京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第20459号 / 人博第809号 / 新制||人||194(附属図書館) / 28||人博||809(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 加藤 眞, 教授 市岡 孝朗 / 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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Genetic predisposition to obesity presents a paradox: how do genetic variants with such a detrimental impact on human health persist through evolutionary time? Numerous hypotheses, for instance the thrifty genotype hypothesis, attempt to explain this phenomenon, yet fail to provide a satisfying answer to the modern obesity epidemic. In this critical review, I appraise existing theories explaining the evolutionary origins of obesity and explore novel biological and sociocultural agents of evolutionary change that may help explain the distribution of obesity and leanness predisposing variants in modern human populations. Gene pleiotropy and adaptations to diverse environmental niches may explain the rise and subsequent selection of obesity risk alleles. The regulation of gene expression by epigenetic mechanisms may serve as a stochastic factor affecting the manifestation of obesity phenotypes. Finally, exposure to malnutrition and disease epidemics in the wake of colonialism, culturally mediated notions of attractiveness and desirability, and diverse mating systems – including forced copulation, consanguinity and polygamy – may play a role in shaping the human genome. In short, I posit that in order to explain ethnic variation in obesity susceptibility, we must examine the origin of physiological adaptations and understand the sociocultural experiences of individuals and populations. As an imperative first step towards the identification of important drivers of obesity gene evolution, this review will inform empirical research focused on testing evolutionary theories by way of population genetics and mathematical modelling. Ultimately, these data will promote a better understanding of the aetiology of obesity and are expected to guide the development of targeted management, treatment, and prevention strategies. / Thesis / Master of Science (MSc)

Viruses may acquire mutations that result in a tropism shift. RNA viruses, such as Coronaviruses (CoVs), are susceptible to tropism shifts. A tropism shift occurs when a virus alters the tissue or cell type it infects, which can have important implications for disease pathogenesis, virulence, transmission, and treatment control. Tropism shifts can occur after cross-species jumps, as well as result from within-host evolution. Beyond the human host, CoVs can be highly pathogenic to a wide variety of wildlife and companion animals. A spillover event from animals to humans, resulting in a tropism shift, has occurred at some point in the evolutionary history of all three highly pathogenic human CoVs: severe acute respiratory syndrome coronavirus (SARS-CoV), middle eastern respiratory syndrome coronavirus (MERS), and severe acute respiratory syndrome 2 (SARS-CoV-2). Therefore, studying the evolution of CoVs in non-human animals may be of critical importance for pandemic prevention. This was the focus of my dissertation, to apply state-of-the-art codon models of evolution to a variety of CoV viral sequences to identify how natural selection may alter viral proteins priming them for tropism shifts. Statistical codon models can infer both which codon sites and genes have been subject to positive or negative selection, effectively differentiating signal between random mutations and those that may impact fitness. These models may also compare selection at homologous sites between different phenotypes (i.e., Spike protein sequences isolated from the gastrointestinal tract and those from macrophages) to identify where selection is acting differently between the phenotypes. In chapter 2 I examined a CoV sequence isolated from hospitalized humans in Malaysia that resembled a Canine Coronavirus (CCoV) to investigate how natural selection had shaped the Spike protein sequence in related animal CoV sequences priming it to jump into humans. In chapter 3 I compared the natural selection signals at specific codon positions in the Spike protein from sequences isolated from two separate feline tropisms (gastrointestinal and macrophage) to identity which adaptive mutations may be associated with the tropism shift and subsequent shift in virulence. This was performed on Feline Coronavirus (FCoVs), where almost 90% of all wild and domestic cats are gastrointestinally infected with FCoVs, and infection becomes highly pathogenic as a result of the shift in tropism to the macrophages. Since intra-host evolution can impact tropism shifts, in Chapter 4 I performed a detailed high-throughout analysis of intra-host evolution of RNAseq data of Equine Coronavirus (ECoV), as well as natural selection analyses of related embecoviruses that have colonized the human host. Taken together, I report on novel signals of natural selection across viral proteins, with an emphasis on Spike, on a diverse set of CoV clades that shed light on the complexities of coronavirus evolution as it relates to tropism shifts. / Biology

