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The aim of this thesis is to assess the populations structure of Anopheles darlingi in French Guiana. A population genetics study on An. darlingi is justified because it is an important vector of malaria in South America and particularly in French Guiana. We need to know more about this mosquito species to reduce transmission of malaria parasites by vector control.The first approach is a methodological study designed to determine whether the capture method (Human landing catch or MosquitoMagnet® with octenol or Lurex™ as attractant) or the time of capture influences the population structure of An. darlingi. This step clarifies whether the collection method could lead to sampling bias. Indeed, if we capture different populations of An. darlingi using different trapping methods or at different times of the day, it becomes impossible to perform genetic structure studies, except with mosquitoes captured with the same type of trap and at the same time each day. Likewise, it becomes impossible to compare studies using different capture methods or different time slots.The second objective is focused on the genetic diversity of An. darlingi populations in French Guiana. Sampling was carried out at 14 sites in French Guiana and one site in representing two different ecological zones: the coast and the forest. Genotyping was performed on a total of 1881 mosquitoes using 8 microsatellite markers. This study allowed to evaluate the population structure of Anopheles in French Guiana. The relevance of this study lies in the fact that it helps us better understand the populations of malaria vectors in the territory and therefore to improve vector control measures.The preliminary methodological study showed that the 3 methods of mosquito collection studied attract and capture the same populations of An. darlingi. Different collection methods can therefore be used to carry out sampling of Anopheles for molecular studies including studies on population genetic structure. Likewise, the time of capture was not associated with variations in Anopheles populations.In French Guiana, we have identified five sub-populations of An. darlingi mosquitoes. The first two “clusters” bring together all the coastal sites: Kourou, Matoury, Cacao, Régina, Blondin, Saint-Georges and Saut-Maripa. The other three clusters form a single entity, they bring together the forest populations: Sikini, Camopi, Alikéné, Dagobert, Dorlin, Midenangalanti and Bois Martin. A distinct population structure of An. darlingi mosquitoes has therefore been identified based on two ecological strata in French Guiana. Coastal sites are probably subject to a passive diffusion of mosquitoes associated with human travel by the only road that crosses French Guiana from West to East along the coast. The forest populations of An. darlingi seem to be structured by passive following the gold miners’ displacements between different illegal gold mining sites.Population structure studies of An. darlingi carried out in this thesis work fill a gap in existing knowledge in the field of entomology/epidemiology in French Guiana. These studies meet the need to understand the dynamics of An. darlingi populations. This structure should be taken into account when designing programs of surveillance and vector control., Cette thèse a pour but d’évaluer la structuration des populations d’Anopheles darlingi en Guyane. Une étude de génétique des populations sur An. darlingi se justifie parce que c’est un vecteur important du paludisme en Amérique du Sud et particulièrement en Guyane. Nous avons besoin de mieux connaitre le vecteur afin d’espérer agir sur la transmission des plasmodies dans le cadre de la lutte antivectorielle.Un premier axe repose sur une étude méthodologique permettant de déterminer si la méthode de capture (capture sur homme ou MosquitoMagnet® utilisant l’octénol ou le Lurex™ comme attractant) ou l'heure de capture influence la structure des populations d’An. darlingi. Cela a permis de préciser si la capture pouvait entrainer un biais d’échantillonnage. En effet, si on capture des populations différentes d’An. darlingi lors de l’utilisation de pièges différents ou lorsqu’on capture à des horaires différents, il devient impossible de faire des études de structure génétique excepté avec des moustiques capturés avec le même type de piégeage et à la même heure. De même, il devient impossible de comparer plusieurs études entre elles si elles n’ont pas utilisé le même mode de capture ou le même créneau horaire. Un second axe est dédié à l’étude, chez An. darlingi, de la diversité génétique des populations à l’échelle de la Guyane. L’échantillonnage a été effectué sur 14 sites en Guyane et un site au Suriname réparti selon deux différents faciès écologiques : le littoral et la forêt. Le génotypage a été obtenu pour un total de 1881 individus à l’aide 8 marqueurs microsatellites. Cette étude permet d’évaluer la structure des populations d’anophèles en Guyane. L’intérêt est de mieux connaitre les populations de vecteurs du paludisme sur le territoire et donc de mieux les contrôler dans le cadre de la lutte antivectorielle.L’étude méthodologique préliminaire a montré que les 3 types de collecte étudiés attirent et capturent les mêmes populations d’An. darlingi. Différentes méthodes de collectes peuvent donc être utilisées pour réaliser l’échantillonnage d’anophèles dans le cadre d’études moléculaires comme des études de structure génétique des populations. De même, l’heure de capture n’a pas été associée à des variations des populations anophéliennes.A l’échelle de la Guyane, nous avons mis en évidence cinq sous populations de moustiques appartenant à l’espèce An. darlingi. Les deux premiers « clusters » regroupent tous les sites du littoral : Kourou, Matoury, Cacao, Régina, Blondin, Saint-Georges et Saut-Maripa. Les trois autres clusters forment une entité. Ils regroupent les populations de la forêt : Sikini, Camopi, Alikéné, Dagobert, Dorlin, Midenangalanti et Bois Martin. Une structuration des populations d’An. darlingi à l’échelle de la Guyane a donc été mise en évidence selon les deux faciès écologiques. Les sites du littoral sont probablement soumis à une diffusion passive de moustiques liée aux déplacements humains par l’unique route nationale qui traverse la Guyane d’ouest en est le long du littoral. Les populations forestières d’An. darlingi semblent s’être structurées par diffusion passive selon les déplacements des orpailleurs entre les sites d’orpaillage illégaux.Les études de structure des populations d’An. darlingi menées dans cette thèse ont permis de combler le manque de connaissances existantes sur le sujet en Guyane. Ces études répondent à un besoin de compréhension de la dynamique des populations d’An. darlingi. Cette structuration doit être prise en compte lors de la conception des programmes de surveillance et de lutte antivectorielle.

