturbés par l’agriculture ancienne se séparent très nettement sur l’axe 1 de l’analyse factorielle des correspondances du tableau espèces x sites, indiquant la présence fréquente d’espèces liées de façon préférentielle à l’un ou l’autre des types d’utilisation ancienne. Parmi les individus présents sur les sites perturbés dominent les espèces vivant au dépens des animaux (coprophages, hématophages, parasitoïdes). A contrario, les populations de la forêt non touchée par l'occupation humaine ancienne sont dominées par les espèces vivant au dépens de la végétation sous toutes ses formes (phytophages, xylophages, saproxylophages). Ces premiers résultats mériteraient d’être étendus à d’autres sites, afin en particulier d’écarter le risque de confusion de facteur entre utilisation ancienne et d’autres paramètres environnementaux., We studied the impact of Roman land-use on species diversity of arthropods in the forest of Thuilley-aux-Groseilles. At 6 sites (3 close to the ancient Roman settlement and 3 in surrounding undisturbed areas), arthropods were captured in 4 different types of traps, during one season of vegetation. Among the 8914 individuals identified, 433 species were determined. Average Shannon diversity per site was high (5.5 binons). There was no important difference between types of ancient land use for the classical diversity indicators (species richness, Shannon index, total number of individuals counted). But, the sets of species found in disturbed and undisturbed sites were clearly separated along the first axis of a factorial correspondence analysis of the species x sites table. Thus, a significant proportion of species preferred one or the other ancient land-use type. In sites close to the settlement, species feeding upon animals in a broad sense (coprophagous, hematophagous, parasitoids) dominated. In remote, undisturbed, sites, species feeding on plants dominated (phytophagous, xylophagous, saproxylophagous). These first results indicate that very ancient land-use probably not only impact soil fertility and plant diversity, but also arthropods community composition. They should be extended to other situations, in order to discard any confusion between the role of ancient land-use and other confounding factors.

The aim of this study was to determine the dynamics of colonisation and composition of the wood-decomposer community in a native forest and four monocultures over time. A fingerprinting method of TGGE (temperature gradient gel electrophoresis) with rDNA amplified by ITS1F and ITS2 primer pairs was optimized and used as a culture-independent approach to determine the dominant fungal species and biodiversity over a two-year period of decomposition of beech-wood samples. The bacterial community after two years was also investigated. Data showed that each tree species, as well as sampling date, displayed the characteristic community structure. There was no strong decrease in microbial species richness or Shannon-Wiener diversity index caused by a change of tree species. Nevertheless, a strong shift in decomposer community structure was evident among the tree species both for fungi and bacteria. The effect of environmental conditions was also significant., L’objectif de cette étude était de caractériser la dynamique de colonisation d’un matériau modèle (du bois de hêtre) par les lignivores au cours de la décomposition, dans une forêt native et sous quatre essences de substitution à la forêt native feuillue. La technique d’empreinte génétique de TGGE (électrophorèse sur gel en gradient de température) ciblée sur l’ADN ribosomique, amplifié par les amorces ITS1F et ITS2, a été optimisée et utilisée pour déterminer les espèces fongiques dominantes ainsi que la diversité totale au cours des deux années d’incubation in situ des échantillons. La diversité bactérienne a également été étudiée sur les échantillons prélevés après deux années d’incubation. Les données indiquent que le peuplement et la durée d’incubation modifient la structure des communautés fongiques. Il n’y a cependant pas de forte diminution du nombre d’espèces ni de l’index de diversité de Shannon-Wiener associée au changement d’essence forestière. Toutefois, il y a une forte évolution dans la structure des communautés de décomposeurs entre les peuplements, à la fois pour les champignons et les bactéries. Les effets des paramètres environnementaux sont discutés.

De l’olivier à l’oléastre : origine et domestication de l’Olea europaea L. dans le Bassin méditerranéen Keywords : VEGETAL PRODUCTIONS, NATURAL RESOURCES AND ENVIRONMENTRésumé : L’olivier occupe la 24 e place des 35 espèces les plus cultivées dans le monde. La diversité phénologique des cultivars est remarquable et l’intérêt économique de l’espèce est majeur. Pourtant peu d’études ont porté sur la domestication de l’olivier et sur les relations entre l’olivier et sa forme sauvage, l’oléastre. Les marqueurs moléculaires rendent possible l’étude de la structure génétique des cultivars, des flux géniques et des relations entre la forme cultivée et sauvage. L’analyse de la diversité actuelle de la sous-espèce europaea d’Olea europea permet de remonter le temps et d’analyser les mécanismes qui ont conduit à cette diversité. Les processus utilisés donnent un panorama de la diversité après les glaciations et permettent de situer globalement les zones refuges qui apparaissent nombreuses et génétiquement très structurées. La comparaison avec la connaissance populaire montre que, chez cette espèce, l’histoire a été enjolivée, probablement pour combler l’absence de données historiques. L’origine de l’olivier à partir de l’oléastre ne fait plus de doute à l’est comme à l’ouest de la mer Méditerranée. Cependant, la diversité de l’oléastre et de l’olivier est maximale à l’ouest. L’archéologie confirmant la présence de l’oléastre à l’ouest, l’origine de la sous-espèce europaea est donc à reconsidérer, The olive tree is the cultivated form of the wild oleaster, both of which belong to the subspecies europaea of Olea europaea and are naturally distributed all around the Mediterranean Sea. In addition to these, some trees escaped from cultivation resemble oleasters by their physiognomy. No specific morphologic marker unambiguously differentiates the three forms. Olive cultivars today show a wide diversity in their morphology and phenology. Olives are important economically in Mediterranean countries, and olive oils carrying the taste and aroma of the fruit are the base of a new gastronomy also economically significant. Olive trees fashion landscapes and prevent erosion, and a social culture is associated with their products. Oleasters are endangered due to recurrent gene flow from the olive tree, human impact on forests and climate change. Olive cultivars result from a long process of selection in diverse environments that have had different cultural practices and traditions ever since the olive tree began accompanying human migration in the Neolithic period. The first domestication had occurred by -5800 B.P. around the eastern Mediterranean basin. Olive cultivars are deeply differentiated according to ultimate use — for oil, table or mixed. Their origins are unknown and the country of origin is only an indication of where they come from. Cultivars and oleasters are wind-pollinated and outcrossing is the rule. Molecular markers have recently made it possible to study the diversity of olive trees and thus to attempt to verify myths and beliefs about their origins. Relations between cultivars can now be established with several types of markers. Domestication events must have appeared in several sites around eastern and western Mediterranean localities since cultivars have inherited cytotypes of local oleasters, and this probably occurred simultaneously. Human migrations displaced cultivars, leading to gene flow: local oleasters generate new forms and new cultivated genotypes. Cytoplasmic markers show at least four separate origins of olive trees from oleasters, and SSRs show at least seven. Molecular markers have enabled us to show that each cultivar corresponds to one clone with a few exceptions. This means that cultivars were propagated from a single tree, with some exceptions that may be due to mixing two or three sister progenies of one tree. Although oleasters originate from seven different refuge areas, gene flow caused by cultivar displacement has disturbed this structure. Some cultivars also have their origin in some of these primary populations but others appeared as hybrids between two or three of these zones. This suggests that gene flow occurred between local oleasters and cultivars introduced by human migrations