京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第22791号 / 人博第962号 / 新制||人||228(附属図書館) / 2020||人博||962(吉田南総合図書館) / 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 瀬戸口 浩彰, 教授 市岡 孝朗, 教授 宮下 英明 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

Orientador: Erick da Cruz Castelli / Resumo: O gene HLA-C está localizado dentro do Complexo Principal de Histocompatibilidade (MHC), a região mais variável do genoma humano. HLA-C codifica moléculas que participam principalmente do processo de apresentação de antígenos intracelulares aos linfócitos T citotóxicos e interage com receptores presentes nas células NK, modulando sua atividade. A variabilidade das moléculas HLA permite a apresentação de diferentes peptídeos por um mesmo indivíduo e aumenta o repertório de peptídeos apresentados por uma população. Além disso, HLA-C é expresso na interface materno-fetal pelo trofoblasto, onde possui uma importante função imunomodulatória por meio da interação com receptores KIR das células NK maternas. Devido a sua dupla função, alguns alelos de HLA-C ou combinações de alelos HLA-C/KIR têm sido associados a diversos contextos fisiológicos e patológicos. Contudo, a variabilidade desse gene tem sido explorada principalmente para os éxons, em especial os éxons 2 e 3, que codificam os domínios de ligação ao peptídeo, enquanto a variabilidade de outros segmentos gênicos importantes (como outros éxons, íntrons e regiões regulatórias) foram pouco estudadas. Este estudo avaliou a variabilidade genética e assinaturas de seleção natural ao longo do gene HLA-C em uma amostra de 418 indivíduos do Brasil e 108 indivíduos do Benin. Considerando as duas populações, detectamos 359 sítios de variação ao longo da região analisada. Os haplótipos promotores, codificadores e de 3’NT apresentaram um... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Human Leucocyte antigen-C (HLA-C) is a classical HLA class I molecule that binds and presents peptides to cytotoxic T lymphocytes in the cell surface. HLA-C has a dual function since it also interacts with KIR receptors expressed in NK and T cells, modulating their activity. The structure and diversity of the HLA-C regulatory regions, as well as the relationship among variants along the HLA-C locus, is poorly addressed, and no population-based study explored the complete HLA-C variability in different population samples. Here we first present a new molecular and bioinformatics method to evaluate the full HLA-C segment, including regulatory sequences. Then, we applied this method to survey the HLA-C diversity in two geographically distinct population samples, one admixed from Brazil (São Paulo State) and one less admixed from Benin. Our results indicate that the HLA-C promoter and 3’UTR are very polymorphic, with the presence of few but highly divergent haplotypes. However, both these regulatory regions present conserved segments that are shared among different primates. Nucleotide diversity was higher in other exonic segments rather than exons 2 and 3, and also higher in the second half of the 3’UTR region. We detected evidence of balancing selection on the entire HLA-C locus and positive selection in exon 1, for both populations. HLA-C motifs previously associated with KIR interaction and expression regulation are similar between both populations, but the frequency of amino ... (Complete abstract click electronic access below) / Doutor

The ability to recover ancient DNA from skeletal material has completely transformed the field of evolutionary anthropology, making it possible to sequence the genomes of individuals who lived thousands of years ago. In addition to solving the long-standing question of admixture between neanderthals and modern humans and uncovering evidence of dramatic migration events throughout human history, ancient DNA has become an important resource for understanding many facets of natural selection, which is often challenging using today's genetic variation alone. Chapter 1 examines the dynamics of negative selection acting against Neanderthal ancestry in modern humans and establishes its limits over long evolutionary timescales. It shows that the previously reported monotonic decline in Neanderthal ancestry over the last fifty-thousand years, thought to be a result of negative selection, is a statistical artifact caused by incorrect assumptions about modern human demographic history, in particular the gene flow between Africa and West Eurasia. Re-estimation of the Neanderthal ancestry proportions over time using a more robust statistic no longer infers a significant decline in Neanderthal ancestry, which is proven to be consistent with simulations of negative selection across a wide range of selection parameters. Chapter 2 describes the first comprehensive analysis of the Y chromosomes of neanderthals and Denisovans. Although Neanderthals and Denisovans form a sister group to modern humans at the autosomal level, Neanderthal Y chromosomes are more similar to modern humans than Denisovan Y chromosomes. In fact, the Y chromosomes of late neanderthals represent a lineage introgressed from an early modern human population. This introgression, which occurred hundreds of thousands of years, completely replaced the Y chromosomes of early neanderthals, reflecting the observations made from mitochondrial DNA. Population genetic simulations of selection and introgression show that although a complete replacement of both mitochondrial DNA and Y chromosomes is unlikely under neutrality, higher deleterious burden of neanderthals predicts a rapid replacement of both loci by their modern human counterparts. Finally, Chapter 3 presents an R package admixer, designed to facilitate the programming of automated, fully reproducible population genetic analyses using ADMIXTOOLS, a suite of programs widely used in ancient DNA research.

