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At Santa Margarita Ranch, California, oak mistletoe (Phoradendron villosum) parasitizes valley oak and blue oak but cannot be found growing on coast live oak despite its abundance and ability to parasitize coast live oak in other areas. It seems as though this species of mistletoe is specializing on certain host oak trees, but the mechanisms of this specialization are unknown. In order to investigate this pattern, we utilized a type of machine learning in GIS called supervised classification as well as a reciprocal transplant study in the field. The three species of oak trees were classified with 87% accuracy using drone imagery and 95% accuracy using open source NAIP imagery. This classification technique could be applied to the whole state of California as long as ground truth points for each species were collected. This could be extremely useful for large scale forest management projects and ecological questions. Unfortunately, the classifier was unsuccessful at distinguishing mistletoe from host and so the number of mistletoe on each host could not be quantified using this technique. The reciprocal transplant study involved collecting mistletoe fruit from individuals growing on each of the three hosts and experimentally applying them back onto all three hosts. This allowed us to test whether there are host races of mistletoe that specialize at growing on certain hosts. We found that seeds from each host origin germinated equally well regardless of where they were dispersed, and seeds survived best on coast live oak, regardless of where they originated from. Based on these results, there must be some mechanism, other than host races, that explains the lack of mistletoe on coast live oaks at Santa Margarita Ranch. Future projects should investigate whether evidence for host races can be found at a later stage of seedling development and the roll of bird dispersers in creating the pattern.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24674号 / 農博第2557号 / 新制||農||1099(附属図書館) / 学位論文||R5||N5455(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 髙野 義孝, 教授 寺内 良平, 教授 吉田 健太郎 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

The twisted-wing parasites (Strepsiptera) are an endoparasitic order of insects with cosmopolitan distribution, which are sister group of Coleoptera. There are about 600 known species up to date. Strepsiptera parasitize seven insect orders (Thysanura, Orthoptera, Blattodea, Mantodea, Hemiptera, Diptera, Hymenoptera). The family Xenidae is one of the most derived groups of Strepsiptera. Its representatives parasitize aculeate Hymenoptera of three families (Vespidae, Sphecidae, Crabronidae). In comparison to the basal groups, there are well-known hosts for genera of the family Xenidae. Therefore, this group is suitable object for study of the evolution of host specialization. Phylogeny of the family Xenidae was constructed on the basis of molecular analysis of three genes. Moreover, the mapping of ancestral host major groups and biogeographic areas was performed using two methods (parsimony, maximum likelihood). According to the results, the family Xenidae is monophyletic group with Old World origin. There were a several independent switches to the same host groups. This significantly changes the existing ideas about evolution of host specialization and requires a taxonomic revision. Within the family Xenidae, there were several cases of dispersal between the Old World and the New World. Furthermore,...

La lutte microbiologique connaît un regain d'intérêt suite aux problématiques soulevée spar les pesticides chimiques en agriculture. L'objectif de ces travaux de thèse est d'étudier le potentiel d'une ressource virale alternative, les Densovirus pathogènes de Lépidoptères,appartenant à la sous famille des Densovirinae, strictement inféodée aux Arthropodes. Nos travaux ont été axés sur trois points (i) décrire le spectre d'hôtes de deux Densovirus candidats et identifier des déterminants de spécificité pour comprendre l'évolution du spectre d'hôtes ; (ii) caractériser des mécanismes de transmission horizontale pour analyser la dynamique de l'infection et (iii) valider des outils de détection des Densovirinae afin d'étudier la diversité génétique virale dans la nature. Le premier axe nous a permis d'identifier (i) un Densovirus candidat qui ne semble être virulent que pour des Lépidoptères ravageurs de culture, et (ii) des déterminants de spécificité à la surface de la capside impliqués le franchissement de la barrière intestinale. Concernant la transmission, nos résultats montrent qu'un Densovirus se propage rapidement dans une population hôte en induisant un comportement cannibale probablement développé par les individus non infectés. Nous avons également caractérisé deux mécanismes de transmission horizontale,par morsures et par un vecteur endoparasitoïde. Enfin, pour