Bobcats (Lynx rufus) are generalist carnivores with an expansive range from southern Canada to northern Mexico, in which 11 - 12 subspecies have been described. Since European settlement, bobcat habitat has become increasingly fragmented due to urbanization and development of agricultural land. Presently, there is little information on the genetic structure of bobcat populations at large spatial scales. Furthermore, it is unknown whether the current isolation of bobcat populations is a historic feature or whether recent landscape alterations have disrupted dispersal among previously connected populations. To address these questions, microsatellite and mitochondrial DNA data were used for relatedness measurements, spatial autocorrelation examinations, Bayesian assignment testing and sequence analysis of bobcats across their range. These analyses showed that, within southern Illinois, females were closely related to one another and males tended to disperse from their natal area. On a regional scale, microsatellite data revealed several distinct genetic groups within the midwest, notably eastern and western bobcat populations. In contrast, mitochondrial DNA analyses resolved little differentiation among bobcat populations, elucidating two-three phylogeographic groups. Taken together, these data reveal that bobcats have not historically, experienced large barriers to dispersal. Rather, recent habitat alterations may be disrupting dispersal over large scales. Genetically defined groups are potential conservation units and should be used for regional management of bobcats.

Subspecies composition and genetic variation are important to the growth and survival of Largemouth Bass and information on these genetic characteristics is required for proper management of the species. In Puerto Rico, a genetic evaluation is needed to develop management plans for Puerto Rico reservoirs and maintain Florida Largemouth Bass at the Maricao Hatchery. Subspecies composition was characterized among reservoirs and the contemporary Maricao Hatchery broodstock in Puerto Rico, and metrics were compared between subspecies and hybrids among reservoir populations. Genetic variation and structure was determined and compared to Largemouth Bass populations in their native range. Florida subspecies were prevalent in all populations and non-introgressed subspecies seemed to be better adapted to the island than introgressed forms. Genetic diversity was lower in Puerto Rico populations and substantial genetic structure among populations was lacking. These results provide genetic information to guide future management and propagation of Largemouth Bass in Puerto Rico.

An analysis of microsatellite variation among individuals of Indian origin was performed to compare the genetic diversity between different regions within India that are divided by spoken language and geographical distance. In addition, the relationship between the Indian and other human populations was examined. Six microsatellite loci -CSF1PO, TPOX, TH01, F13A01, FESFPS and vWA were amplified and typed in a total of 149 individuals representing a broad geographical distribution within the Indian subcontinent. Contingency analyses of allele frequency distributions between North and South Indian populations revealed a significant difference at the vWA locus. The lack of significant differences at the other five loci may indicate a considerable amount of gene flow between these two populations or that these polymorphisms existed before the split between Northern and Southern populations. The South Indian population (n = 37) revealed the presence of an allele at the vWA locus that was not detected in either the North Indian (n = 103) or Caucasian (n = 212) populations. The absence of this allele in the North and the presence in the South may indicate a population specific allele and gives support to the hypothesis that India was occupied by an earlier Dravidian population before the more recent arrival of the Aryans who lacked this allele. Genetic distance failed to reveal any significant distances between North and South Indian populations. Phylogenetic analyses, although not significant, indicated that the two populations were not monophyletic. A correlation between genetic and geographic distance between the Northeast, Northcentral, Southeast and Southwest regions of India revealed a correlation coefficient of r = -0.53 which was not significant. The negative correlation is solely due to the fact that the two most geographically closest populations, Salem and Cochin, show the greatest genetic distance (0.442) between them. This is consistent with the fact that social factors play an important role in the genetic structuring of Indian populations. Genetic distance analyses revealed significant distance values between the Indian, Caucasian and African populations and showed the Indian population to be genetically closer to the Caucasian population. These results are consistent with earlier studies using gene frequency data and mitochondrial DNA. Overall, the results of the genetic distance and phylogenetic analyses showed that six microsatellite loci were able to distinguish between African and non-African populations, but more loci need to be utilized to differentiate between non-African populations. / Thesis / Master of Science (MS)