Natural selection and other components of evolutionary theory are known to be particularly challenging concepts for students to understand. To help illustrate these concepts, we developed a simulation model of microevolutionary processes. The model features all the components of Hardy-Weinberg theory, with population size, selection, gene flow, nonrandom mating, and mutation all being demonstrated in the simulations. By using this freely available computer model, students can develop and test hypotheses with replicated virtual experiments. Because the model is an agent-based simulation, there is biologically realistic variability in the results. Students using the model see results both numerically and graphically and these are reinforced by an animation of the virtual fish in the simulated experiment.

BACKGROUND: Studies that aim to understand the processes that generate and organize plant diversity in nature have a long history in ecology. Among these, the study of plant-plant interactions that take place indirectly via pollinator choice and floral visitation has been paramount. Current evidence, however, indicates that plants can interact more directly via heterospecific pollen (HP) transfer and that these interactions are ubiquitous and can have strong fitness effects. The intensity of HP interactions can also vary spatially, with important implications for floral evolution and community assembly. SCOPE: Interest in understanding the role of heterospecific pollen transfer in the diversification and organization of plant communities is rapidly rising. The existence of spatial variation in the intensity of species interactions and their role in shaping patterns of diversity is also well recognized. However, after 40 years of research, the importance of spatial variation in HP transfer intensity and effects remains poorly known, and thus we have ignored its potential in shaping patterns of diversity at local and global scales. Here, I develop a conceptual framework and summarize existing evidence for the ecological and evolutionary consequences of spatial variation in HP transfer interactions and outline future directions in this field. CONCLUSIONS: The drivers of variation in HP transfer discussed here illustrate the high potential for geographic variation in HP intensity and its effects, as well as in the evolutionary responses to HP receipt. So far, the study of pollinator-mediated plant-plant interactions has been almost entirely dominated by studies of pre-pollination interactions even though their outcomes can be influenced by plant-plant interactions that take place on the stigma. It is hence critical that we fully evaluate the consequences and context-dependency of HP transfer interactions in order to gain a more complete understanding of the role that plant-pollinator interactions play in generating and organizing plant biodiversity.

