<p>Centromeres are the chromosomal loci where microtubule spindles bind, via the kinetochore, during mitosis and meiosis. Paradoxically the centromere, as a functional unit, is essential to guarantee faithful chromosome segregation, whereas its underlying DNA sequences and associated kinetochore proteins are fast evolving. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. In spite of their importance, very little is known about the degree to which centromeric tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from species using publicly available genomic sequence and our own data. We found that despite an overall lack of sequence conservation, centromeric tandem repeats from diverse species showed similar modes of evolution. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. In addition, we performed a survey of fungi genomes for the presence of high-copy tandem repeats, but found little evidence to suggest that high-copy centromeric repeats are a common feature feature in fungi, with the possible exception of the <i>Zygomycota</i>. phylum. Finally, in most species the kinetochore assembles at a single locus, but in some cases the kinetochore forms along the entire length of the chromosomes forming holocentric chromosomes. Following a literature review we estimate that holocentricity is very common and has evolved at least thirteen times.

<p>The goal of this dissertation was to better clarify the sensory and cognitive capabilities and limitations of a size-constrained animal. Because visually-guided behaviors are more experimentally tractable than behaviors guided by other sensory modalities, I chose to study a small animal with an unusually good visual system and a suite of apparently visually-guided behaviors, the jumping spider <i>Lyssomanes viridis</i> (Salticidae). Jumping spiders' principal eyes, which are adapted for the perception of shape and pattern, have the highest measured acuity of any arthropod, but also the narrowest field of view, making salticids a particularly interesting study system for measuring the capabilities and limitations of a tiny animal with small yet apparently highly functional eyes. For my dissertation, I examined the amount and type of visual information gathered in high-stakes encounters; i.e. species and sex recognition and male-male contests over females. In salticids, the wrong assessment of species and sex or fighting ability carries with it the risk of injury or even death. Thus, more information, and especially high-resolution information, should be particularly adaptive in such encounters, and should provide us with a good proxy of the perceptual and cognitive capabilities and limitations of this small animal. </p><p>In chapter two, I assayed the amount and type of visual information gathered in the context of species and sex recognition, and tested for crossmodal interactions between pheromones and visual cues. Using computer-animated stimuli, I found that, although males took the time necessary to visually scan both the face and legs of other spiders before deciding whether to threaten, court, or ignore them, their conspecific visual recognition templates were fairly coarse, and resulted in them making numerous misidentifications and frequently courting heterospecific salticids. This was especially true in the presence of conspecific female pheromones. Pheromones appeared to exert further top-down effects on visual recognition of conspecifics by bringing visual recognition templates into working memory, as was inferred from the fact that males spent less time examining conspecific images in the presence of conspecific female pheromones. Pheromones also increased the probability that a non-conspecific spider bearing even a slight resemblance to a conspecific female spider would be recognized and courted as a conspecific female. However, pheromones usually did not hasten the recognition of non-conspecific images; this indicates that males' poorer recognition accuracy in the presence of pheromones was not a result of males' spending less time visually examining non-conspecific images. </p><p>In chapter three, I looked for correlations between various visual features and contest success in order to determine what types of visual information opponents could theoretically use to assess their opponents' resource holding potential in contests over females. I found that all measured size-related traits correlated strongly with contest success, but that coloration did not, except in the rare cases in which a smaller male won a contest. In these encounters, males who won, despite being smaller, had less red chelicerae than their opponents. Finally, in chapter four, I used the results of chapter three to begin assessing whether the traits that correlate with contest success are actually assessed by males, and in particular, whether they are assessed visually. To do this, I presented males with various sizes of computer-animated opponents, and found that males were less likely to threaten larger opponents. Thus, males seem to be using visual cues to gather information about the size of their opponents. Whether they evaluate overall size, or more specifically, the size of their opponents' weapons, will be addressed in future work.</p> / Dissertation

<p> In this work, I describe my doctoral work studying the regulation of transcription with both computational and experimental methods on the natural genetic variation in a population. This works integrates an investigation of the consequences of polymorphisms at three stages of gene regulation in the developing fly embryo: the diversity at <i>cis</i>-regulatory modules, the integration of transcription factor binding into changes in chromatin state and the effects of these inputs on the final phenotype of embryonic gene expression.</p>

<p> This study used fine-scale phylogeography of populations of side-blotched lizard, <i>Uta stansburiana</i> to determine concordance with previously identified phylogeographic patterns in the Transverse Mountain Range of Southern California. Mitochondrial DNA analysis revealed clade distributions that both agreed and conflicted with previously identified clade breaks. This study revealed two new distinct clade breaks that transect the San Gabriel Mountains and detected haplotype mixtures in populations sampled between the San Gabriel and San Bernardino Mountains. Genetic landscape GIS analyses identified areas of genetic divergence and diversity for this species. This combined analysis enabled the discovery of a suture zone between the San Gabriel and San Bernardino Mountains that represents a phylogenetic crossroads with high levels of diversity and divergence and complex phylogeographic structure. My results suggest the importance of the use of fine-scale phylogeographic analysis in the discovery of new clade boundaries within a geologically complex and hyper-diverse region.</p>

<p> Signaling theory originated in evolutionary biology and explains the mechanisms behind the honest communication of information between organisms. Communication scholars are increasingly turning to signaling theory as a way to test evolutionary explanations for human behavior. The present study tests if receiver-dependent costly signals can be used to predict the moment of aggressive behavior in video game environments. High status (but not high trait aggression) male subjects were fastest to engage in combat against a low voice pitch male opponent - but only when subject skill was high. This result underscores the importance of video game skill as a variable of interest as well as the need for video games researchers to tease out when real-world behaviors map to video game contexts.</p>