Fragmentation acting over geological times confers wide, biogeographical scale, genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a major European forest tree and to resolve its demographic history, we describe and model its spatial genetic structure and gene 30 genealogy. We then test which Pleistocene event, whether recent or ancient, could explain its widespread but patchy geographic distribution using population genetic data, environmental data and realistic demographic timed scenarios. The taxon of interest is a conifer forest tree, Pinus nigra (Arnold), the European black pine, whose populations are located in the mountains of southern Europe and North Africa, most frequently at mid35 elevation. We used a set of different genetic markers, both neutral and potentially adaptive, and either bi-parentally or paternally inherited, and we sampled natural populations across the entire range of the species. We analysed the data using frequentist population genetic methods as well as Bayesian inference methods to calibrate realistic, demographic timed scenarios. Species with geographically fragmented distribution areas are expected to display strong among40 population genetic differentiation and low within-population genetic diversity. Contrary to these expectations, we show that the current diversity of Pinus nigra and its weak genetic spatial structure are best explained as resulting from late Pleistocene or early Holocene fragmentation of one ancestral population into seven genetic lineages, which we found to be the main biogeographical contributors of the natural black pine forests of today. Gene flow among the different lineages is strong across forests 45 and many current populations are admixed between lineages. We propose to modify the currently accepted international nomenclature made of five subspecies and name these seven lineages using regionally accepted subspecies-level names.

International audience; The pollen beetles, Brassicogethes aeneus (Fabricius, 1775), is one of the most significant pests of oilseed rape. To shed light on past and present pollen beetle demography (dispersal, population size), twelve microsatellite markers were developed and population genetic diversity and structure were analyzed at different spatial scales in France and in Europe from 433 individuals collected in 18 winter oilseed rape fields. RESULTS: The genetic differentiation among the population samples was low but significant between the Estonian sample and the rest of Europe. Isolation by distance was only significant at the European scale. The genetic variability was similar among the 18 population samples. Demographic inferences suggested a recent expansion of B. aeneus population size over Europe, possibly corresponding to an increase of oilseed rape crop’s area during the last decades. CONCLUSION: Current population size and dispersal are not straightforward to estimate from the distribution of genetic variability in B. aeneus over Europe because of the complexity of the demographic history of the pests. Nevertheless, as gene flow was important enough to prevent strong genetic differentiation at large geographical scales, the management of pollen beetle populations should likely be thought at the European continental level.

The pathovar viticola of Xanthomonas citri causes bacterial canker of grapevine. This disease was first recorded in India in 1972, and later in Brazil in 1998, where its distribution is currently restricted to the northeastern region. A multilocus sequence analysis (MLSA) based on seven housekeeping genes and a multilocus variable number of tandem repeat analysis (MLVA) with eight loci were performed in order to assess the genetic relatedness among strains from India and Brazil. Strains isolated in India from three related pathovars affecting Vitaceae species and pathogenic strains isolated from Amaranthus sp. found in bacterial canker-infected vineyards in Brazil were also included. MLSA revealed lack of diversity in all seven genes and grouped grapevine and Amaranthus strains in a monophyletic group in X. citri. The VNTR (variable number of tandem repeat) typing scheme conducted on 107 strains detected 101 haplotypes. The total number of alleles per locus ranged from 5 to 12. A minimum spanning tree (MST) showed that Brazilian strains were clearly separated from Indian strains, which showed unique alleles at three loci. The two strains isolated from symptomatic Amaranthus sp. presented unique alleles at two loci. STRUCTURE analyses revealed three groups congruent with MST and a fourth group with strains from India and Brazil. Admixture among populations were observed in all groups. MST, STRUCTURE and e-BURST analyses showed that the strains collected in 1998 belong to two distinct groups, with predicted founder genotypes from two different vineyards in the same region. This suggest that one introduction of grape planting materials contaminated with genetically distinct strains took place, which was followed by pathogen adaptation. Genome sequencing of one Brazilian strain confirmed typical attributes of pathogenic xanthomonads and allowed the design of a complementary VNTR typing cheme dedicated to X. citri pv. viticola that will allow further epidemiological survey of this genetically monomorphic pathovar. Made available in DSpace on 2019-11-29T18:07:54Z (GMT). No. of bitstreams: 1 Xanthomonascitripv.viticolaAffectingGrapevineinBrazil2019.pdf: 3096692 bytes, checksum: ec2b3ffb0c06180736f471cfff22e23f (MD5) Previous issue date: 2019