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Understanding the genetic basis of adaptive evolution, and how natural selection has shaped patterns of polymorphism and divergence within and between species are enduring goals of evolutionary genetics. In this thesis, I used whole genome re-sequencing data to characterize the genomic signatures of natural selection along different evolutionary timescales in three Populus species: Populus tremula, P. tremuloides and P. trichocarpa. First, our study shows multiple lines of evidence suggesting that natural selection, due to both positive and purifying selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. Second, we characterize the evolution of genomic divergence patterns between two recently diverged aspen species: P. tremula and P. tremuloides. Our findings indicate that the two species diverged ~2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. We further explore different mechanisms that may explain the heterogeneity of genomic divergence, and find that variation in linked selection and recombination likely plays a key role in generating the heterogeneous genomic landscape of differentiation between the two aspen species. Third, we link whole-genome polymorphic data with local environmental variables and phenotypic variation in an adaptive trait to investigate the genomic basis of local adaptation in P. tremula along a latitudinal gradient across Sweden. We find that a majority of single nucleotide polymorphisms (SNPs) (&gt;90%) identified as being involved in local adaptation are tightly clustered in a single genomic region on chromosome 10. The signatures of selection at this region are more consistent with soft rather than hard selective sweeps, where multiple adaptive haplotypes derived from standing genetic variation sweep through the populations simultaneously, and where different haplotypes rise to high frequency in different latitudinal regions. In summary, this thesis uses phylogenetic comparative approaches to elucidate how various evolutionary forces have shaped genome-wide patterns of sequence evolution in Populus. / <p>The research in this thesis was supported by the Swedish research council (to Pär K. Ingvarsson) and the JC Kempe Memorial Scholarship Foundation (to Jing Wang). The PhD study of Jing Wang in Sweden was funded by the State Scholarship from China Scholarship council.</p>

Stellenbosch University. Faculty of Arts and Social Sciences. Dept. of Visual Arts / Thesis (MA (VA)) -- Stellenbosch University, 2006. / ENGLISH ABSTRACT: Cultural evolution & genre: an investigation of three South African graphic narratives of the South African Border war (1975-1988) Magister in Fine Arts thesis, Department of Fine Arts, Stellenbosch University This study analyses three South African graphic narratives in the context of culture evolving in the Darwinian sense. It is deemed necessary to consider evolutionary theory in such a study of graphic narratives as it considers the development of culture as resulting from a process of evolution akin to natural selection. Special attention is paid to the theory of memetics, in the field of evolutionary epistemology, and its proposal to model cultural evolution. While this model relies on evolutionary theory, the development of culture is seen as evolving separately from biological evolution. This evolutionary perspective on culture is combined with the concepts of discourse and genre in social semiotics and media studies to investigate the changes in the depiction of the Border war in South African graphic narratives. As such this study focuses on the strategic viewpoint of cultural evolution, the role of memes in genre and its interaction with the evolution of discourse. This approach is offered as a useful method to analyse cultural artefacts. / AFRIKAANSE OPSOMMING: Kulturele evolusie & genre: 'n ondersoek van drie grafiese verhale van die Suid-Afrikaanse Grensoorlog (1975-1988) Magister in Beeldende Kunste tesis, Oepat1ement Beeldende Kunste, Universiteit van Stellcnbosch Hicrdie studic ontleed drie Suid-Afrikaanse graficse verhale in die konteks van kultuur wat evolueer in die Oarwinistiese sin. Oit word belangrik gereken om evolusieteorie in so 'n studie van grafiese verhale in ag te neem aangesien die ontwikkeling van kultuur as die resultaat van 'n proses van evolusie, verwand aan natuurlike seleksie, geag word. Spesiale aandag word geskenk aan die teorie van meme, in die veld van evolusieepistemologie, en die teorie se voorstel om kulturele evolusie te modelleer. Terwyl so 'n teorie op evolusieteorie steun, word die ontwikkeling van kultuur beskou as 'n afsonderlike proses van natuurlike seleksie. Hierdie evolusienere perspektief op kultuur word verenig met die konsepte van diskoers en genre in sosiale semiotiek en media studies om die veranderende uitbeelding van die Grensoorlog in Suid-Afrikaanse gratiese verhale na te vors. Sodanig fokus hierdie studie op die strategiesc oogpunt van kulturele evolusie, die rol van meme in genre en die interaksie met die ontwikkeling van diskoers. Hierdie benadering word aangebied as 'n waardevolle metode om kulturele artefakte te ontleed.

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The central goal of this thesis is to provide additional criteria towards implementing open-ended evolution in an artificial system. Methods inspired by biological evolution are frequently applied to generate autonomous agents too complex to design by hand. Despite substantial progress in the area of evolutionary computation, additional efforts are needed to identify a coherent set of requirements for a system capable of exhibiting open-ended evolutionary dynamics. The thesis provides an extensive discussion of existing models and of the major considerations for designing a computational model of evolution by natural selection. Thus, the work in this thesis constitutes a further step towards determining the requirements for such a system and introduces a concrete implementation of an artificial evolution system to evaluate the developed suggestions. The proposed system improves upon existing models with respect to easy interpretability of agent behaviour, high structural freedom, and a low-level sensor and effector model to allow numerous long-term evolutionary gradients. In a series of experiments, the evolutionary dynamics of the system are examined against the set objectives and, where appropriate, compared with existing systems. Typical agent behaviours are introduced to convey a general overview of the system dynamics. These behaviours are related to properties of the respective agent populations and their evolved morphologies. It is shown that an intuitive classification of observed behaviours coincides with a more formal classification based on morphology. The evolutionary dynamics of the system are evaluated and shown to be unbounded according to the classification provided by Bedau and Packard’s measures of evolutionary activity. Further, it is analysed how observed behavioural complexity relates to the complexity of the agent-side mechanisms subserving these behaviours. It is shown that for the concrete definition of complexity applied, the average complexity continually increases for extended periods of evolutionary time. In combination, these two findings show how the observed behaviours are the result of an ongoing and lasting adaptive evolutionary process as opposed to being artifacts of the seeding process. Finally, the effect of variation in the system on the diversity of evolved behaviour is investigated. It is shown that coupling individual survival and reproductive success can restrict the available evolutionary trajectories in more than the trivial sense of removing another dimension, and conversely, decoupling individual survival from reproductive success can increase the number of evolutionary trajectories. The effect of different reproductive mechanisms is contrasted with that of variation in environmental conditions. The diversity of evolved strategies turns out to be sensitive to the reproductive mechanism while being remarkably robust to the variation of environmental conditions. These findings emphasize the importance of being explicit about the abstractions and assumptions underlying an artificial evolution system, particularly if the system is intended to model aspects of biological evolution.