Powdery mildew caused by <i>Blumeria graminis</i> f. sp. <i>tritici</i> is one of the most devastating diseases in wheat (<i>Triticum aestivum</i>) worldwide. Hypersensitive, race specific genes primarily have been deployed to control the disease, however recent efforts have shifted to breeding for more durable resistance, such as "adult plant resistance" (APR). Molecular markers and quantitative trait loci (QTL) associated with APR to powdery mildew must first be validated and QTL effects evaluated in different genetic backgrounds and breeding populations to be useful in marker-assisted selection (MAS) programs. Eighteen simple sequence repeat (SSR) markers previously mapped near the three QTL in Massey for APR to powdery mildew were evaluated for association with APR for powdery mildew in a recombinant inbred line (RIL) breeding population derived from a cross between USG 3209 and a moderately susceptible cultivar Jaypee, wherein Massey is the resistance source for APR in USG 3209. Thirteen new SSR markers were added to the pre-existing genetic linkage maps near the three QTL associated with APR in the Becker by Massey (BM) population. Interval mapping analysis of mildew severity data collected in 2002 (F_5:6) and 2003 (F_6:7) field experiments with marker genotype data obtained in 2003 (F_6:7) confirmed the presence of three QTL for APR on chromosomes 1B, 2A, and 2B in the USG 3209 by Jaypee (UJ) population. The QTL on chromosomes 1B, 2A, and 2B explained 12% to 13%, 59% to 69%, and 22% to 48% of the phenotypic variance for powdery mildew severity in the UJ RIL populations, respectively, in the two field experiments. The efficiency of MAS was examined using powdery mildew data collected in 2002 and 2003 field experiments and also from a greenhouse experiment in 2004 (F_7:8), wherein adult plants of the 293 RILs were evaluated for disease severity using a composite of five different isolates of <i>B. graminis</i>. Selection of RILs possessing the QTL on chromosome 2A and to a lesser extent the one on chromosome 1B was effective in identifying powdery mildew resistance in both greenhouse and field experiments, whereas the effect of the QTL on chromosome 2B was insignificant in the greenhouse. Overall, selecting RILs with QTL on chromosomes 2A and 2B was most successful in identifying highly resistant RILs compared to selecting RILs having other combinations of two or three QTL combinations. The RILs possessing both QTL on chromosomes 2A and 2B had mean mildew severities of 4.4% and 3.2% in 2002 and 2003 field experiments, respectively. Breeders implementing MAS programs for APR to powdery mildew via selection of RILs containing the two QTL on chromosomes 2A and 2B likely will obtain RILs having high levels of resistance in the field. However, combining all three QTL may ensure greater durability of APR, on the basis that resistance conferred by QTL on chromosome 2A and 1B are genetically stable across all environments in this study. / Master of Science

L'esturgeon européen Acipenser sturio (Linnaeus, 1758) était un poisson commun de nos fleuves jusqu'au début du 20e siècle. Toutes ses populations sont maintenant éteintes sauf une qui survit dans le bassin Gironde-Garonne-Dordogne en France. Les données disponibles sur l'espèce restent très partielles car elles proviennent quasi exclusivement de cette population relictuelle. Au cours de cette thèse, plus d'une centaine d'échantillons anciens d'esturgeons restes archéologiques ou spécimens naturalisés conservés dans les muséums d'histoire naturelle ont été analysé grâce aux méthodes de la paléogénétique. Ces analyses génétiques ont été réalisées sur l'ADN mitochondrial (surtout la Dloop) ainsi que sur cinq loci microsatellites qu'il a été nécessaire d'adapter aux méthodes d'étude de l'ADN ancien. Les données paléogénétiques obtenues ont permis d'étudier : 1) les relations de l'esturgeon européen avec les autres espèces d'esturgeons vivant ou ayant vécu en Europe, en particulier l'esturgeon de l'Adriatique A. naccarii et l'esturgeon atlantique A. oxyrinchus. 2) la diversité génétique de l'esturgeon européen sur l'ensemble de son ancienne aire de répartition. 3) la diversité génétique d'une population d'esturgeon européen au cours du temps la population du Rhône, d'une période où elle était florissante jusqu'à son extinction. L'ensemble de ces données ont été discuté à la lumière de la conservation de l'espèce, qui est aujourd'hui en danger critique d'extinction. / The European sturgeon Acipenser sturio (Linnaeus, 1758) was a common fish of our rivers until the beginning of the 20th century. All populations are now extinct except one which survives in the Gironde-Garonne-Dordogne basin in France. Data available on this species are only partial because they only stem from this relictual population. During this thesis, more than one hundred ancient sturgeon samples archaeological remains or naturalized museum specimens were analysed by paleogenetics means. These genetics anlyses were carried out on mitochondrial DNA (mainly the Dloop) and five microsatellites loci which were adapted to ancient DNA methodologies. Paleogenetics data that we obtained were used to study : 1) A. sturio interactions with other sturgeon species which live or lived in Europe, especially the Adriatic sturgeon A. naccarii and the atlantic sturgeon A. oxyrinchus. 2) the genetic diversity of A. sturio all over its former geographical range. 3) genetic diversity of a population of the European sturgeon through time the Rhone River population from a period it was flourishing until its extinction. All these data were considered in the light of the species conservation, since A. sturio is now critically endangered.

