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<p> Adaptive Laboratory Evolution (ALE) methodologies are used for studying microbial adaptive mutations that optimize host metabolism. The Systems Biology Research Group (SBRG) at the University of California, San Diego, has implemented high-throughput ALE experiment automation that enables the group to expand their experimental evolutions to scales previously infeasible with manual workflows. The data generated by the high-throughput automation now requires a post-processing, content management and analysis framework that can operate on the same scale. We developed a software system which solves the SBRG's specific ALE big data to knowledge challenges. The software system is comprised of a post-processing protocol for quality control, a software framework and database for data consolidation and a web platform named ALE Analytics for report generation and automated key mutation analysis. The automated key mutation analysis is evaluated against published ALE experiment key mutation results from the SBRG and maintains an average recall of 89.6% and an average precision of 71.2%. The consolidation of all ALE experiments into a unified resource has enabled the development of web applications that compare key mutations across multiple experiments. These features find the genomic regions <i> rph, hns/tdk, rpoB, rpoC</i> and <i>pykF</i> mutated in more than one ALE experiment published by the SBRG. We reason that leveraging this software system relieves the bottleneck in ALE experiment analysis and generates new data mining opportunities for research in understanding system-level mechanisms that govern adaptive evolution.</p>

<p><i>Pediomelum esculentum</i> (commonly prairie turnip) is a perennial legume of the Great Plains, consisting of a deep taproot and large edible tuber, and has served as a nutritious staple in Native American diets. The tuber is capable of storing up to 20 percent protein by weight. <i> P. esculentum</i> is a legume, but not a prominent nodule former; instead, it grows in nitrogen-limited soils and produces large amounts of protein. This suggests the involvement of biological nitrogen fixation. We have investigated the presence of diazotrophic endophytes in <i>P. esculentum</i>. Bacteria were isolated from wild plants on nitrogen free media, identified with their partial 16S rRNA gene sequences, and screened for the presence of the nitrogen fixation gene <i>nifH</i>. Select isolates were applied as a co-inoculum to seedlings grown under gnotobiotic conditions in a growth chamber with no nitrogen source. Seedlings in both the inoculated and uninoculated group developed nodules and showed no signs of nitrogen stress. Bacteria isolated from the nodules and tubers of both groups were closely related to the same <i>Bacillus</i> bacterium isolated from seeds germinated under sterile conditions, according to partial <i>16S rRNA </i> sequences. Bright field and fluorescence imaging revealed bacteria present in the intercellular space of four-week-old tubers and in the sterile germinated seeds. Sectioning and imaging of the nodules show a central nodule vasculature and infected cells extending inwards to the main root vasculature. Nitrogen fixation in the plants was indirectly confirmed by acetylene reduction. Our results suggest <i>P. esculentum</i> has formed a unique symbiosis with a nitrogen fixing <i>Bacillus</i> bacterium that transmits vertically in the seeds and induces nodules. </p>

<p> The deep sea is the Earth&rsquo;s largest ecosystem and harbors a unique and largely endemic fauna. Although most research has focused on the ecological mechanisms that allow coexistence, recent studies have begun to investigate how this remarkable fauna evolved.. My work quantifies geographic patterns of genetic variation and investigates potential mechanisms that shape evolution in the deep ocean. </p><p> Bathymetric genetic divergence is common in the deep sea with population structure typically decreasing with depth. The evolutionary mechanisms that underlie these patterns are poorly understood. Geographic patterns of genetic variation indicated that the protobranch bivalve <i>Neilonella salicensis </i> was composed of two distinct lineages separated bathymetrically. Genetic diversity was greater in the lower-bathyal clade of <i>N. salicensis </i> than the upper to mid-bathyal clade. In a co-occurring mid-bathyal protobranch <i>Malletia johnsoni,</i> population differentiation was greater among samples than the confamilial lower-bathyal <i>Clencharia abyssorum,</i> though, genetic diversity was similar. These patterns suggest general trends do not always hold and fine scale patterns of gene flow need to be thoroughly investigated. </p><p> Little is known about the ecological or evolutionary mechanisms that might promote divergence or maintain population structure. Oxygen minimum zones (OMZs), which cover enormous regions of the deep ocean, might hamper gene flow by precluding larval dispersal. To test this, genetic patterns of the wood-boring bivalve <i>Xylophaga washington</i> were quantified across the northeastern Pacific OMZ. Results indicate two clades were apparent, one throughout the OMZ and one within and below it, possibly segregated by a historically stronger OMZ or other environmental factors that vary with depth. A similarly uninvestigated evolutionary factor with potentially large impacts is selection on mitochondrial DNA. Positive selection is apparent in the mitochondrial DNA of shallow water and deep-sea crabs, shrimp, and fishes, possibly related to any of the myriad factors that differ between the two habitats. </p><p> The deep sea is biogeochemically important and is highly impacted by climate change and anthropogenic factors. Genetic patterns in this habitat are very complex. This work suggests gene flow is inhibited at many scales, both across bathymetric gradients and within small bathymetric ranges.</p><p>