étudier la prévalence virale,nous avons mis au point un protocole basé sur le principe d'une PCR nichée que nous avons testé sur des insectes collectés dans la nature. Ceci nous a permis de dresser un inventaire de la diversité d'insectes, sans toutefois révéler à ce jour la présence de Densovirinae. Ces résultats constituent les premières connaissances pour l'élaboration d'un modèle épidémiologique qui nous permettra d'évaluer l'impact sur l'environnement d'utiliser un Densovirus en tant qu'agent de lutte microbiologique. / Microbial control has a renewed interest due to issues raised by chemical pesticides inagriculture. The aim of this work is to propose a new viral resource, Densoviruses pathogenicfor Lepidoptera belonging to Densovirinae sub‐family restricted to arthropods. We focus onthree axes, (i) we described the host range of two Densovirus candidates, and identified hostspecificity determinants to understand host range evolution; (ii) we characterized themechanisms driving the horizontal transmission of Densovirus to model the dynamic of theinfection; and (iii) we validated tools to detect Densovirinae to study the viral geneticdiversity in natura. The first point lead us to identify (i) a Densovirus potentially pathogeniconly for lepidopteran pests, and (ii) few determinants of specificity localized at the surface ofthe capsid that are essential for the midgut recognition, although this barrier of specificity isnot the only one. Concerning horizontal transmission, our results show that a Densovirus canspread rapidly within a host population, inducing a cannibalistic behavior probablydeveloped by non infected individuals. We also characterize two mechanisms involved intransmission, by biting and by an endoparasitoïd vector. To study the densoviral prevalence,we develop a nested PCR and test it on insect sampling. This allowed us to describe theinsect diversity. No Densovirinae have been detected so far. These results are the first steptoward building an epidemiology model that may allow to evaluate the impact of using aDensovirus as a biological control tool.

Primers for 10 polymorphic DNA microsatellite loci were developed and characterized for the endangered oyster mussel Epioblasma capsaeformis from the Clinch River, TN. Microsatellite loci also were amplified for individuals collected from the following additional populations or species: (1) E. capsaeformis from Duck River, TN; (2) E. florentina walkeri from Indian Creek, upper Clinch River, VA; (3) E. florentina walkeri from Big South Fork Cumberland River, TN; and (4) E. torulosa rangiana from Allegheny River, PA. Allelic diversity ranged from 9-20 alleles/locus, and averaged 13.6/locus for all 5 populations investigated. Average expected heterozygosity (HE) per locus ranged from 0.78-0.92, and averaged 0.86. A genetic characterization of extant populations of E. capsaeformis and E. florentina walkeri was conducted to assess taxonomic validity and to resolve conservation issues related to recovery planning. These mussel species exhibit pronounced phenotypic variation, and are difficult to characterize phylogenetically using DNA sequences. Monophyletic lineages, congruent with phenotypic variation among species, were obtained only after extensive analysis of combined mitochondrial (1378 bp of 16S, cytochrome-b, ND1) and nuclear (515 bp of ITS-1) DNA sequences. In contrast, analysis of variation at 10 hyper variable DNA microsatellite loci showed moderate to highly divergent populations based on FST values, which ranged from 0.12-0.39. Quantitative genetic variation was observed in fish host specificity, with transformation success of glochidia of E. capsaeformis significantly greater (p<0.05) on the greenside darter Etheostoma blennioides, and that of E. f. walkeri significantly greater (p<0.05) on the fantail darter E. flabellare. Lengths of glochidia differed significantly (p<0.001) between species, with sizes ranging from 241-272 μm. Underwater photographs of mantle-pads and micro-lures of female mussels documented fixed phenotypic variation between species. The texture and color of the mantle-pad of E. capsaeformis is smooth and bluish-white, while that of E. f. walkeri is pustuled and brown, with tan mottling. Based on extensive molecular, morphological, and life history data, a population of E. capsaeformis from the Duck River, TN is described and proposed as a separate species, and a population of E. f. walkeri from the upper Clinch River, VA is described and proposed as a separate subspecies. Genetic management guidelines were developed to assess taxonomic status, genetic variation of donor-recipient populations targeted for augmentation, and field and laboratory protocols to maximize genetically effective population size, minimize genetic changes in captive-reared progeny, and prevent the release of juvenile mussels into non-native drainages. A pragmatic approach to species recovery is advocated; one that incorporates the principles of conservation genetics into breeding programs, but prioritizes the immediate demographic needs of critically endangered mussel species. / Master of Science

