Gene duplications can facilitate genetic innovation, reduce pleiotropy and catalyze reproductive incompatibilities and speciation. Therefore, the molecular and transcriptional fate of duplicate genes plays an important role in the evolutionary trajectory of entire genomes and transcriptomes. Using the polyploid African clawed frog Xenopus, I have investigated mechanisms that promote the retained expression of duplicate genes (paralogs) after whole genome duplication. The studies herein estimated molecular evolution and characterized expression divergence of thousands of duplicate genes and a singleton ortholog from a diploid outgroup. In this thesis, I have discussed the multiple mechanisms for the retention of duplicate genes in a polyploid genome and examined the potential effects that gene characteristics before duplication have on the odds of duplicate gene persistence. I have also explored the use of microarrays for comparative transcriptomics between duplicate genes, and between diverged genomes. The main objectives of my thesis were to better understand the genetic mechanisms that promote the retained expression of gene duplicates. My research utilized the duplicated genome from the allopolyploid clawed frog Xenopus. Genome duplication in clawed frogs offers a compelling opportunity to study factors that influence the genetic fates of gene duplicates because many paralogs in these frogs are of the same age, permitting one to control for the influence of time when evaluating the impact of duplication. My work has major impacts on several biological fronts including evolutionary genomics and comparative transcriptomics, and also on technical aspects of using microarrays. I have provided among the most comprehensive studies of its kind, in terms of examining molecular and regulatory aspects of thousands of expressed duplicates of the same age, and exploring various alternative hypotheses to explain how these genes are retained. / Thesis / Doctor of Philosophy (PhD)

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The cell cycle of eukaryotes consists of alternation between growth and DNA replication (interphase), and DNA distribution and cell-division (mitosis or M-phase). This process is regulated by a complex network of biochemical reactions. A core part of this network, called the "Cell Cycle engine" is evolutionarily conserved. The dimer of CDK1 (a protein kinase) and Cyclin proteins (the regulatory components), called M-phase Promoting Factor (MPF), and its key regulatory proteins Cdc25 and Wee1, are central parts of this cell cycle engine. Maintaining the fidelity of the DNA during the cell cycle is critical for successful propagation of the cell lineage. In the presence of unreplicated DNA, the cell cycle engine''s progress into mitosis is slowed down (or halted) by regulation of MPF activity through Cdc25 and Wee1. This regulatory event, called the unreplicated DNA checkpoint, was modeled in a rudimentary fashion in the Novak and Tyson (1993) model of frog eggs. Since then, many new experiments have uncovered relevant parts of this network. Here, we include these parts into a detailed model of the unreplicated DNA checkpoint in the cell cycle of frog-egg extracts. This work and future studies of the unreplicated DNA checkpoint will lead to its better understanding and hopefully to some strategies for tackling cancer. / Master of Science

Wetlands play a vital role in regional and global biogeochemistry by controlling the movement and cycling of nutrients and carbon. While individual wetlands may provide these ecosystem services, high density wetland landscapes, referred to as wetlandscapes, can have far reaching aggregate effects on elemental cycling and solute transport. Here we use forested Delmarva bays or wetlands as a study ecosystem to explore physical and biological controls on wetland chemistry within forested wetlandscapes. The Delmarva wetlandscape consists of thousands of geographically isolated wetlands on the Delmarva Peninsula, United States, which despite their proximity to each other have highly variable sizes, shapes, hydrology, vegetative cover, and biological communities. This physical and biological variation makes the Delmarva wetlandscape an ideal ecosystem to understand spatio-temporal heterogeneity and drivers of biogeochemistry. In this dissertation, I demonstrate that water chemistry within the Delmarva wetlandscape is heterogeneous both within and between surface water and groundwater systems (Chapter 2). Surface water chemistry was primarily influenced by temporal factors (season and month), followed by local hydrology. In contrast, groundwater