No description available.

„Alles ist Prozess“ – so könnte man meinen, rückt doch der Prozess als Beschreibungskategorie und damit die Prozessualität der jeweils betrachteten Phänomene in den letzten Jahrzehnten immer stärker in den Fokus wissenschaftlicher und außerwissenschaftlicher Reflexionen. Heute werden Prozesse in allen Bereichen – Natur, Technik, Wirtschaft, Politik, Gesellschaft und Kultur – nicht mehr nur diagnostiziert oder gedeutet, vielmehr werden sie überwacht, zu steuern und zu regulieren versucht, sie werden ‚optimiert‘, ‚gemanaged‘ und nicht zuletzt will Veränderung auch ‚kommuniziert‘ sein.

Lizards of the viviparous genus Niveoscincus contributed importantly to a classic model for the evolution of placentation of squamate reptiles. This model predicts that: (1) placental function is correlated with placental structural complexity and (2) the type of chorioallantoic placenta attributed to three species of Niveoscincus (N. metallicus, N. ocellatus, N. pretiosus) is intermediate in complexity to a highly placentotrophic type of placenta. Recent studies of two of these species (N. metallicus, N. ocellatus) revealed additional variation in placental structure, as well as variation in the level of placentotrophy; N. metallicus is predominantly lecithotrophic, while N. ocellatus is highly placentotrophic. We used light microscopy to study placental ontogeny in two biennially reproducing species of Niveoscincus (N. greeni, N. microlepidotus) and placental morphology in late stage embryos of N. pretiosus. These data, in combination with prior studies, provide descriptions of placental structure for six of the eight species assigned to this lineage. The genus Niveoscincus has greater variation in placental structure than any other squamate lineage. We recognize four distinct groupings among these six species based on placental structure. The most highly placentotrophic species, N. ocellatus, has a complex placental morphology, yet shares these structures with a predominantly lecithotrophic species, N. microlepidotus. Thus, among species of Niveoscincus, placental structural complexity is not an infallible predictor of overall placental function. J. Morphol. 270:485-516, 2009.

Stephen Jay Gould, a great scientist and evolutionary biologists, suggested that if we could replay the tape of life, we would not have observed similar course of events because evolution is stochastic and if affected by several events. Since then, the possibility that evolution is repeatable or predictable has been debated. Studies using large-scale evolution experiments, long-term data for individual populations, and controlled experiments in nature, have demonstrated phenotypic and genetic convergence in several taxa. These studies suggest that despite some randomness, predictable evolutionary patterns can emerge on a large temporal and spatial scale. However, a few cases also exist where evolution is unpredictable and stochastic. One way to understand evolutionary predictability better can be to have quantitative estimates of predictability at different heirarchical levels (mutations, genetic, phenotypic). This can help better understand if evolution is predictable and the extent to which it is predictable. My dissertation uses Lycaeides butterflies to identify and quantify evolutionary predictability in different contexts such as on a geographic scale, temporal scale and genomic scale. I accomplished this by sequencing and annotating the genomes of these butterflies across a vast geographic range and on a temporal scale and by comparing natural and experimental populations. My results show that different mechanisms can assist evolution of organisms to adapt to novel environmental challenges, and that the evolutionary changes can be somewhat predictable. Through this work I demonstrate three main findings: first, quantitative estimates of evolutionary predictability indicate that degree of predictability is variable and is highly context-dependent. Second, we can predict evolutionary patterns on a spatial as well as temporal scale, and can predict patterns in nature by controlled laboratory experiments. Additionally, genomic changes underlying repeatability vary across the genome. Lastly, the approach of quantifying predictability can help us better understand the mechanisms which drive evolution and how organisms will evolve in response to similar environmental pressures. These results suggest that evolution can be constrained and if we actually replay the tape of life, we could see a considerably similar outcome in biodiversity compared to what Gould predicted.