Les microsporidies sont des pathogènes intracellulaires obligatoires apparentés aux champignons. Elles infectent de nombreux animaux, dont le nématode Caenorhabditis elegans. La première microsporidie isolée d’une souche de C. elegans sauvage a été nommée Nematocida parisii. L’interaction entre N. parisii et C. elegans est devenue un puisant modèle pour l'étude des interactions hôte-pathogène. Cependant, ce modèle a été récemment découvert et de nombreux détails sur son écologie et sa biologie restaient inconnus. Notamment, nous ignorions l’incidence et la diversité des infections microsporidiennes chez C. elegans et autres nématodes dans la nature.A partir d’une collection de nématodes, de la famille des Rhabditidae, échantillonnés dans le monde entier, j’ai recensé un panel de 47 nématodes présentant des symptômes d’infection par des microsporidies. J’ai caractérisé moléculairement la diversité de ce parasite infectant ces nématodes et déterminé que N. parisii est la microsporidie la plus souvent responsable des infections chez C. elegans dans la nature. J’ai également décrit et nommé six nouvelles espèces de Nematocida. Au cours de mes travaux, j’ai aussi défini deux nouveaux genres de microsporidies génétiquement distincts de Nematocida, appelés Enteropsectra et Pancytospora. Mes travaux ont de plus détaillé la diversité qui existe chez les microsporidies parasites de nématodes. Ces microsporidies présentent des différences en terme de taille et forme de leurs spores, de leur tropismes tissulaire et intracellulaire chez l’hôte, de leur voie de sortie des cellules hôtes mais aussi de spectre d’hôtes. Mes résultats ont démontré que, dans la nature, les infections de C. elegans et autres nématodes par les microsporidies sont répandues et diverses.De plus, j’ai estimé la variation naturelle pour la sensibilité de C. elegans à l'infection par N. ausubeli. J’ai notamment comparé 10 souches naturelles de C. elegans en utilisant des tests de consommation alimentaire. Deux souches de C. elegans, JU1249 et JU2825, présentaient des niveaux contrastés de sensibilité, ce que j’ai interprété comme étant une différence de niveau de tolérance aux infections. Ces deux souches se sont révélées être de bons candidats pour une future caractérisation des loci génétiques associés à la variation de sensibilité de C. elegans aux infections microsporidiennes. Enfin, j’ai observé un effet surprenant de l'infection de C. elegans par les microsporidies. En effet, la présence du pathogène est capable de supprimer le déclin progressif de la fécondité à haute température chez certaines lignées de C. elegans. / Microsporidia are fungi-related intracellular pathogens that infect a great variety of animals, including the nematode Caenorhabditis elegans. The first microsporidia isolated from wild C. elegans was named Nematocida parisii in 2008. C. elegans and N. parisii have been used as a powerful model for the study of host-pathogen interactions. However, it was unclear how widespread and diverse microsporidia infections are in C. elegans or other related nematodes in the wild.By sampling rhabditid nematodes worldwide, we established a collection of 47 nematodes that displayed putative microsporidia infections. We characterized molecularly these infections and determined that N. parisii (or N. ironsii) is the most common microsporidia infecting C. elegans in the wild. We further described and named six new Nematocida species. In addition, we defined two new genera of nematode-infecting microsporidia, named Enteropsectra and Pancytospora, which are genetically distinct from Nematocida. Further investigations showed that these microsporidia are diverse in terms of spore size and shape, host tissue tropism, host cell intracellular localization, cellular exit route, host specificity pattern, etc. Overall, these findings illustrate the widespread and diverse microsporidia infections in C. elegans and related nematodes in the wild.We further assayed the natural variation of C. elegans in sensitivity to N. ausubeli infection, by comparing 10 C. elegans strains using food consumption tests. Two C. elegans strains, JU1249 and JU2825, displayed the largest sensitivity differences, which were suggested to be a result of the different tolerance between the two strains. These two strains are proven to be good candidates for future studies on the genetic loci associated with C. elegans sensitivity variation to microsporidian infections. Furthermore, I observed an exciting effect of host-pathogen interaction. Microsporidia infection is able to suppress the progressive decline in fertility in some C. elegans with the mortal germline phenotype (Mrt).