Les pullulations de « papillon cendre » du genre Hylesia, appartenant à la famille des Saturniidae, constituent un problème récurrent de santé publique en Guyane et au Venezuela. En effet, pour protéger ses oeufs des prédateurs, la femelle possède des soies détachables extrêmement urticantes qu’elle est susceptible de libérer dans l’atmosphère. L’augmentation des sources de lumière artificielle depuis la fin du 19ème siècle liée à l’urbanisation croissante attire ces papillons nocturnes vers les villes et les villages, où la libération des soies urticantes est susceptible d’affecter l’Homme en générant une douloureuse affection de peau, la « papillonite ». Malgré les enjeux sociaux et économiques liés à la présence récurrente de ces papillons en zones urbaines, leur biologie et leur écologie reste peu connue. Les pullulations de « papillon cendre » attribuées à l’espèce H. metabus constituent un problème récurrent de santé publique en Guyane et au Venezuela. La définition de méthodes spécifiques de régulation des populations s’avère donc très urgente mais nécessitait au préalable de vérifier que seule l’espèce H. metabus est impliquée dans ces épisodes d’urtication et de préciser la structure des populations de ces insectes. Il était également important de préciser les mécanismes de reconnaissance des partenaires sexuels chez cette même espèce. Ces questions ont été les objectifs principaux de cette thèse. L’utilisation d’outils moléculaires a permis de montrer que seule l’espèce Hylesia metabus était impliquée dans les récents épisodes d’urtication en Guyane et au Venezuela. L’étude a également démontré que les populations guyanaises de cette espèce se distinguaient au plan génétique des populations du Vénézuela, et surtout qu’elles se structuraient en 2 sousensembles génétiques distincts entre la côte et l’intérieur de la Guyane. Tous les insectes collectés durant les épisodes de pullulation appartenaient au sous-ensemble côtier. Une approche basée sur l’étude du comportement de reproduction a été utilisée afin de préciser la temporalité d’émission de la phéromone sexuelle et ouvre de nouvelles perspectives pour l’identification de cette phéromone. / The genus Hylesia (Lepidoptera Saturniidae) are moths of human health importance in Venezula and French Guiana, inducing epidemic outbreaks of lepidopterism, a puriginous dermatitis caused by the urticating properties of the females’ abdominal setae. Adult female releases extremely urticating setae in the surrounding air, causing itchy dermatitis known as ‘papillonite’. Hylesia are attracted by artificial light source which are increasing since the end of the 19th century due to urbanization resulting in serious invasion event in towns and villages. Despite of the impact on human health, many aspects of the biology and their ecology remain unclear. The definition of specific methods of population regulation is thus very urgent but it was necessary first of all to verify that only the species H. metabus is involved in these episodes of urtication and to specify the population structure of these insects. It was also important to clarify the mechanisms for recognizing sexual partners in this same species. These questions were the mainobjectives of this thesis.The use of molecular tools has shown that a single species, Hylesia metabus, was involved in recent episodes ofurtication in Guyana and Venezuela. The study also demonstrated that the Guyanese populations of this species aregenetically distinct from the Venezuelan populations, and especially that they are structured in 2 distinct genetic subgroupsbetween the coast and the interior of French Guiana. All insects collected during outbreaks belonged to thecoastal subset. An approach based on the study of reproductive behavior has been used to clarify the temporality ofemission of the sex pheromone and opens new perspectives for the identification of this pheromone

