The subject of this thesis is the study of a system of multiple simultaneously spreading diseases, or strains of diseases, in a structured host population. The disease spread is modelled using the well-studied SEIR compartmental model; host population structure is imposed through the use of random graphs, in which each host individual is explicitly connected to a predetermined set of other individuals. Two different graph structures are used: Zipf power-law distributed graphs, in which individuals vary greatly in their number of contacts; and Poisson distributed graphs, in which there is very little variation in the number of contacts. Three separate explorations are undertaken. In the first, the extent to which two SEIR processes will overlap due to chance is examined in the case where they do not affect each other's ability to spread. The overlap is found to increase with increased heterogeneity in the number of contacts, all things equal. Introducing differences in infection probability or a delay between introducing the two strains produces more complex dynamics. I then extend the model to allow strains to modify each other's transmissibility. This is found to lead to modest changes in the size of the outbreak of affected strains, and larger effects on the size of the overlap. The extent of the effect is found to depend strongly on the order in which the strains are introduced to the population. Zipf graphs experience somewhat larger reductions in outbreak size and less reduction of overlap size, but overall the two graphs experience similar effects. This is due to the reduced effect of modification in key high-degree vertices in the Zipf graph being offset by higher local clustering. Finally, I introduce recombination and competition by replacement into the model from the first project. The number of recombinant strains that arise is found to be either very low or very high, with chance governing which occurs. Recombinant strains in Zipf distributed graphs have a significant chance of failing to spread, but not in Poisson distributed graphs. Replacement competition in the presence of a growing number of strains is found to both increase the chance of a strain failing to spread, and to reduce the overall size of outbreaks. This effect is equal in both graph types.

New insight to the population structure of the tapeworm Ligula intestinalis were obtained using genomic data by represented genomoc methods (ddRAD and high-throughput sequencing)

At least since the Neolithic, humans have largely lived in networks of small, traditional communities. Often socially isolated, these groups evolved distinct languages and cultures over microgeographic scales of just tens of kilometers. Population genetic theory tells us that genetic drift should act quickly in such isolated groups, thus raising the question: do networks of small human communitiesmaintain levels of genetic diversity over microgeographic scales? This question can no longer be asked in most parts of the world, which have been heavily impacted by historical events that make traditional society structures the exception. However, such studies remain possible in parts of Island Southeast Asia and Oceania, where traditional ways of life are still practiced. We captured genome-wide genetic data, together with linguistic records, for a case-study system-eight villages distributed across Sumba, a small, remote island in eastern Indonesia. More than 4,000 years after these communities were established during the Neolithic period, most speak different languages and can be distinguished genetically. Yet their nuclear diversity is not reduced, instead being comparable to other, evenmuch larger, regional groups. Modeling reveals a separation of time scales: while languages and culture can evolve quickly, creating social barriers, sporadic migration averaged over many generations is sufficient to keep villages linked genetically. This loosely-connected network structure, once the global norm and still extant on Sumba today, provides a living proxy to explore fine-scale genome dynamics in the sort of small traditional communities within which the most recent episodes of human evolution occurred.

MHC glycoproteins are an essential part of adaptive immunity and may also play a role in mate choice. In addition, MHC genes are the most variable of all known genes. For these reasons, they have been intensively studied for several last decades. However, research is complicated due to extreme variability and frequent duplications. The Eurasian beaver seems to serve as an interesting model. It underwent a dramatic bottleneck culminating in the end of 19th century, when only about 1,200 individuals survived in several isolated relic populations. Thanks to numerous reintroductions, beavers of various origin meet in newly established populations. However, knowledge of beaver MHC was very limited. Only a single MHC gene has been investigated in a detail, and some relic populations were not sampled. Utilising additional relic populations and additional MHC locus, I verified a significant reduction of the variability of beaver MHC genes and also found signs of selection in the past. Then I sequenced MHC loci in two newly formed populations. I confirmed the ongoing selection by the disruption of cytonuclear equilibrium and the advantage of divergent alleles. We therefore can have a unique insight into the several periods of the history of beaver populations: In the past, MHC diversity was shaped by a...

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第17774号 / 理博第3897号 / 新制||理||1562(附属図書館) / 30581 / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 渡辺 勝敏, 教授 曽田 貞滋, 教授 疋田 努 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24456号 / 理博第4955号 / 新制||理||1707(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 渡辺 勝敏, 教授 曽田 貞滋, 教授 中務 真人 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Hierarchical sampling from populations, incipient and recognized varieties within Phacelia dubia and P. maculata has revealed high levels of intraspecific polymorphism in chloroplast DNA. Much of the variation is partitioned between populations as evidenced by population-specific variants at fixation in all three populations of P. dubia var. interior and in both populations of P. maculata. Nine of 16 populations were polymorphic for cpDNA haplotypes. A total of 16 haplotypes was found in a sample of 106 individuals; the most common occurred in eight of the 16 populations and in 31 per cent of the individuals in the entire sample. A phylogenetic analysis revealed four basic plastome types. The two major groups of plastomes were separated by four independent base-pair mutations which suggests an ancient split in the evolution of plastid genomes. Representatives from each major plastome division were found in each of five populations spanning two allopatric varieties of P. dubia. The geographical distribution of haplotypes and lack of evidence for recent admixture argue against migration as a source of the polymorphism. It is more likely that the current taxonomic varieties are descendants of a polymorphic common ancestor.

No description available.

Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritionally value (high in protein and mineral content) and ability to thrive in harsh climates (drought, extreme elevations, etc.) make it an important regional food crop throughout the Andean region. The objectives of this study were to develop genetic markers and to quantify genetic diversity within cañahua. A set of 43 wild and cultivated cañahua genotypes and two related species (C. quinoa and C. petiolare) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic sequences produced by 454 pyro-sequencing of cañahua genomic DNA. In addition, another and 424 C. quinoa based microsatellite markers were evaluate as potential cross-species marker loci. A total of 48 polymorphic microsatellite marker loci were identified which detected a total of 168 alleles with an average of 3.5 alleles per marker locus and an average heterozygosity value of 0.47. A cluster analysis, based on Nei genetic distance, grouped the cultivated cañahua into a single dominant branch clearly separated from wild cañahua genotypes and the outgroup species. Within the cultivated genotypes, two dominant subclades were present that were further partitioned by AMOVA analysis into five model-based clusters. Significant correlations were found between genetic distance and morphological traits. The isolation by distance test displayed no significant correlation between geographic collection origin and genotypic data, suggesting that cañahua populations have moved extensively, presumably via ancient food exchange strategies among native peoples of the Andean region. The molecular markers reported here are a significant resource for ongoing efforts to characterize the extensive Bolivian and Peruvian cañahua germplasm banks, including the development of core germplasm collections needed to support emerging breeding programs.

No description available.