Les mécanismes expliquant le maintien de la diversité végétale dans les forêts tropicales sont mal connus. Une hypothèse particulièrement étudiée est l’hypothèse Janzen-Connell qui postule que ces mécanismes sont essentiellement causés par les interactions entre les plantes et leurs ennemis naturels, en particulier les organismes pathogènes. Dans cette thèse, nous nous sommes donc intéressés aux agents pathogènes présents dans les sols d’une forêt guyanaise et à leur lien de spécificité avec les plantes. Dans le cas où l’hypothèse Janzen-Connell serait vérifiée, on peut s’attendre à ce que les plantes structurent les communautés de micro-organismes pathogènes. Nos travaux se sont focalisés sur les Oomycètes et en particulier les Phytophthora, pathogènes des arbres très importants, mais nous nous sommes aussi intéressés aux champignons pathogènes. Ainsi, nous avons développé et comparé des jeux d’amorces PCR spécifiques des Phytophthora et des Péronosporomycètes afin d’étudier ces organismes par metabarcoding. Ces amorces ont ensuite servi à étudier la diversité des communautés de Phytophthora dans des échantillons de sols de deux sites forestiers de Guyane Française prélevés au pied d’arbres appartenant à 10 familles végétales. Une faible diversité a été retrouvée, avec seulement 8 taxons en tout, et la très large dominance d’un complexe d’espèces Phytophthora heveae. La structuration par la plante-hôte de ces communautés est plutôt faible. Dans une étude complémentaire, nous avons analysé la diversité des Oomycètes et des champignons pathogènes dans les sols et les litières de six plantations monospécifiques et au sein d’une forêt naturelle de Guyane. La structuration par l’hôte s’est avérée nulle pour les Oomycètes et faible pour les champignons pathogènes. Enfin, nous n’avons pas réussi à déclencher expérimentalement des mortalités ou dépérissements par des Oomycètes sur le wacapou, une espèce d’arbre guyanaise, via des inoculations de sols de forêt. Au final, les résultats de cette thèse ne supportent pas l’hypothèse selon laquelle les Oomycètes seraient d’importants acteurs du maintien de la diversité végétale dans les forêts tropicales. Par ailleurs, ils nous interrogent sur la faible diversité de ce groupe de microorganismes dans les sols et litières dans un hotspot de diversité végétale. / The mecanisms implied in the maintenance of plant diversity in tropical forests are still poorly known. One particularly studied hypothesis is the Janzen-Connell hypothesis, which posits that these mecanisms are essentially caused by the interactions between plant and their natural enemies, including pathogenic organisms. In this thesis, we looked at the pathogenic organisms present in the soils of a Guyanese forest, and the specificity of their interactions withplants. In the case where the Janzen-Connell hypothesis would be verified, we could expect that pathogenic micro-organisms communities would be structured by plants. Our works focused on Oomycetes and especially the Phytophthora, which are very important pathogens of trees, but we also took an interest on pathogenic Fungi. Thus, we developed PCR primer sets specific of the Phytophthora and Peronosporomycete groups, in order to study these organismsthroughmetabarcoding. These primers were then used to investigate the community of Phytophthora in soils sampled from two French Guiana sites, near trees belonging to 10 families. A low diversity was described, with a total of only 8 taxas, and the overwhelming dominance of the species complex P. heveae. A weak host effect was detected. In a complementary study, we looked at the diversity of Oomycetes and Fungi in soils and litters of six monospecific tree plantations and a Guianese natural forest. Structuration by host appeared to be null for Oomycetes and weak for pathogenic Fungi. Finally, we did not success in trying to experimentally provoke, through forest soil inoculations, Janzen-Connell mortalities due to Oomycetes on the Wacapou, a Guianese tree species. In the end, the results of this thesis do not support the hypothesis that Oomycetes may be important agents of the maintenance of tree diversity in tropical forests. Moreover, they bring some questions about the low diversity of this group of micro-organisms in a tree diversity hotspot.

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