Parasitic copepods including Lepeophtheirus salmonis have been the focus of strong concern for the health of wild and farmed salmonids in the Pacific and Atlantic Oceans. Salmon are highly valuable species from both socioeconomic and ecological perspectives. The host-parasite dynamics of Lepeophtheirus salmonis and the Atlantic and Pacific salmonids have changed over evolutionary time to the point that both Atlantic and Pacific salmon and Atlantic and Pacific Lepeophtheirus salmonis are genetically distinct. Recent human interference with the natural population dynamics of this parasite and its hosts may have altered the population genetic structure of Lepeophtheirus salmonis, particularly because salmon farms may provide more stable conditions for parasite population growth. High abundance of Lepeophtheirus salmonis on salmon farms causes damage to the farmed salmon and leads to increased infection intensities in nearby wild hosts. Some Atlantic Lepeophtheirus salmonis have developed resistance to the anti-parasitic drugs they are repeatedly exposed to. No drug resistance has yet been detected within the Pacific Ocean, where only one drug is available, and heavily relied on, to treat Lepeophtheirus salmonis infections. Control of Lepeophtheirus salmonis abundance on Pacific salmon farms is important to maintain the health of farmed salmon and is also important to protect wild salmonids from increased infections originating from salmon farms. The goal of this thesis was to characterize and employ a large suite of molecular markers to assess the population structure of Lepeophtheirus salmonis in the Pacific Ocean. Until this point, the primary focus of Lepeophtheirus salmonis population genetics research has been limited to the Atlantic Ocean and has relied on a small number of available molecular markers. Available expressed sequence tag DNA libraries were screened to identify putative polymorphic loci, which were then experimentally evaluated. We characterized 22 novel microsatellite loci and 87 single nucleotide polymorphisms within 25 nuclear loci for Lepeophtheirus salmonis. We used these genetic markers, as well as 5 microsatellite loci previously developed for use in Atlantic Lepeophtheirus salmonis population studies, to genotype 562 Lepeophtheirus salmonis that were collected from12 Pacific Ocean sampling locations. We compared Lepeophtheirus salmonis genotypes among: (1) seven wild host populations and five farmed host populations within the Pacific Ocean; (2) geographically separated wild host populations, ranging from the Bering Sea to the southwest end of Vancouver Island, British Columbia; and (3) temporally separated cohorts of farmed Atlantic salmon from two geographically distant farm locations on the northwest coast of Vancouver Island and the Campbell River area east of central Vancouver Island. Our analyses failed to resolve significant population structure among sampled Pacific Lepeophtheirus salmonis and, therefore, supports a hypothesis of high gene flow throughout the Northeast Pacific Ocean. It is important to understand the biology and population dynamics of Lepeophtheirus salmonis because it is a consequential parasite of wild and farmed salmonids in the Pacific Ocean. Both the molecular tools developed for this study and the population genetics information generated from this study have contributed to our overall understanding of the evolutionary history and population dynamics of Lepeophtheirus salmonis. / Graduate

This thesis investigates aspects of the community ecology of rabbit parasites with particular emphasis upon the gut helminths, utilising a 23 (later extended to 26) year time series of rabbits and their parasites. A clearer understanding of parasite communities can lead to more effective biological control strategies. Rabbits are regarded as a serious pest species throughout Europe and the Antipodes and the use of the myxomatosis virus, as a biological control agent, has already been tried and failed. However, a clearer picture of the parasite community may offer future possibilities for control. Additionally, the rabbit is a good model for other grazing species, as it carries a similar gut helminth community. Drug resistance is an increasing problem in a wide range of parasites. A clearer appreciation of parasite communities could also aid in the search for effective and environmentally sound pathogen control strategies (e.g. via cross immunity or competition with benign species). Theoretical models have revealed the importance of aggregation to the stability of the host parasite relationship, to parasite evolution and to interspecific parasite interactions. A number of models have considered the effect of varying aggregation upon these dynamics with differing outcomes to those where aggregation was a fixed parameter. Here the stability of the distribution for each of the rabbit helminths was examined using Taylor's power law. The analyses revealed that aggregation was not a stable parameter but varied with month, year, host sex, host age, and host myxomatosis status. Evidence for the existence of interspecific parasite interactions in natural systems has been equivocal. Factors influencing parasite intensity were evaluated for the gut helminth. A network of potential interactions between the parasites was revealed. Only month was shown to be of greater influence on the community. Following, from the above analyses, a community model was constructed which incorporated both seasonal forcing and interspecific parasite interactions, with interaction mediated via host immunity. One unexpected emergent property was an interaction between the seasonality and the immune decay rate with slower immune decay resulting in a shift of the immune response out of phase with the species against which it was produced. The model was also used to assess the potential effects of two control strategies, an anticestodal and a single species vaccine. The vaccine had greater effects on the whole community than the anticestodal because of the immune- mediated interactions. The host is also an integral part of the community as the parasite dynamics are linked with that of their host. Therefore an assessment of the parasites' impact upon host condition and fecundity was also undertaken. This revealed a variety of positive and negative associations between the parasites and their host, with potential implications for future host control strategies. This study has shown that ignoring parasite-parasite or parasite-host interactions and interactions of both the host and the parasite with the external environment, could result in a poor description of the community dynamics. Such complexities need to be considered and incorporated into theory if future control strategies for either host or parasites are to be effective.