chemistry was strongly influenced by water level below ground surface and interaction with organic soil layers. These results are important in understanding both internal wetlandscape water chemistry dynamics and export of solutes such as dissolved organic matter (DOM) to adjacent river ecosystems. Further, these results suggest that local biological and hydrological factors strongly affect surface water chemistry in wetlands. To explore these factors, I used an observational approach to determine the role of larval amphibians on wetland biogeochemistry (Chapter 3) and employed high-resolution chemistry sensors to study the effect of hydrological changes on surface water dissolved organic matter concentrations (Chapter 4). Animal waste can contribute substantially to nutrient cycling and ecosystem productivity, yet little is known of the biogeochemical impact of animal excretion in wetland habitats. A common and abundant amphibian in Delmarva wetlands are wood frog (Lithobates sylvaticus) tadpoles. I found that wood frog tadpole aggregations elevated nutrient recycling, microbial metabolism, and carbon cycling in Delmarva wetlands. These results provide evidence for the functional and biogeochemical role of tadpole aggregations in wetland habitats, with important implications for ecosystem processes, biodiversity conservation, and ecosystem management. To further explore the role of hydrology on DOM concentrations, I utilized high-resolution fluorescent dissolved organic matter sensors (fDOM) and applied river solute transport frameworks and metrics to wetland catchments. I found that there was heterogeneity in wetland response to changing hydrology and that seasonality and potentially bathymetry influences fDOM concentrations. Together, these studies inform our understanding of wetlandscape heterogeneity and DOM export, as well as biological and hydrological drivers of biogeochemistry. / Doctor of Philosophy / Wetlands control the movement of nutrients and carbon at local, regional, and global scales. There is a large body of knowledge demonstrating the importance of wetlands to the transport of dissolved water constituents, such as dissolved organic matter (DOM) and nutrients. However, there is little information on what controls surface water chemistry in these wetland landscapes and less is known about belowground water chemistry. In this study I examined the role of water level, wetland shape, and time (i.e., year, month of the year, and season) on surface and groundwater chemistry in wetlands. I found that water chemistry was different between surface and groundwater and that differences were primarily due to seasons or months in surface water wetlands, while water level and flooding of organic matter-rich soil layers controlled groundwater chemistry. These results indicate that there are differences in water chemistry between surface water and groundwater that are controlled by unique drivers. These results also suggested that biological processes such as animal presence may influence wetland chemistry. To understand the role of animals in wetland chemistry, I studied the effect of wood frog (Lithobates sylvaticus) tadpole waste on nutrient concentrations in wetlands and found large tadpole groups are significant recyclers of nitrogen and phosphorous, which were used by microbes as nutrients, leading to enhanced leaf litter break-down in wetlands. These findings imply that tadpoles have an important role in wetland ecosystems by creating locations of enhanced nutrient and carbon cycling and that conservation of amphibian species may also preserve ecosystem processes in wetlands. Additionally, my initial study suggested that hydrology influences DOM concentrations in wetlands. I used high-frequency chemistry sensors to detect fluorescent dissolved organic matter (fDOM) concentrations, which represents a fraction of DOM. I found that relationships and patterns in fDOM concentration were complex, and that season and wetland shape were important in wetland DOM dynamics. Overall, this dynamic behavior across seasons and between wetlands indicates that wetland response to water levels can drive differences in water chemistry between wetlands and is important in our understanding of wetland response to storm events. The information gained from these studies is important in understanding how large wetland landscapes function and control movement of nutrients and carbon. Further, my research has uncovered the role of animal species in controlling nutrient and carbon cycling in wetland environments as well as the complex response of fDOM to water level changes in individual wetlands.