The etiology and main pathways for the spread of lavender decline, an infectious disease affecting French lavender production since the 1960s, have remained unclear, hampering the development of efficient control strategies. An extensive survey of lavender fields led to the conclusion that “Candidatus Phytoplasma solani” was chronically infecting declining lavenders and was associated with large infectious populations of Hyalesthes obsoletus planthoppers living on the crop itself. Lavender appeared to be the main reservoir host for lavender-specific phytoplasma strains, an unusual feature for this phytoplasma, which usually propagates from reservoir weeds to various economically important crops. These results point out the necessity to protect young lavender fields from the initial phytoplasma inoculum coming from surrounding lavender fields or from infected nurseries and to promote agricultural practices that reduce the development of H. obsoletus vector populations., Lavender decline compromises French lavender production, and preliminary data have suggested the involvement of “Candidatus Phytoplasma solani” in the etiology of the disease. In order to evaluate the epidemiological role of “Ca. Phytoplasma solani,” a 3-year survey was conducted in southeastern France. “Ca. Phytoplasma solani” was detected in 19 to 56% of the declining plants, depending on seasons and cultivars, and its prevalence was correlated with symptom severity. Autumn was more favorable than spring for phytoplasma detection, and “Ca. Phytoplasma solani” incidence was higher in Lavandula angustifolia than in Lavandula intermedia hybrids. Detection of the phytoplasma fluctuated over months, supporting the chronicity of infection. Three “Ca. Phytoplasma solani” secY genotypes, S17, S16, and S14, were the most prevalent in lavender fields and were also detected in nurseries, whereas strains detected in surrounding bindweed and wild carrots were mostly of the S1 and S4 genotypes. This suggests that lavender is the main pathogen reservoir of the epidemic. Adults and nymphs of the planthopper vector Hyalesthes obsoletus were commonly captured in lavender fields and were shown to harbor mainly the prevalent phytoplasma genotypes detected in lavenders. The “Ca. Phytoplasma solani” genotype S17 was transmitted to Catharanthus roseus periwinkle by naturally infected H. obsoletus. Finally, the inventory of the bacterial community of declining lavenders that tested negative for “Ca. Phytoplasma solani” by 16S rRNA deep sequencing ruled out the involvement of other phloem-limited bacterial pathogens. IMPORTANCE The etiology and main pathways for the spread of lavender decline, an infectious disease affecting French lavender production since the 1960s, have remained unclear, hampering the development of efficient control strategies. An extensive survey of lavender fields led to the conclusion that “Candidatus Phytoplasma solani” was chronically infecting declining lavenders and was associated with large infectious populations of Hyalesthes obsoletus planthoppers living on the crop itself. Lavender appeared to be the main reservoir host for lavender-specific phytoplasma strains, an unusual feature for this phytoplasma, which usually propagates from reservoir weeds to various economically important crops. These results point out the necessity to protect young lavender fields from the initial phytoplasma inoculum coming from surrounding lavender fields or from infected nurseries and to promote agricultural practices that reduce the development of H. obsoletus vector populations.

The Crau Plain grasshopper,PrionotropisrhodanicaUvarov, 1923 (Orthoptera: Pamphagidae: Thrinchinae), is a rare grasshopper species endemic to the Crau Plain, a steppic habitat in France with unique floristic and faunistic communities. During recent decades, the area covered by these steppic grasslands has been highly reduced and fragmented due to the development of irrigation-based agriculture, roads, as well as industrial and military complexes. The restricted distribution, low population density and poor dispersal ability ofP.rhodanica, combined with the destruction of its habitat, has led to the classification of this species as critically endangered in the IUCN Red List of Threatened Species. Decreases in habitat quality due to intensive grazing in the remnant grassland patches constitute an additional threat forP.rhodanicathat can impact population dynamics at a relatively small-scale. In this work, we focused on a small area of about 3 km2occupied by one of the largest subpopulations observed in 2000–2001. We conducted a single-time snapshot intensive survey of grasshopper density and genetic variation at 11 microsatellite markers. We used a recent method, MAPI, to visualize the spatial genetic structure as a continuous surface and to determine, with the simultaneous use of spatial cross-correlograms, whether the normalized difference vegetation index, which informs on the balance between vegetation productivity and grazing intensity, can explain grasshopper population structure at such a fine scale. We found that both population density and gene flow were strongly and positively correlated to habitat quality (higher productivity of grasslands and/or lower sheep grazing). The spatial scales of interaction between these variables were estimated to be highly similar, in the range of 812–880 meters. This result suggests thatP.rhodanicais very sensitive to the quality of the grasslands it inhabits.

Investigations into life history of microorganisms that cause plant diseases have been limited mostly to contexts where they are in interaction with plants, and with cropped or otherwise managed vegetation. Therefore, knowledge about the diversity of plant pathogens, about potential reservoirs of inoculum and about the processes that contribute to their survival and adaptation is limited to these contexts. The agro-centric perspective of plant pathogen life histories is incoherent with respect to the capacity of many of them to persist as saprophytes on various substrates. In this context we have investigated the ubiquity of the broad host range necrotrophic fungus Botrytis cinerea, outside of agricultural settings and have determined if the populations in these natural habitats can be distinguished phenotypically and phylogenetically from populations isolated from diseased crops. Over a period of 5 years, we isolated B. cinerea from 235 samples of various substrates collected in France including rainfall, snowpack, river, and lake water, epilithic biofilms in mountain streams, leaf litter and plant debris, rock surfaces, bird feathers and healthy wild plants from outside of agricultural fields. All substrates except rock surfaces harbored B. cinerea leading us to establish a collection of purified strains that were compared to B. cinerea from diseased tomato, grapes and various other crops in France. Phylogenetic comparisons of 321 strains from crop plants and 100 strains from environmental substrates based on sequences of 9 microsatellite markers revealed that strains from crops and the environment could not be distinguished. Furthermore, the genetic diversity of strains outside of agriculture was just as broad as within agriculture. In tests to determine the aggressiveness of strains on tomato stems, the mean disease severity caused by strains from environmental substrates was statistically identical to the severity of disease caused by strains from tomato, but was significantly greater than the severity caused by strains from grape or other crops. Our results suggest that highly diverse populations of this plant pathogen persist outside of agriculture in association with substrates other than plants and that this part of their life history is compatible with its capacity to maintain its potential as plant pathogen.