This study involves a measure of the variability of descendants from a cross between Ustilago hordei race 7 and race 11, on two varieties of barley, Trebi and Odessa. Components of variability were defined, statistically described and compared. Biometrical analyses uncovered the action of significant additive and non-additive genetic effects. Differential interactions between treatments and varieties revealed the existence of at least one virulence gene. Specific polygenes and the virulence gene were found to produce significant interactions with different environmental conditions. Homogeneity of variance of the genetic components of the F2 from three randomly chosen F1 dikaryotic lines demonstrated the highly homozygous condition of the parental teliospores. Covariance - variance regression analysis was used to study the dominance and epistatic differences between treatment dikaryons. There is evidence for ambidirectional dominance. The number of effective factors operating against the varieties, Trebi and Odessa, were estimated to be between 4-6 and 1-2 respectively. / Science, Faculty of / Botany, Department of / Graduate

Chez les vertébrés, la réponse immunitaire acquise représente un mécanisme sophistiqué de réponse face aux parasites dont l‟une des particularités est la possibilité qu‟il offre aux mères de transférer certains de ses effecteurs à leurs nouveau-nés. Pourtant, malgré un intérêt croissant pour les effets maternels, les déterminants écologiques et évolutifs du transfert d‟anticorps maternels n‟ont pas encore été beaucoup étudiés. L‟analyse d‟un cadre théorique spécialement développé pour inclure le transfert transgénérationnel d‟immunité montre que l‟évolution de la capacité à transférer une immunité temporaire aux jeunes dépend des caractéristiques de l‟hôte et du parasite. En particulier, l‟augmentation de l‟espérance de vie de l‟hôte favorise l‟évolution de réponses immunitaires acquises, et la protection conférée par ces réponses est aussi supposée durer plus longtemps chez les hôtes longévifs. En accord avec cette prédiction, une étude de vaccination transgénérationnelle chez une espèce d‟oiseau de mer longévive a permis de mettre en évidence une demi-vie des anticorps maternels particulièrement longue. Les conditions sociales sont aussi un élément clé, et chez une espèce de mammifère, j‟ai pu montrer qu‟elles permettent un élargissement du répertoire d‟anticorps maternels. Le transfert d‟anticorps maternels est aussi à même de modifier les dynamiques épidémiologiques et pourrait présenter un atout non négligeable si la vaccination était utilisée en conservation. Enfin, ce mécanisme pourrait être mis à profit pour estimer l‟exposition des mères, et ainsi inférer la dispersion entre différentes zones d‟habitat / In vertebrate species, acquired immune response represents a sophisticated protection mechanism against parasites that has the particularity of enabling mothers to transmit part of its effectors to their newborns. Yet, despite an increasing interest in maternal effects, ecological and evolutionary determinants of the transfer of maternal antibodies remain poorly studied. The analysis of a theoretical framework specially developed to include a transgenerational transfer of immunity show that the evolution of an ability to temporarily protect offspring depends on the characteristics of both the host and the parasite. In particular, increasing the life span of the host favors the evolution of acquired immune responses and increases the duration of the protection offered by these mechanisms. Accordingly, a transgenerational vaccination study in a long-lived seabird revealed a particularly long half-life of maternal antibodies. Social conditions also proved important in a mammal species as they can allow for the broadening of the repertoire covered by maternal antibodies. The transfer of maternal antibodies could also modify epidemiological dynamics and could bbe an interesting asset if vaccination was used as a conservation tool. Finally, this mechanism could be used to estimate the exposure of mother and thus infer the dispersal rate between different habitat patches.

Das Problem der Rekonstruktion einer gemeinsamen evolutionären Entwicklung zwischen Wirts- und Parasitenspezies ist in der Forschung weit diskutiert. Dabei wird der Komplexität einer solchen Berechnung besondere Bedeutung beigemessen. In dieser Arbeit wird ein algorithmischer Ansatz vorgestellt, welcher auf Basis dynamischer Programmierung eine Rekonstruktion zweier phylogenetischer Stammbäume und einer gegebenen Abbildung von Parasiten auf zugehörige Wirte erzeugt. Grundlage dieser Berechnung ist ein ereignis-basiertes Modell der Koevolution, bei dem jedem Ereignis ein Kostenwert zugeordnet ist. Gesucht wird nach Rekonstruktionen, welche die Gesamtkosten der aufgetretenen Ereignisse minimieren. Es wird eine Vorgehensweise vorgestellt, mit welcher sich die Kosten der Ereignisse automatisch berechnen lassen. Dazu wurde ein Gütemaß entwickelt, um verschiedene Rekonstruktionen bezüglich der bei ihrer Berechnung verwendeten Ereigniskostenverteilung bewerten zu können. Im Gegensatz zu bisherigen Arbeiten unterstützt der vorgestellte Ansatz zudem die Verwendung von Stammbäumen mit mehrfach verzweigenden Knoten. Die algorithmischen Überlegungen wurden in einem Javaprogramm namens DynamicTreeMap umgesetzt. / The problem of reconstructing the common evolutionary development between host- and parasite species has been strongly discussed in research. Hereby a special meaning has been attributed to the complexity of such a calculation. In this thesis an algorithmic approach based on dynamic programming will be introduced, that creates a reconstruction of two phylogenetic genealogical trees and a given mapping of parasites on appropriate hosts. The foundation of this calaculation is an event-driven model of coevolution where costs are assigned to each event. The algorithm searches for reconstructions, which minimize the total costs of all occurred events. A method will be introduced which calculates the event-costs automatically. Therefore a quality rate has been developed, to evaluate different reconstructions concerning the used event-costs. Unlike present approaches genealogical trees with multiple branching nodes can be considered. The described approach has been implemented in a java program named DynamicTreeMap.

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第18605号 / 人博第701号 / 新制||人||167(附属図書館) / 26||人博||701(吉田南総合図書館) / 31505 / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 加藤 眞, 教授 市岡 孝朗, 教授 瀬戸口 浩彰, 教授 宮本 嘉久, 教授 新宮 一成 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DGAM

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