Este trabalho busca entender a diversificação craniana dos macacos do Velho Mundo (Catarrhini) integrando duas abordagens para o estudo da evolução de caracteres complexos: a genética quantitativa e a integração morfológica. A investigação tem três objetivos principais: 1) comparar a magnitude e o padrão das relações entre os caracteres cranianos entre todos os Catarrhini; 2) testar a hipótese de que deriva genética é o único agente responsável pela diversificação craniana; 3) explorar as conseqüências evolutivas da associação entre caracteres. De posse de um banco de dados bastante representativo da diversidade dos macacos do Velho Mundo (39 medidas cranianas de cerca de 6.000 crânios de mais de 130 espécies), gerei as matrizes de correlação e de variância/covariância, que resumem as relações entre os caracteres, e comparei-as entre vários grupos. Comparei-as também a expectativas derivadas de modelos teóricos de evolução por deriva genética, além de simular a ação de seleção natural sobre essas matrizes para observar o comportamento evolutivo dos diversos padrões de associação entre caracteres. De maneira geral, o padrão das relações é o mesmo entre todos os Catarrhini, mas a magnitude com que os caracteres estão associados varia bastante. Isso tem conseqüências evolutivas importantíssimas, pois grupos com baixas magnitudes tendem a responder na mesma direção em que a seleção atua (alta flexibilidade evolutiva), enquanto que altas magnitudes estão associadas, independentemente da direção da seleção, a respostas ao longo do eixo de maior variação, que no caso dos Catarrhini corresponde à variação no tamanho (baixa flexibilidade evolutiva). A diversificação inicial do grupo parece ter sido gerada por seleção natural, mas nos níveis de gênero e espécie, deriva genética é o processo predominante; a exceção são os cercopitecíneos, onde há evidência de seleção também nesses níveis. Com base nesses resultados, proponho um modelo que associa a magnitude geral da correlação entre caracteres aos possíveis caminhos evolutivos que uma população pode seguir. Apesar de este trabalho estar empiricamente restrito aos macacos do Velho Mundo, esse modelo é válido para os mamíferos como um todo e pode ser testado em outros grupos, aumentando nossa compreensão de como a associação entre caracteres afeta a evolução dos seres vivos. / This is a study on the cranial diversification of the Catarrhini, a large group of primates that includes all Old World monkeys and apes, bringing together two approaches to investigate the evolution of complex characters: quantitative genetics and morphological integration. It has three main goals: 1) to compare magnitudes and patterns of inter-trait relationships in the skull among catarrhines; 2) to test the null hypothesis that genetic drift is the sole agent responsible for cranial diversification; 3) to explore the evolutionary consequences of inter-trait associations. With a large and representative cranial database of Old World monkeys and apes (39 measurements of around 6,000 skulls from more than 130 species), I generated and compared correlation and variance/covariance matrices, which summarize inter-trait relationships, among several Catarrhini groups. I compared some of those matrices to expectations derived from theoretical models of evolution through genetic drift, and simulated natural selection to observe the evolutionary behavior of each matrix. From a broad perspective, the patterns of relationships are the same among all catarrhines, but the magnitudes are quite variable. This has very important evolutionary consequences, because groups with low overall magnitudes tend to respond in the same direction of selection (high evolutionary flexibility), while higher magnitudes, regardless of the direction of selection, are associated to responses along the axis of highest variation, which in this case corresponds to size variation (low evolutionary flexibility). The initial diversification of catarrhines seems to have been generated by natural selection, but drift probably played a major role at the genus and species level; the exception are the cercopithecines, for which there is evidence for selection also in those levels. Based on these results, I propose a model that links the overall magnitude of inter-trait correlations to the possible evolutionary paths of a given population. This study is empirically restricted to Old World monkeys and apes, but the model has been proved valid to a broader sample of mammals and can be tested for other groups, contributing for our understanding of how complex characters evolve.