We present statistical methods based on matrix factorization problems. A first method allows efficient inference of population structure from genetic data and including geographic proximity information. A second method corrects the association studies for confounding factors. We present in this manuscript the models, as well as the theoretical aspects of the inference algorithms. Moreover, using numerical simulations, we compare the performance of our methods with those of existing methods. Finally, we use our methods on real biological data. Our methods have been implemented and distributed as R packages: tess3r and lfmm., Nous présentons des méthodes statistiques reposant sur des problèmes de factorisation matricielle. Une première méthode permet l'inférence rapide de la structure de populations à partir de données génétiques en incluant l'information de proximité géographique. Une deuxième méthode permet de corriger les études d'association pour les facteurs de confusion. Nous présentons dans ce manuscrit les modèles, ainsi que les aspects théoriques des algorithmes d'inférence. De plus, à l'aide de simulations numériques, nous comparons les performances de nos méthodes à celles des méthodes existantes. Enfin, nous utilisons nos méthodes sur des données biologiques réelles. Nos méthodes ont été implémentées et distribuées sous la forme de packages R : tess3r et lfmm.

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.

During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.

paper originating from a presentation made at the 13th International Plant Virus Epidemiology Symposium held at Avignon, France June 6-10, 2016; Cultivar choice is at the heart of cropping systems and resistant cultivars should be at the heart of disease management strategies whenever available. They are the easiest, most efficient and environmentally friendly way of combating viral diseases at the farm level. Among the melon genetic resources, Vat is a unique gene conferring resistance to both the melon aphid Aphis gossypii and the viruses it carries. The ‘virus side’ of this pleiotropic phenotype is seldom regarded as an asset for virus control. Indeed, the effect of Vat on virus epidemics in the field is expected to vary according to the composition of aphid populations in the environment and long-term studies are needed to draw a correct trend. Therefore, the first objective of the study was to re-evaluate the potential of Vat to reduce viral diseases in melon crops. The second objective was to investigate the potential of Vat to exert a selection pressure on virus populations. We monitored the epidemics of Cucurbit aphid-borne yellows virus (CABYV), Cucumber mosaic virus (CMV), Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV) in two melon lines having a common genetic background, a resistant line (R) and a susceptible line (S), in eight field trials conducted in southeastern France between 2011 and 2015. Vat had limited impact if any on WMV epidemics probably because A. gossypii is not the main vector of WMV in the field, but a favorable impact on CMV, yet of variable intensity probably related to the importance of A. gossypii in the total aphid population. Vat had a significant impact on CABYV epidemics with mean incidence reduction exceeding 50% in some trials. There was no effect of Vat on the structure of virus populations, both for the non-persistent WMV transmitted by numerous aphid species and for the persistent CABYV transmitted predominantly by A. gossypii.

Le genre Pseudomonas, inclut plusieurs espèces de bactéries phytopathogènes, comme les Pseudomonas syringae qui provoque la bactériose, maladie conduisant généralement à la mort des arbres fruitiers. A l’heure actuelle, les moyens de lutte contre P. syringae sont très réduits ou inexistants. Ainsi, des méthodes alternatives ou le rôle de certains éléments comme la présence de réservoirs de la bactérie sont en cours d’étude. Partant de l’hypothèse que le couvre-sol pourrait être une source d’inoculum de P. syringae, l’objectif du stage est de savoir si le couvre-sol joue un rôle dans le développement du chancre bactérien en verger d’abricotier. Les prélèvements de couvre-sol et des feuilles ont été réalisés dans un verger expérimental au domaine de Gotheron dans la Drôme. Tous les échantillons ont été analysés en biochimie (test oxydase et fluorescence), en microbiologie (dénombrement sur milieux TSA et KBC), en biologie moléculaire (PCR, gel d’électrophorèse, séquençage) et en bio-informatique. Ces différentes étapes ont permis de sélectionner les bactéries P. syringae et de déterminer les phylogroupes ainsi que les clades, et de pouvoir comparer les génomes des bactéries. Le couvre-sol en inter-rang dans les vergers d’abricotier comporte en grande majorité des populations du phylogroupe 2. Le phylogroupe 2 comprend plusieurs clades avec des bactéries pathogènes de l’abricotier. L’arbre quant à lui comporte principalement des populations du phylogroupe 1, dont le rôle dans le développement de la maladie reste à préciser. Le couvre-sol ne semble pas jouer un rôle prépondérant dans le développement de la bactériose de l’abricotier., The bacteria from the genus Pseudomonas are vascular, including several pathogenic species as Pseudomonas syringae who cause the bacterial canker. This disease usually lead the fruit trees to death. Currently, the means of fighting against P. syringae are reduced or nonexistent. So, alternative methods or the role of some elements as ground-cover are under study. On the assumption of ground-cover is a source of inoculum of P. syringae, the goal of this internship is to know if the ground-cover play a role in the development of the bacterial canker in Apricot orchards. The sampling of ground-cover and leaves were realized in an experimental orchard in Gotheron (Drôme). All the samples were analyzed in biochemistry (oxidase test and fluorescence), in microbiology (count in culture TSA and KBC), in molecular biology (PCR, electrophoresis gel, sequencing) and in bioinformatics. These different steps allowed to select P. syringae bacteria and to determine phylogroups as well as clades, and to be able to compare the genomes of bacteria. Ground-cover in inter-row in apricot orchard consist in a large majority of phylogroups 2. The phylogroups 2 consist of different pathogenic bacteria for apricot. The trees consist of the phylogroups1, which the goal in the development of the disease must be clarify. So, Ground-cover don’t play a role in the development of the bacterial canker in apricot orchard.