Thesis (MSc)--University of Stellenbosch, 1982. / ENGLISH ABSTRACT:This study deals with the development of the ethmoidal region of Ascaphus truei Stejneger with special interest to the development of the nasal sacs, the diverticulum medium and the Jacobson's organ. This is to gather more information regarding the phylogeny of the structures. The opinions concerning the phylogenetical migration of the Jacobson's organ, are corroborated by the development of the organ in Ascaphus. The possible origin of the diverticulum medium from the nasal end of the nasolacrimal duct also is commented on. / No Afrikaans abstract available

Le slasher est un sous-genre du film d'horreur reposant sur une figure de tueur masqué punissant en apparence la sexualité adolescente. Très populaire auprès du public adolescent de 1978 à 1984, il serait, selon de nombreux critiques, une expression de sadisme « gratuit ». Cependant, toute production culturelle possède une légitimité qui peut lui être conférée en trouvant une clé de lecture adéquate. Cette clé est selon-nous un archétype culturel que nous nommons foolkiller, et qui figure une victime marginale sanctionnant les actes irresponsables mettant en danger les membres les plus faibles de la communauté. Cet archétype convoque l'imaginaire médiéval du charivari, un rite de justice folklorique punissant les manquements à la morale. Pour parvenir à cette référence, il est nécessaire de montrer que le slasher a masqué un genre plus large qui gravite autour d'une victime humiliée se vengeant de ses persécuteurs et qui inclue des films comme Willard (1971), Carrie (1976), ou encore Fade to Black (1980). Or, on peut trouver une formulation prototypique de cette histoire dans Hop-Frog (1849), une nouvelle d'Edgar Poe racontant la vengeance d'un bouffon difforme persécuté par un roi sadique. Nous envisageons cette nouvelle comme un artefact prototypique de l'archétype culturel du foolkiller dont le genre masqué par le slasher est une expression contemporaine. L'étude de cette nouvelle et de ses références culturelles permet de comprendre le fonctionnement de l'archétype et son apparition en réponse à une crise sacrificielle au sens où l'entend René Girard. Une crise du même genre est repérable dans la culture américaine des années 1970, ce qui explique la résurgence de l'archétype à cette période. / The slasher movie is a horror film sub-genre featuring a masked killer supposedly punishing teenage sexuality. Extremely popular among teens from 1978 to 1984, it is generally discarded by serious critics as a spectacle of gratuitous violence. However, the genre can be granted some legitimacy once it is seen as a contemporary form of a cultural archetype which we call "foolkiller". This archetype revolves around a freak avenging its own humiliation at the hands of bullies and punishing irresponsible acts endangering the weakest people in a community. Culturally speaking, this archetype has roots in the medieval practice of "rough music", a masked demonstration organized to humiliate some wrongdoer and to punish moral transgressions in the community. In order to access this cultural reference, it is necessary to show that the attention given the slasher film has concealed the existence of another genre, comprising slasher films but also movies such as Willard (1971), Carrie (1976), and Fade to Black (1980), whose protagonist is a victim avenging its persecution. This plot can also be found in "Hop-Frog", a short-story written by Edgar Allan Poe in 1849. It tells the story of a jester dwarf bullied by a cruel king. We argue that this tale is a prototypical artifact of the foolkiller archetype, which also informs the genre concealed by the slasher film. The cultural frame of this short story enables us to understand how the archetype functions and its relationship to what René Girard calls a "sacrificial crisis". Such a crisis is at work within 1970's American culture, which explains why the archetype reappears during this time.The slasher movie is a horror film sub-genre featuring a masked killer supposedly punishing teenage sexuality. Extremely popular among teens from 1978 to 1984, it is generally discarded by serious critics as a spectacle of gratuitous violence. However, the genre can be granted some legitimacy once it is seen as a contemporary form of a cultural archetype which we call "foolkiller". This archetype revolves around a freak avenging its own humiliation at the hands of bullies and punishing irresponsible acts endangering the weakest people in a community. Culturally speaking, this archetype has roots in the medieval practice of “rough music”, a masked demonstration organized to humiliate some wrongdoer and to punish moral transgressions in the community. In order to access this cultural reference, it is necessary to show that the attention given the slasher film has concealed the existence of another genre, comprising slasher films but also movies such as Willard (1971), Carrie (1976), and Fade to Black (1980), whose protagonist is a victim avenging its persecution. This plot can also be found in "Hop-Frog", a short-story written by Edgar Allan Poe in 1849. It tells the story of a jester dwarf bullied by a cruel king. We argue that this tale is a prototypical artifact of the foolkiller archetype, which also informs the genre concealed by the slasher film. The cultural frame of this short story enables us to understand how the archetype functions and its relationship to what René Girard calls a "sacrificial crisis". Such a crisis is at work within 1970's American culture, which explains why the archetype reappears during this time.