La compréhension de la structure génétique et de la dynamique des populations, ainsi que les mécanismes moléculaires régissant les interactions entre l’hôte et le pathogène sont des éléments clefs pour la gestion des maladies. Au cours de cette étude nous avons cherché à développer dans un premier temps des marqueurs microsatellites à partir de données issues du séquençage d’un isolat de Ganoderma boninense. Ces marqueurs microsatellites nous ont permis d’étudier la structuration génétique et l’histoire démographique de G. boninense. Le génotypage d’un sous-échantillonnage issus de missions de récolte en Malaisie et à Sumatra nous a permis de mettre en évidence deux groupes principaux au sein de l’Asie du Sud-Est. Nous avons ensuite concentré notre attention sur la région regroupant la Malaisie péninsulaire et l’île de Sumatra, zone historique de développement de la culture industrielle du palmier à huile et d’apparition de la pourriture basale du stipe due à G. boninense, qui semble former une seule population. Nous avons examiné à une échelle géographique plus restreinte cette zone géographique afin de mettre en évidence une potentielle sous structure au sein de cette population. En testant l’effet du fond génétique du palmier d’origine de chaque individu, du nombre de génération de palmier précédent le moment de la récolte de l’individu, ou de la distance géographique sur une possible sous-structure des individus au sein de la zone historique, nous avons mis en évidence qu’aucune sous-structure génétique n’émergeait. En revanche, La comparaison de plusieurs scénarios d’évolution démographique a permis de mettre en évidence un phénomène d’expansion très ancien bien antérieur au début du développement de la culture industrielle du palmier à huile. Pour finir, la comparaison des données transcriptomiques entre des isolats agressifs et non agressifs a permis de souligner la présence d’une centaine de gènes différentiellement exprimés possédant une annotation fonctionnelle. Les résultats de ces deux approches pourront permettre une meilleure gestion de la maladie ainsi que l’amélioration des programmes développement et de gestion des résistances. / The understanding of genetic structuration and population dynamic, as well as the molecular mechanisms ruling host/pathogen interaction, are key elements for disease management. During this study, as first step, we were looking to develop microsatellites markers from genomic data obtained from sequencing of a Ganoderma boninense pure strain. Those markers allowed studying genetic structuration and demographic history of G. boninense. Genotyping of a subset of samples from sampling mission in Malaysia and Sumatra have highlighted two main groups in South-East Asia. Then, we focused on a region gathering peninsular Malaysia and Sumatra together, as it is both historical region of industrial oil palm culture development and the first region of basal stem rot observation caused by G. boninense, and to appear as a single population. We examine this region at a lower scale in order to highlight a potential genetic substructure in this population. We tested for effect of genetic tree background of each sample, number of planting generation before sampling and geographical distance between sample in order to observe a potential correlation between genetic substructure and one of those factors. As no correlation appeared, we concluded that this population does not have a genetic substructure. On the other hand, the comparison between several demographic evolution scenarios have shown a strong support for a past expansion event further back in time from the beginning of industrial oil palm culture development. To conclude, the exploration of transcriptomic data between strains owning aggressive or non-aggressive profile showed the differential expression of a hundred genes owning a functional annotation. Results from both approaches will allow the development of better disease management and a better resistance selection and management program.