<p> The formation and maintenance of romantic pair bonds is a well-represented topic in human evolutionary sciences. This extensive body of work, drawn mostly from the field of evolutionary psychology, has proposed mechanisms for attracting a mate (e.g., resource display, physical cues), attaining a mate (e.g., intrasexual competition), and keeping a mate (e.g., competitor derogation, emotional manipulation). However, this evolutionary model of human pair bonding has not fully addressed relationship termination. If we accept that we have an evolved suite of behaviors that encourage and facilitate pair bonding, then we must also look to breakups and ask whether evolution has played a role in shaping &ldquo;heartbreak&rdquo;&mdash;the post-relationship grief (PRG) which many individuals endure.</p><p> The evolutionary model of human mating predicts divergent mating &ldquo;agendas&rdquo; for men and women. The first step in our research program was to conduct a modest pilot study to address how and when PRG differs between men and women. This pilot study is included as Chapter One for convenience. Having concluded that many of the existing suppositions about breakups were not supported by our initial inquiry, we set out to expand and revise the current model so that it can be used to make accurate predications regarding a more complex suite of variables (e.g., life history, sexuality). Chapter Two explains the logic and implications of this expansion via the example of a specific breakup scenario: the loss of a woman&rsquo;s partner to a romantic rival.</p><p> After presenting the possible evolutionary cause and adaptive benefits of PRG, we next tested both new and existing hypotheses as they relate to biological sex differences (Chapter Three) and life history variation (Chapter Four) in PRG. This quantitative foundation for ongoing qualitative study concludes with an overview of PRG in a population that is sorely underrepresented in evolutionary literature&mdash;individuals whose sexual orientation is not exclusively heterosexual.</p>

<p> It is often presumed that evolutionary reduction is tantamount to deconstruction, or even destruction, because relaxed selective forces have been insufficient to maintain the organ in its original state. However, studies on reduction are often limited by a lack of diversity, both of related species exhibiting reduction and of the reduced form itself. There have also been very few studies on the reduction of compound eyes, despite the fact that their near ubiquity among arthropods alone makes them perhaps the most common type of eye. Bat flies (Streblidae and Nycteribiidae) are a group of dipterans that exhibit variable degrees of compound eye reduction, and therefore provide the opportunity to study reduction of this organ in a phylogenetic context. The first chapter of this work reports on behavioral experiments demonstrating that the eyes of one bat fly species, <i>Trichobius frequens</i>, are functional, and that they neither exhibit phototaxis typical of other dipteran species, nor move toward a light source. The second chapter uses molecular phylogenetics to identify a correlation between eye and wing morphology. The results also suggest that secondary to their eye reduction, bat flies (at least in the case of New World specie, including <i>Trichobius spp.</i>) have secondarily experienced a shift in the structure of their facets that is convergent with other insects whose eyes have been selected for increased sensitivity. In the final chapter, histological and optical analyses of <i>T. frequens </i> eyes are used to reveal significant structural changes to the microstructure of its ommatidia that increase sensitivity at the expense of acuity. Many of these changes are also convergent with similar adaptations that have been demonstrated to increase sensitivity in organisms that function in reduced light environments. The results of these analyses suggest that reduction in <i> T. frequens</i> eyes may have been part of an active remodeling process resulting from a shift in the relative importance of sensitivity and acuity. As this is a process of reduction not generally considered, the findings here turn our attention to alternative hypotheses that should be considered when studying evolutionary reduction of any organ.</p>

<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>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

<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>