Crypsis can be an important mechanism of predator avoidance for organisms. However, many species exhibit sexual dichromatism, in which the males possess a suite of colorations in order to attract female attention. The resulting differences in crypsis between the males and females can provide insight into the relative strengths of the sexually and naturally selective forces shaping the coloration of the organism, as well as clues regarding potential sensory biases of the selecting sex. In this study, I examine variation in the coloration of four Pacific Northwest populations of the sexually dimorphic and dichromatic polygynous species of jumping spider Habronattus oregonensis and compare the coloration of different body regions of the spiders to their habitats. I also investigate differences in relative size of a male sexual ornament, the enlarged first leg tibia. Field work for this study was conducted in June and July of 2009. The three main foci of this study are 1) to compare the degree of color matching of females and their habitat to the degree of color matching of males and their habitat, evaluating whether sexual selection on males has reduced their degree of crypsis relative to that of females, 2) if there is indeed a difference in crypsis between the sexes, to gauge whether there are similar divergences from crypsis among the populations - both in the quantitative amount of divergences as well as the colorimetric direction of such divergences, and 3) whether there is any variation in sexual ornament size among populations. Male first leg tibia size is a sexual character that is presumably not influenced by habitat coloration; differences in male tibia allometry among populations would provide supporting evidence for the hypothesis that sexual selection is indeed maintaining phenotypic differences among the populations, regardless of habitat location and color. I found a high degree of conformity of hue and chroma between male and female spiders and their habitats, with three notable exceptions. The most extreme difference in coloration between spider and habitat was that of the Gorge and Siskiyou population male anteriors. The anteriors had proportionally less green and more ultraviolet reflectance than their habitat. Second, the Mt. Hood and Tillamook population male abdomens diverged from their habitat in a similar, although less pronounced manner to that of the Gorge and Siskiyou population male anteriors: they had proportionally less green and more UV reflectance. Third, female abdomens of all populations were highly variable in chroma, despite having hues that generally matched their habitat. Tibia area relative to body size of Gorge and Siskiyou population males was significantly smaller than that of Mt. Hood and Tillamook population males. The lower level of background hue matching among males compared to females implies that sexual selection has directly conflicted with natural selection, resulting in impaired crypsis. While the reduced crypsis of the Gorge and Siskiyou population males is centered on their anterior (the primary body region presented to the females during courtship), the deviations from crypsis in the Mt. Hood and Tillamook population males are highest on their abdomen, although the degree of contrast is lower than that of the Gorge and Siskiyou population anteriors. These differences in coloration between the Mt. Hood and Tillamook population male abdomens and their habitats are in the same colorimetric direction as those of the Gorge and Siskiyou population anteriors and their habitat; this may indicate a sensory bias of the females, conserved in all four populations, selecting for male reflectance with a higher UV to green ratio. The fact that Mt. Hood and Tillamook population male abdomens have a more modest reduction in background matching compared to Gorge and Siskiyou population male anteriors may be due to the search methods of flying predators (e.g., spider wasps); the dorsum would presumably be more conspicuous to predators than the anterior, and would thus be subject to more intense selection for crypsis despite sexual selection to the contrary. The variability of abdomen coloration of females of both morphs may indicate that selection for crypsis is less strong among females than among males. One possible reason for this would be if females spent less time in the exposed courtship habitat than males, a conclusion implied by a highly male-skewed sex ratio encountered during field collections. Like the differences in coloration between different males of different populations, the significant differences in male tibia size also imply variability in the intensity of sexual selection. Relative importance of male coloration and tibia size may be weighted differently among populations, operating under similar constraints on reductions in survival accrued by developing these characters. The high degree of variation found among the populations implies that there is a degree of reproductive isolation among the chromatically and morphologically dissimilar populations. However, the similarity of the environments in which the populations existed, the close geographic proximity of some of the dissimilar populations, and the lack of any substantial geographic boundaries between the populations imply that this isolation is not maintained through extrinsic factors. Rather, it would seem that the interpopulational diversity is maintained by sexual selection. However, evidence from morphology and coloration suggest that the generation of this diversity is not evolving exclusively under sexual selection pressure, but rather is constrained to a degree by natural selection.

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Francisella tularensis is the etiological agent of tularemia, a zoonotic disease with worldwide prevalence. F. tularensis is a highly pathogenic organism and has been designated as a potential biothreat agent. Currently there are four recognized subspecies of F. tularensis: tularensis (type A), holarctica (type B), mediasiatica, and novicida. In addition, genomic studies have further subdivided type A tularensis into two subclassifications, type A.I and type A.II. These two subclassifications differ in geographic distribution with type A.I appearing mainly in the Eastern United States and type A.II appearing mainly in the Western United States. Because of differences of virulence among the subspecies, it is important to be able to quickly identify each of the subspecies rapidly and accurately. This work describes the development of a multiplex real-time polymerase chain reaction (PCR) assay which was shown to be ~98% successful at identifying the known subspecies of F. tularensis. Furthermore, F. tularensis is thought be a genome in decay (losing genes) because of the relatively large number of pseudogenes present in its genome. We hypothesized that the observed frequency of gene loss/pseudogenes may be an artifact of evolution in response to a changing environment, and that genes involved in virulence should be under strong positive selection. Eleven arbitrarily chosen virulence genes were screened for positive selection along with 10 arbitrarily chosen housekeeping genes. Analyses of selection yielded one housekeeping gene and 7 virulence genes which showed significant evidence of positive selection. Our results suggest that while the loss of functional genes through disuse could be accelerated by negative selection, the genome decay in Francisella could also be the byproduct of adaptive evolution, as evidenced by several of its virulence genes which are undergoing strong, positive selection.