<p>Much of plant growth is directly or indirectly regulated by the plant hormone auxin. Although some genes involved in the auxin pathway have been characterized, there are still gaps in our knowledge of this genetic pathway. Recently, the orthologous maize genes <i>BARREN STALK2</i> (<i> BA2</i>) and rice gene <i>LAX PANICLE2</i> (<i>LAX2</i>) have been cloned and characterized. Maize <i>ba2</i> and rice <i> lax2</i> mutant plants both show significant flaws in axillary meristem (AM) initiation, suggesting a role in auxin regulation. In support of this hypothesis, <i>LAX2</i> interacts with the auxin regulating <i> LAX PANICLE1</i> (<i>LAX1</i>) protein. My research reconstructs the evolutionary history of the <i>BA2</i>/<i>LAX2</i> lineage and tests for conservation of <i>BA2</i>/<i>LAX2</i> mRNA expression in diverse grasses. My results indicate that the <i> BA2</i>/<i>LAX2</i> gene family&mdash;comprising <i>BA2 </i>/<i>LAX2</i>, <i>BA2</i>/<i>LAX2-Like1</i> (<i>BA2</i>/<i>LAX2L1</i>), and <i>BA2</i>/<i> LAX2-Like2</i> (<i>BA2</i>/<i>LAX2L2</i>)&mdash;is restricted to monocots, and shows evidence of two independent gene duplication events. During its evolution, the <i>BA2</i>/<i>LAX2</i> gene family appears to have gained a PDZ Protein Binding motif, which may allow it to interact with other proteins besides <i>BA1</i>/<i> LAX1</i>. My expression analyses show that <i>BA2</i>/<i> LAX2</i> genes are expressed during multiple stages of inflorescence development, and this expression is conserved across multiple grass species. A unique floral expression pattern appears to have evolved at the base of the Joinvilleaceae lineage. My study further supports the hypothesis that <i> BA2</i>/<i>LAX2</i> genes are functioning in multiple AM pathways. </p>

<p>At the end of the nineteenth century Charles Sanders Peirce wrote that "chance begets order" - indeterministic or `chancy' processes can underlie orderly and seemingly deterministic processes. Indeed, Peirce argues that indeterminism is the seed of all order in the natural world. The dissertation explores this theme in three parts. The first chapter reconstructs and elaborates Peirce's objections against necessitarianism, the position that all natural laws are perfectly orderly, deterministic. The second chapter examines and elaborates Ronald Aylmer Fisher's sophisticated analogy between gas models from statistical mechanics and his own population genetics models. The final chapter treats a contemporary indeterministic account of biological fitness and examines several points on which intuitions from deterministic theories misinterpret this quintessentially indeterministic position. The dissertation motivates an indeterministic theory of natural law and reinvigorates its implications for hierarchical models of the natural world.</p> / Dissertation

Thesis (Ph.D.)--University of California, San Francisco, 2009. / Source: Dissertation Abstracts International, Volume: 70-10, Section: B, page: 5941. Adviser: Pao-Tien Chuang.

<p> Unraveling the molecular etiology of a novel phenotype is still a major challenge. Mammalian pregnancy, a novel phenotype, preserves its stepwise evolution in extant species, which gives us additional tools to use to begin to unravel its evolution. Within this thesis, the evolution of three components of pregnancy are explored- the regulation of <i>TAP2</i> expression, the regulation of HLA-F expression, and the possible role of transposable elements in rewiring the regulatory networks underlying major gene expression shifts at the maternal-fetal interface.</p><p>

<p> Climate change is ostensibly one of the greatest modern selective pressures, and species with sensitive life histories or physiologies must adapt, migrate, or buffer its effects to persist. Some 15&ndash;37% of species are expected to be endangered or extinct by 2050. The most vulnerable include habitat specialists, local endemics, and species with low intrinsic growth rates. Yosemite toads (<i>Anaxyrus canorus</i>) are one such alpine endemic, having been extirpated from up to 69% of their historical range. Several features of their natural history make them vulnerable: small population sizes, high larval mortality, infrequent breeding, and specialized, patch-limited habitat prone to premature desiccation. In addition to their role as ecosystem flagships, Yosemite toads provide a model system for the many other specialists with similar life histories that are challenged by environmental change. The goal of this dissertation is to understand how historical evolutionary processes such as lineage divergence and secondary admixture, along with current levels of genetic connectivity, are expected to shape the future of Yosemite toad persistence in the face of climate change. The first chapter reconstructs phylogeographic patterns of lineage formation and fusion during repeated bouts of Pleistocene glaciation, and showcases a role for refugia in ecological divergence. The second chapter examines three contact zones as replicate tests of the hypothesis that loci associated with incipient speciation are distinct from those that readily cross ancient lineage boundaries. The third chapter models modern genetic connectivity as a network of environmental and climatic interactions, using a novel approach that incorporates phylogeographic structure. The fourth chapter forecasts the future selective pressure of climate change, and predicts where connectivity may be a mitigating force to restore genetic diversity. My dissertation provides an example of how conservation strategies can incorporate the many temporal processes (ancient, recent, and current) that have shaped current genetic diversity patterns, and use a &ldquo;total evidence&rdquo; approach to predict future adaptive potential.</p><p>