The variation of genome content and structure across the tree of life is astounding and can provide clues to understand the process of evolution. Overall, this helps us understand the history of life and how organisms have fundamentally changed and adapted to their environments. Gene duplication is an important mechanism for molecular evolution because it provides opportunity for functional novelty and molecular innovation. Gene duplication creates new functional gene copies with different selective pressures that allow them to take on new or specialized functions. Throughout this work, I explored the interplay between genetic changes, molecular phenotype, and the selection of duplicate gene copies. I particularly focused on the genetic opportunity, consequences, and selective pressures of the mechanisms for short-term and long-term duplicate copy retention. I modeled the stochastic processes of mutation and selection and their effect on duplicate gene copy retention. Specifically, I modeled the interplay between subfunctionalization and dosage balance and found that selection may cause genes that are sensitive to dosage balance effects to experience delayed subfunctionalization, but ultimately lead to higher levels of subfunctionalization. These findings suggest that subfunctionalization may not occur as a purely neutral process. Next, I used survival analysis methods to model patterns of duplicate gene retention in genomes experiencing consecutive whole genome duplication events. I modeled three hypotheses to explain patterns of duplicate gene retention including the Independence Hypothesis, the Gene Duplicability Hypothesis, and a novel Mutational Opportunity Hypothesis. Under the Gene Duplicability and Mutational Opportunity hypotheses, the expected patterns of duplicate gene retention after consecutive whole genome duplication events are greatly affected by the ages of the whole genome duplication events and the functional properties of the genomic content that influence opportunity and selection. Additionally, I describe how statistical model testing techniques can be applied to investigate which hypothesis is consistent with patterns of retention in real-world phylogenetic datasets. I used these described techniques to explore the hypotheses’ parameter space consistent with a modest dataset of fish and plant lineages. These results suggest that a gene duplicate’s retention after whole genome duplication events may be influenced by its functional properties. Key findings underscore the multifaceted nature of duplicate gene retention, influenced by a myriad of factors including genetic opportunity, selective pressures, and evolutionary context. By dissecting the underlying mechanisms driving duplicate gene retention, this dissertation advances our understanding of the evolutionary dynamics shaping genome evolution and functional diversity across diverse biological systems. / Biology

<p>Evolutionary dynamics can be notoriously complex and difficult to analyze. In this dissertation I describe a population genetic regime where the dynamics are simple enough to allow a relatively complete and elegant treatment. Consider a haploid, asexual population, where each possible genotype has been assigned a fitness. When mutations enter a population sufficiently rarely, we can model the evolution of this population as a Markov chain where the population jumps from one genotype to another at the birth of each new mutant destined for fixation. Furthermore, if the mutation rates are assigned in such a manner that the Markov chain is reversible when all genotypes are assigned the same fitness, then it is still reversible when genotypes are assigned differing fitnesses. </p><p>The key insight is that this Markov chain can be analyzed using the spectral theory of finite-state, reversible Markov chains. I describe the spectral decomposition of the transition matrix and use it to build a general framework with which I address a variety of both classical and novel topics. These topics include a method for creating low-dimensional visualizations of fitness landscapes; a measure of how easy it is for the evolutionary process to `find' a specific genotype or phenotype; the index of dispersion of the molecular clock and its generalizations; a definition for the neighborhood of a genotype based on evolutionary dynamics; and the expected fitness and number of substitutions that have occurred given that a population has been evolving on the fitness landscape for a given period of time. I apply these various analyses to both a simple one-codon fitness landscape and to a large neutral network derived from computational RNA secondary structure predictions.</p> / Dissertation