The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations., SCOPUS: ar.j, info:eu-repo/semantics/published

Potato virus Y (PVY) is one of the rare members of the genus Potyvirus for which the genetic diversity is structured by the plant species of origin. This structure has been explained by the occurrence in some crop species of barriers to infection by PVY isolates originating from other plant species. A particularly strong barrier to infection has been shown between PVY isolates from pepper (Capsicum spp.) and potato (Solanum tuberosum). PVY isolates from potato belong mainly to clades N and O and are poorly or not infectious at all in pepper. By contrast, PVY isolates from pepper belong mainly to clade C1 and are poorly or not infectious at all in potato. Recent surveys and genetic analyses, however, have revealed that PVY isolates of clades N and/or O can be quite frequent in pepper crops. Conversely, PVY isolates of clade C1 are almost absent in potato crops. However, we showed that PVY isolates of clade C1 from pepper are infectious in a potato cultivar devoid of the resistance gene Nc tbr . It has also been shown that, among pepper, tomato and tobacco genotypes carrying eIF4E-mediated recessive resistances, PVY evolution in one crop species could favour its future adaptation to other species. Altogether, these results suggest a lack of strong barriers to PVY host change between solanaceous crops. The contrast with older studies could be due to a range of factors, including an insufficient sampling effort in previous studies (too few isolates collected and characterised, too few plant genotypes assayed), to recent changes among PVY populations and/or to the contrasted behaviour of different genotypes within a plant species upon PVY inoculation.

To estimate the genetic diversity for a better understanding of the spread of Botrytis cinerea, we genotyped with nine microsatellite markers 174 isolates collected from four greenhouses during three growing seasons in the region of Bejaia. Four of these isolates were detected as Botrytis pseudocinerea according to the allele size at locus Bc6. For all other isolates further studied, all loci were polymorphic, with the mean number of alleles per locus ranging from 2.77 to 5.22.Considerable genetic variability was detected in all subpopulations (D*>0.87; Hnb>0.40). Based on the standardized index of association analysis, significant but low levels of clonality occurred, not excluding the possibility of recombination (rD= 0.07, P

Development of SNPs markers from pooled Rad-seq data and high-throughput genotyping, applied to the study of several harvested population genetics in the Upper-Maroni (French guiana). 17. Journées Ouvertes de Biologie, Informatique et Mathématiques

National audience; Blights and cankers of fruit trees caused by Pseudomonas syringae generate significant economic losses worldwide. Given the epiphytic lifestyle of P. syringae orchard ground covers represent a potential source of inoculum of P. syringae for fruit trees. They also represent a reservoir of bacterial diversity that could be beneficial for plant health via natural antagonistic and competitive interactions within the microbial flora. This microbial reservoir could be exploited for the development of ecological engineering practices, specifically the management of ground covers to reduce their negative impact on plant health and in particular as a source of pathogenic strains of P. syringae. Within the species P. syringae there is a very high genetic variability, and strains are distributed into 13 phylogroups (Berge et al., 2014) with very marked differences in pathogenicity among some of these phylogroups. Until now the only method for phylogenetic identification was the sequencing of specific and conserved genes. We have now replaced this with a PCR-based method allowing fast and accurate identification of 9 of the 13 current phylogroups (Borschinger et al., submitted). Here we will present the results of an exploratory study of P. syringae populations hosted by different compartments from 4 kiwifruit and 3 apricot orchards located in the southwest of France. The analysis of the phylogenetic structure of the P. syringae populations isolated from samples of ground cover, buds, leaves, twigs, irrigation water and soil, indicates a very large inter- and intra-orchard variability. Populations are largely constituted by an assembly of strains belonging to different phylogroups. Similarities between the phylogenetic structures of populations, and genetic similarities between strains, from different samples suggests a connection between these different compartments.

Cucurbits are widely grown in different provinces of Turkey. However their production is restricted by plant viruses. ZYMV is one of the most economically important viruses of cucurbit crops worldwide, including in Turkey. Several strains have been defined based on their biological, serological and molecular variability –particularly in the coat protein (CP) coding region. One molecular cluster (A1) appears highly prevalent worldwide, but other clusters (A4, A5) have been observed recently in several European and Mediterranean countries, probably in relation to recent introductions. However the situation in Turkey remains unknown. The aim of this research was thus to characterize the molecular variability of ZYMV in Turkey and look for the presence of emerging strains.

Le groupe des Pseudomonas syringae est très divers, au niveau phénotypique, génétique et de ses habitats. Récemment, 13 phylogroupes et 23 clades qui prennent en compte la diversité génétique et celle des habitats de cette bactérie ubiquiste ont été décrits (Berge et al., 2014). Des outils moléculaires permettant d’identifier les P. syringae et leur phylogroupes ont été développés au laboratoire (Borschinger et al., soumis), et nous permettent de travailler sur de relativement grands effectifs d’isolats bactériens. Avec ces outils, en réalisant nous-même des prélèvements dans des vergers ciblés en 2014 et 2015, et en collaboration avec le CTIFL qui a réalisé deux importantes prospections en 2011-2012, nous avons exploré la diversité des P. syringae rencontrés dans 36 vergers d’abricotiers de la vallée du Rhône, où le chancre bactérien était présent, et ce dans différents compartiments : le sol, le couvre-sol, les débris de culture, la plante (greffon) à différents stades de son développement, les racines (porte-greffe), la plante avec ou sans symptômes déclarées. Les résultats obtenus montrent que, parmi les 2436 isolats collectés, les isolats potentiellement pathogènes proviennent de 4 phylogroupes différents qui montrent une grande diversité; par ailleurs, certains phylogroupes sont ubiquistes et d’autres spécialisés. Le sol, le couvre-sol, les débris de culture, la plante (avec ou sans symptômes visibles) sont des réservoirs potentiels de la maladie. Les conséquences en termes d’étiologie et détection du chancre bactérien de l’abricotier sont discutées.