Dans ce projet, nous nous sommes intéressés à l’invasion du nématode du pin, Bursaphelenchus xylophilus, un ver microscopique responsable de la maladie du dépérissement du pin et causant la perte de millions d’arbres annuellement à travers le monde. Notre objectif global était d’affiner nos connaissances sur ce cas d’invasion et particulièrement d’établir l’histoire d’invasion des populations européennes. Nous avons analysé la diversité génétique neutre d’échantillons de populations naturelles de nématode du pin de l’aire native et de différentes zones envahies à l’aide de méthodes de génétique des populations. Ces analyses ont essentiellement mis en évidence que (i) l’aire native du nématode du pin est fortement structurée à fines échelles spatiales et présente une diversité génétique faible à modérée, suggérant un rôle important de la dérive génétique, non compensée par la dispersion, (ii) les populations européennes présentent une diversité génétique extrêmement faible, suggérant un seul évènement d’introduction en Europe, et que (iii) l’Amérique du Nord est la source la plus probable des populations envahissantes européennes, non le Japon et la Chine. Ce projet souligne l’intérêt que les nématologistes et les généticiens des populations ont à collaborer. La génétique des populations a en effet permis de clarifier l’histoire de l’invasion des populations européennes et ce modèle nématode, du fait de son cycle de vie complexe résultant en un cas extrême de faible diversité génétique, a permis de s’interroger sur des méthodes et analyses couramment utilisées en génétique des populations. / In this project, we were interested in the invasion of the pinewood nematode, Bursaphelenchus xylophilus, a microscopic worm responsible for the pine wilt disease and causing the annual loss of millions of trees worldwide. Our global objective was to improve our knowledge on this case of invasion and particularly to clarify the invasion history of European populations. After developing the microsatellite markers needed for our study, we analysed the genetic diversity of samples of natural populations from both the native area and invaded areas thanks to population genetics methods. These analyses revealed that (i) the native area is strongly genetically structured at fine scales and displays a low to moderate genetic diversity, suggesting an important role of the genetic drift, not compensated by dispersal, (ii) the European populations exhibit an extremely low genetic diversity, indicating a unique event of introduction in Europe and (iii) North America is the most probable source of European populations compared to China and Japan. This project is finally a good example of the benefits of collaboration between nematologists and population geneticists. Population genetics allowed to clarify the invasion history of European populations and this “nematode” model, because of its complex life cycle resulting in an extreme case of low genetic diversity, provided the opportunity to question methodologies in population genetics that are routinely used.

International Telemetering Conference Proceedings / October 20-23, 2003 / Riviera Hotel and Convention Center, Las Vegas, Nevada / The NMSUSat is part of the AFRL/NASA University Nanosatellite program. The constellation will consist of a main microsatellite that will have a command link from ground and a telemetry link to ground while a picosatellite will act as a sensor reporting data to the microsatellite. Innovative command and data handling will be incorporated at low cost and greater accessibility. In this paper we present the necessary communications and control architecture for the space segment and the ground segment of the nanosatellite.

Land conversion is one of the greatest threats to terrestrial ecosystems around the world, and understanding its impacts on the biota is crutial for the management and conservation of species in and around human-modified landscapes, particularly in those where local declines can quickly translate into the extinction of endemic species or Evolutionary Significant Units.I investigated how habitat loss and fragmentation impacted dispersal and extinction risk in three small vertebrates (a phrynosomatid lizard Urosaurus nigricaudus, and two heteromyid rodents Chaetodipus arenarius and Dipodomys simulans), in a highly fragmented agricultural valley from the Sonoran Desert in the Baja California Peninsula, Mexico, where reptiles and rodents show high endemism and phylogenetic diversity. After reconstructing the history of habitat loss at the valley during the last 60 years, my approach involved the development and genotyping of 10 DNA microsatellite loci in 800 individuals from the three species that were sampled from continuous and fragmented habitat and analyzed using various population genetic methods.Although genetic diversity was not significantly affected by habitat loss and fragmentation, I observed an increase in genetic structure, relatedness, the spatial scale of individual movement and reversal of sex-biased dispersal in the three species, compared to continous habitat. I found evidence of a large and spatially localized extinction debt in the lizard, that showed individual dispersal restricted to<400 m in the fragmented habitat, while the two heteromyids seemed capable of dispersing over distances of few kilometers. Several observations supported a higher extinction risk in kangaroo rats compared to pocket mice. Continuous areas surrounding the fragmented landscape where identified as important sources of individuals to habitat fragments located nearby. Even the vegetation associated with a narrow wash across the fragmented landscape appeared to act as a corridor as high levels of dispersing individuals were inferred in the three species over a scale of several kilometers. This study provided an approach to evaluate the effects of distinct landscape features in preventing or allowing individual dispersal in multiple co-distributed species towards their conservation in human-modified landscapes.