The RNA World hypothesis describes a period of time during the origins of life in which RNA molecules performed all catalysis and were the only form of information storage. A great deal of evidence has been obtained in support of this hypothesis, however a few key demonstrations are lacking. The first demonstration is of a molecule capable of self-replication that could have plausibly arisen from the prebiotic soup. Previously in the Lehman Laboratory, a 198-nucleotide RNA was discovered that could be fragmented into as many as four pieces ranging from 39 - 63 nucleotides in length. When these pieces were incubated together in a test tube, they re-formed the necessary covalent bonds to regenerate the full-length 198-nucleotide RNA. Furthermore, the full-length RNAs were catalytically active and made copies of themselves from the remaining pieces in solution, providing a model system of self-replication. I was able to remove >10% of the total length of the RNA, which substantially reduced the catalytic activity of the full-length molecule. I discovered several mutations that restored catalytic activity by improved folding and increased catalytic rates using in vitro selection. A subset of these mutations was found to aid in the assembly of the shortened full-length RNA from smaller fragments than were possible in the original system, enhancing the prebiotic relevance of this system. A second demonstration to bolster the RNA World hypothesis would be showing that RNA is capable of harvesting energy from its environment by performing oxidation and reduction reactions. Again using in vitro selection, I have completed five rounds of selection geared towards identifying a ribozyme that reduces benzoic acid to benzaldehyde using Zn2+ and NADH. Results to date suggest the selection is working and it should be continued for another five to ten generations. Finally, I have discovered an RNA sequence that forms knots during transcription, a phenomenon heretofore undocumented in RNA. This new topology has implications for RNA stability by rendering RNA more resistant to hydrolysis, and could impact catalysis through formation of more complex, knotted active sites. Taken together, these findings have improved our understanding of RNA folding and catalysis, and the plausibility of the RNA World.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第17831号 / 農博第2016号 / 新制||農||1016(附属図書館) / 学位論文||H25||N4788(農学部図書室) / 30646 / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 中坊 徹次, 准教授 田川 正朋, 准教授 豊原 治彦 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

No description available.

No description available.

Discovering the targets of selection in a genome is fundamental for understanding how adaptation has affected the biological processes that lead to population and species diversity. However, very few variants in proteins are known to be adaptive. For example, in humans, fewer than 30 such adaptive missense variants are known. It is surprising that in the 5-6 million years since human divergence from chimpanzee so few adaptive missense variants would have accumulated, and so it is unclear whether such adaptive variants have never occurred or whether current methods cannot detect such changes. Are there such adaptive variants in the coding region of the genome? Alternatively, is everything found in non-coding regions, which is often largely thought of as “junk DNA”? These questions represent a grand challenge in the field of evolutionary biology. This work helps to resolve this paradox and shows that there, in fact, may be much more coding adaptation that was previously not detectable. We do this by developing and testing the idea that long term evolutionary patterns of genomic differences between species can be used to identify alleles that affect the fitness of individuals in a population.Many methods that aim to detect selection are often limited as to the timescale during which they are applicable, e.g., long-term or short-term only. In bridging this gap, we build on the Evolutionary Probability (EP) method, a method that uniquely integrates long term evolutionary history to provide a probability of observation under neutrality. We develop an approach that benefits from the strengths of both types of methods by leveraging long term evolutionary information from EP and short-term evolutionary information from population polymorphisms to identify alleles affected by selection. High-throughput analysis of variation for functional change is not possible given the immense sequencing data output that is increasing each day. Thus, we employ an in silico approach. We perform simulations of neutral evolution to identify thresholds of neutrality for EP. We also analyze various bona fide datasets of both neutral, adaptive, and deleterious variation found in humans comprising of hundreds of thousands of individual variants in humans alone. We find that our approach is reliably able to identify evolutionarily unexpected, non-neutral (affected by selection) alleles and requires only sequence alignments. Known adaptive variants are successfully identified, and a vast majority of disease variants are found to be evolutionarily forbidden underscoring the role of coding variation in human divergence as much more than previously thought. In fact, applying our approach across the human exome, we find that the amount of adaptation in humans is likely multiple orders of magnitude greater than previously believed. A catalog of the discovered candidate adaptive polymorphisms is available through an online personal genomics web resource. The new approach has also been shown to be generalizable to any sequence alignment, given that sufficient evolutionary time has elapsed among the species. Overall, our findings offer insight into the adaptive landscape of coding variants in humans, as well as provide a look into the role of long-term evolutionary history into generating disease in contemporary human populations, prompting a rethinking of the role of adaptation in human evolution. / Biology

No description available.