National audience; More than 70 viruses infect cucurbits worldwide. Among the most common and agronomically important are several potyviruses: ZYMV, WMV, PRSV. Besides these viruses that have a worldwide distribution and present distinct biological, serological and molecular features, several viruses closely related to PRSV that could constitute highly divergent strains of this virus or related species have been defined, and could represent new threats for agriculture.

The genetic consequences of range expansions have generally been investigated at wide geographical and temporal scales, long after the colonization event. A unique ecological system enabled us to both monitor the colonization dynamics and decipher the genetic footprints of expansion over a very short time period. Each year an epidemic of the poplar rust (Melampsora larici‐populina) expands clonally and linearly along the Durance River, in the Alps. The colonization dynamics observed in 2004 showed two phases with different genetic outcomes. Upstream, fast colonization maintained high genetic diversity. Downstream, the colonization wave progressively faltered, diversity eroded, and differentiation increased, as expected under recurrent founder events. In line with the high dispersal abilities of rust pathogens, we provide evidence for leapfrog dispersal of clones. Our results thus emphasize the importance of colonization dynamics in shaping spatial genetic structure in the face of high gene flow.

The Pyrenean desman (Galemys pyrenaicus) is a small, semiaquatic mammal endemic to the Pyrenean Mountains and the northern half of the Iberian Peninsula where it lives in cold and well-oxygenated flowing mountain streams. This species is currently classified as vulnerable on the IUCN Red List and has been undergoing habitat loss and fragmentation for decades, inevitably impacting its distribution. A recent genetic study, based on mitochondrial and intronic sequences, showed that the genetic variability of the Pyrenean desman is very low in the Pyrenees. In this study, we investigated the potential existence of genetic structure and gene flow at a smaller scale using 24 polymorphic microsatellite loci. As the Pyrenean desman is a very elusive species, we supplemented our tissue sample collection with samples of feces collected in the French range of this species. We successfully identified 70 individuals based on 355 fecal samples. Bayesian analyses revealed 3 genetic and geographic clusters (1 eastern, 1 central, and 1 western, including 3 genetic subclusters), with origins tracing back only 200 years. These clusters were characterized by low levels of genetic diversity and high inbreeding coefficients. Although gene flow among clusters appeared to be limited, populations seem to have exchanged alleles recently. Therefore, connectivity between watersheds should be enhanced to maintain genetic diversity and potentially improve the long-term survival of the Pyrenean desman in France.

Plant qualitative (i.e. total) resistance to viruses is an efficient way of protecting crops, but it is often broken down by the emergence of adapted virus variants, able to infect those resistant plants. This evolutionary phenomenon can occur particularly quickly in monocultures deployed in vast areas. Different strategies have been studied, aiming at increasing the durability of resistant crops, such as the use of multiline cultivars or cultivar mixtures in space and time. Here we study a complementary strategy that can yield interesting results in terms of yield increase and resistance durability. It exploits the evolutionary principles governing virus populations for the management of plant resistance, particularly regarding the effect of genetic drift on the evolution of plant viruses.

Pseudomonas syringae est agent phytopathogène-environnemental reconnu comme modèle remarquable. Nous avons isolé cette bactérie phytopathogène bien au-delà des zones d’agriculture, dans de nombreux substrats sur plusieurs continents constituant une collection unique au monde (>7000 souches). Une classification de cette bactérie intégrant toute la diversité et délimitant clairement les frontières est nécessaire. Les hybridations ADN/ADN et le séquençage de génomes trop lourds, les phénotypes peu fiables, et le concept de pathovar inopérant, nous conduisent à utiliser le typage MLST pour cette classification qui délimite actuellement 24 clades au sein d’au moins 14 phylogroupes. La robustesse du résultat est confirmée par les données de génomique. Pour chaque phylogroupe, les phénotypes reliés au pouvoir pathogène ont été caractérisés.[br/] A partir de ces données génotypiques et phénotypiques, les spécificités des phylogroupes ont été déterminées et un système de classification extensible à d’éventuels nouveaux groupes a été proposé. Un outil simple d’identification par analyse d’un seul gène de ménage est proposé (Berge et al. 2014). Grâce à la génomique comparative, nous avons développé des PCR spécifiques permettant l’identification au groupe P. syringae entier (Guilbaud et al.) et aux phylogroupes (Borschinger et al.) pour un crible moyen-débit de P. syringae permettant d’établir la structure des populations sur de nombreux échantillons. [br/] Cette classification nous permet d’aborder des questions sur l’écologie des agents phytopathogènes et leur stratégie d’adaptation dans différents environnements.

The melon Vat gene confers resistance to the aphid species Aphis gossypii and resistance to non-persistent viruses (CMV, WMV…) when inoculated by this species. It is however ineffective in blocking the transmission of viruses inoculated by other aphid species. Its effect on non-persistent virus epidemics is thus expected to be limited when A. gossypii is not the main aphid species visiting the melon crop. On the contrary, although not documented, its effect on the persistent virus CABYV mainly vectored by A. gossypii is expected to be strong.[br/] The first objective of the study was to evaluate the effect of Vat on virus epidemics and on the genetic structure of virus populations in field conditions.[br/] The second objective was to investigate the benefit of combining Vat resistance and an appropriate management of field margins to regulate the populations of aphids and/or their virus load. Indeed, literature suggests that flower strips can participate in pest biological control by favoring natural enemies, and strips of non-host plants can protect crops from non-persistent viruses by allowing aphids to probe on healthy plants and thus to lose their virus load before reaching the crops.

Watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) is a serious pathogen of cucurbit crops with a worldwide distribution. It has a wide host range (>170 species) and it is transmitted non-persistently by several aphid species. Previous molecular analyses based on full-length WMV sequences indicated the presence of 3 major groups, namely G1, G2 & G3. Until 2000 in the Mediterranean basin only G1 and G2 groups were observed, with many G1-G2 recombinants. The third group (G3 or ‘‘EM’’ for emerging) probably originating from Asia was first observed in south-eastern France in 2000. Despite the occurrence of WMV in Greece at least since 1983, no information was available on its genetic variability.

Visualisation of spatial networks based on pairwise metrics such as (dis)similarity coefficients provides direct information on spatial organization of biological systems. However, for large networks, graphical representations are often unreadable as nodes (samples), and edges (links between samples) strongly overlap. We present a new method, MAPI (Mapping Averaged Pairwise Information), allowing translation from spatial networks to variation surfaces.

Blights and cankers of fruit trees caused by Pseudomonas syringae generate significant economic losses worldwide. Given the epiphytic lifestyle of P. syringae orchard ground covers represent a potential source of inoculum of P. syringae for fruit trees. They also represent a reservoir of bacterial diversity that could be beneficial for plant health via natural antagonistic and competitive interactions within the microbial flora. This microbial reservoir could be exploited for the development of ecological engineering practices, specifically the management of ground covers to reduce their negative impact on plant health and in particular as a source of pathogenic strains of P. syringae. Within the species P. syringae there is a very high genetic variability, and strains are distributed into 13 phylogroups (Berge et al., 2014) with very marked differences in pathogenicity among some of these phylogroups. Until now the only method for phylogenetic identification was the sequencing of specific and conserved genes. We have now replaced this with a PCR-based method allowing fast and accurate identification of 9 of the 13 current phylogroups (Borschinger et al., submitted). Here we will present the results of an exploratory study of P. syringae populations hosted by different compartments from 4 kiwifruit and 3 apricot orchards located in the southwest of France. The analysis of the phylogenetic structure of the P. syringae populations isolated from samples of ground cover, buds, leaves, twigs, irrigation water and soil, indicates a very large inter- and intra-orchard variability. Populations are largely constituted by an assembly of strains belonging to different phylogroups. Similarities between the phylogenetic structures of populations, and genetic similarities between strains, from different samples suggests a connection between these different compartments.

Cucurbits are economically important vegetable in Turkey. Cucurbit crops are seriously affected by many viruses including Cucurbit aphid-borne yellows virus (CABYV). CABYV, a widespread polerovirus causing yellowing symptoms on older leaves that were previously associated to nutritional or physiological disorders. CABYV was first identified in 1988 in France, now, CABYV is widely spread in the whole Mediterranean region (Lecoq and Desbiez 2012). In Turkey, CABY reported firstly by Yardımcı and Özgönen (2007) as serologicaly. The purpose of this study was to characterize the molecular variability of CABYV in Turkey, through determining partial coat protein (CP) nucleotide sequences of (CABYV) isolates of Turkey.

The genetic structure of Potato virus Y (PVY) and Tobacco etch virus (TEV) (Potyvirus) populations was investigated in pepper fields in two regions in Turkey. The diversity of PVY and TEV populations according to coat protein (CP) and VPg coding regions showed some similarity. All the isolates built a monophyletic group due to a single introduction event or multiple introductions of genetically similar isolates. All the isolates of both viruses showed evidence to the diversification for a long time. Based on VPg and CP sequences, all PVY isolates corresponded to clade C1. Turkish potyvirus isolates were only able to break the pvr21 resistance allele and therefore belonged to pathotype (0, 1). The Pvr4 dominant gene was found to be efficient and durable against PVY but not at all efficient against TEV. Consequently, the pvr22 resistance allele, efficient resistance against PVY and TEV pathotype (0, 1) isolates, would be the most suitable strategy to control potyviruses.

The bacterium Pseudomonas syringae has been historically recognized as an important plant pathogen. However, the description of its ecology is moving away from that of a ubiquitous epiphytic plant pathogen to one of a multifaceted bacterium sans frontières that can survive in various ecosystems linked to the water cycle. Discovery of the aquatic facet of its ecology has led to a vision of its life history that integrates temporal scales spanning billions of years; and spatial scales traversing catchment basins, continents and the whole planet. Phenotypic and molecular characterization of about 800 strains from a wide range of substrates revealed a diversity of traits and abilities, including subverting the attacks and defense responses of the cohabitants of the various environments they occupy and setting off major environmental processes (e.g. rain and snowfall) that influence climate. This new ecological perspective has also yielded insights into epidemiological phenomena linked to disease emergence and into potential conflicts between its beneficial role in climate processes and its negative impact on the health of crops. Overall, it sets the stage for the integration of more comprehensive contexts of ecology and evolutionary history to elucidate the selective pressures that have shaped the biology of P. syringae into a highly diversified metapopulation of strains. We will present our current approach at elucidating the ecology and evolutionary history of this bacterial species and we will solicit discussions to further assess the drivers of its evolution.

National audience

We introduce a set of latent factor models dedicated to landscape genomics and ecological association tests. It includes statistical methods for correcting principal component maps for effects of spatial autocorrelation (spFA); methods for estimating ancestry coefficients from large genotypic matrices and evaluating the number of ancestral populations (sNMF); and methods for identifying genetic polymorphisms that exhibit high correlation with some environmental gradient or with the variables used as proxies for ecological pressures (LFMM). We also developed a set of open source softwares associated with the methods, based on optimized C programs that can scale with the dimension of very large data sets, to run analyses of population structure and genome scans for local adaptation.; Nous introduisons un ensemble de modèles à facteurs latents dédié à la génomique du paysage et aux tests d'associations écologiques. Cela comprend des méthodes statistiques pour corriger des effets d'autocorrélation spatiale sur les cartes de composantes principales en génétique des populations (spFA), des méthodes pour estimer rapidement et efficacement les coefficients de métissage individuel à partir de matrices de génotypes de grande taille et évaluer le nombre de populations ancestrales (sNMF) et des méthodes pour identifier les polymorphismes génétiques qui montrent de fortes corrélations avec des gradients environnementaux ou avec des variables utilisées comme des indicateurs pour des pressions écologiques (LFMM). Nous avons aussi développé un ensemble de logiciels libres associés à ces méthodes, basés sur des programmes optimisés en C qui peuvent passer à l'échelle avec la dimension de très grand jeu de données, afin d'effectuer des analyses de structures de population et des cribles génomiques pour l'adaptation locale.

International audience; Despite the fundamental role that soil invertebrates (e.g. earthworms) play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci) and mitochondrial markers (COI). Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations.

We introduce a set of latent factor models dedicated to landscape genomics and ecological association tests. It includes statistical methods for correcting principal component maps for effects of spatial autocorrelation (spFA); methods for estimating ancestry coefficients from large genotypic matrices and evaluating the number of ancestral populations (sNMF); and methods for identifying genetic polymorphisms that exhibit high correlation with some environmental gradient or with the variables used as proxies for ecological pressures (LFMM). We also developed a set of open source softwares associated with the methods, based on optimized C programs that can scale with the dimension of very large data sets, to run analyses of population structure and genome scans for local adaptation., Nous introduisons un ensemble de modèles à facteurs latents dédié à la génomique du paysage et aux tests d'associations écologiques. Cela comprend des méthodes statistiques pour corriger des effets d'autocorrélation spatiale sur les cartes de composantes principales en génétique des populations (spFA), des méthodes pour estimer rapidement et efficacement les coefficients de métissage individuel à partir de matrices de génotypes de grande taille et évaluer le nombre de populations ancestrales (sNMF) et des méthodes pour identifier les polymorphismes génétiques qui montrent de fortes corrélations avec des gradients environnementaux ou avec des variables utilisées comme des indicateurs pour des pressions écologiques (LFMM). Nous avons aussi développé un ensemble de logiciels libres associés à ces méthodes, basés sur des programmes optimisés en C qui peuvent passer à l'échelle avec la dimension de très grand jeu de données, afin d'effectuer des analyses de structures de population et des cribles génomiques pour l'adaptation locale.

We introduce a new method to study the relationships between population genetic structure and environment. This method is based on Bayesian hierarchical models which use both multi-loci genetic data, and spatial, environmental, and/or cultural data. Our method provides the inference of population genetic structure, the evaluation of the relationships between the structure and non-genetic covariates, and the prediction of population genetic structure based on these covariates. We present two applications of our Bayesian method. First, we used human genetic data to evaluate the role of geography and languages in shaping Native American population structure. Second, we studied the population genetic structure of 20 Alpine plant species and we forecasted intra-specific changes in response to global warming. STAR; Nous présentons une nouvelle méthode pour étudier les relations entre la structure génétique des populations et l'environnement. Cette méthode repose sur des modèles hiérarchiques bayésiens qui utilisent conjointement des données génétiques multi-locus et des données spatiales, environnementales et/ou culturelles. Elle permet d'estimer la structure génétique des populations, d'évaluer ses liens avec des covariables non génétiques, et de projeter la structure génétique des populations en fonction de ces covariables. Dans un premier temps, nous avons appliqué notre approche à des données de génétique humaine pour évaluer le rôle de la géographie et des langages dans la structure génétique des populations amérindiennes. Dans un deuxième temps, nous avons étudié la structure génétique des populations pour 20 espèces de plantes alpines et nous avons projeté les modifications intra spécifiques qui pourront être causées par le réchauffement climatique.

National audience

National audience

National audience; Watermelon mosaic virus (WMV, Potyvirus) is widespread in cucurbit crops in France since its first description 40 years ago. WMV has a relatively wide host range, including several weeds that can constitute winter reservoirs for the virus. Since 2000, new “emerging” (EM) isolates of WMV inducing more severe symptoms, particularly on zucchini squash, were introduced, probably from Asia. Within a few years, they have almost completely replaced in south-eastern France the “classic” (CL) isolates present before. In order to understand the causes for this rapid population shift, we studied the biological properties of CL and EM isolates. There was no evidence for a general better fitness of EM isolates regarding their host range, accumulation and aphid transmission in cucurbit hosts. A modeling approach based on epidemiological data from experimental plots suggested a dissymmetry in favor of EM vs. CL strains regarding their relative capacity of over-infections of plants already infected by the other type of strains, albeit this was not confirmed in greenhouse experimental tests. However, EM isolates appeared to present better aphid transmission rates from some non-cucurbit hosts than CL isolates in conditions of mixed infections, suggesting that non-cucurbit reservoirs could be an important driver of the evolution of viral populations.