<p>Gene regulatory networks (GRNs) provide a systems-level orchestration of an organism’s genome encoded anatomy. As biological networks are revealed, they continue to answer many questions including knowledge of how GRNs control morphogenetic movements and how GRNs evolve. Morphogenesis is a complex orchestration of movements by cells that are specified early in development. </p><p> The activation of an upstream GRN is crucial in order to orchestrate downstream morphogenetic events. In the sea urchin, activation of the endomesoderm GRN occurs after the asymmetric 4th cleavage. Embryonic asymmetric cell divisions often are accompanied by differential segregation of fate-determinants into one of two daughter cells. That asymmetric cleavage of the sea urchin micromeres leads to a differential animal-vegetal (A/V) nuclear accumulation of cell fate determinants, β-Catenin and SoxB1. Β-Catenin protein is localized into the nuclei of micromeres and activates the endomesoderm gene regulatory network, while SoxB1 is excluded from micromeres and enters the nucleus of the macromeres, the large progeny of the unequal 4th cleavage. Although nuclear localization of β-Catenin and SoxB1 shows dependence on the asymmetric cleavage, the mechanics behind the asymmetrical division has not been demonstrated. In Chapter 3, we show that micromere formation requires the small RhoGTPase, Cdc42 by directing the apical/basal orientation of the mitotic spindle at the apical cortex. By attenuating or augmenting sea urchin Cdc42 function, micromere divisions became defective and failed to correctly localize asymmetrically distributed determinants. As a consequence, cell fates were altered and multiple A/V axes were produced resulting in a “Siamese-twinning” phenotype that occurred with increasing frequency depending on the quantitative level of perturbation. Our findings show that Cdc42 plays a pivotal role in the asymmetric division of the micromeres, endomesoderm fate-determinant segregation, and A/V axis formation.</p><p> This dissertation also characterizes, at high resolution, the repertoire of cellular movements contributing to three different morphogenetic processes of sea urchin development: the elongation of gut, the formation of the primary mouth, and the migration of the small micromeres (the presumptive primordial germ cells) in the sea urchin, Lytechinus variegatus. Descriptive studies of the cellular processes during the different morphogenetic movements allow us to begin investigating their molecular control. </p><p>In Chapter 4, we dissected the series of complex events that coordinate gut and mouth morphogenesis. Until now, it was thought that lateral rearrangement of endoderm cells by convergent extension was the main contributor to sea urchin archenteron elongation and that cell divisions were minimal during elongation. We performed cell transplantations to live image and analyze a subset of labeled endoderm cells at high-resolution in the optically clear sea urchin embryo. We found that the endomesoderm cells that initially invaginate into the sea urchin blastocoel remained contiguous throughout extension, so that, if convergent extension were present, it was not a major contributor to elongation. We also found a prevalence of cell divisions throughout archenteron elongation that increased the number of cells within the gut linearly over time; however, we showed that the proliferation did not contribute to growth, and their spindle orientations were randomized during divisions and therefore did not selectively contribute to the final gut length. When cell divisions were inhibited, we saw no difference in the ability of the cells within the gut to migrate in order to elongate. Also in Chapter 4, we describe our observations of the cell biological processes underlying primary mouth formation at the end of gastrulation. Using time-lapse microscopy, photo-convertible Kaede, and an assay of the basement membrane remodeling, we describe a sequential orchestration of events that leads to the fusion of the oral ectoderm and the foregut endoderm. Our work characterizes, at higher resolution than previously recorded, the temporal sequence and repertoire of the cellular movements contributing to the length of the sea urchin larval gut and tissue fusion with the larval primary mouth.</p><p> In Chapter 5, the migration of the small micromeres to the coelomic pouches in the sea urchin embryo provides an exceptional model for understanding the genomic regulatory control of morphogenesis. An assay using the robust homing potential of these cells reveals a “coherent feed-forward” transcriptional subcircuit composed of Pax6, Six3, Eya, and Dach1 that is responsible for the directed homing mechanism of these multipotent progenitors. The linkages of that circuit are strikingly similar to a circuit involved in retinal specification in Drosophila suggesting that systems-level tasks can be highly conserved even though the tasks drive unrelated processes in different animals.</p><p> The sea urchin gene regulatory network (GRN) describes the cell fate specification of the developing embryo; however, the GRN does not describe specific cell biological events driving the three distinct sequences of cell movements. Our ability to connect the GRN to the morphogenetic events of gastrulation, primary mouth formation, and small micromere migration will provide a framework for characterizing these remarkable sequences of cell movements in the simplest of deuterostome models at an unprecedented scale.</p> / Dissertation

abstract: Gene-centric theories of evolution by natural selection have been popularized and remain generally accepted in both scientific and public paradigms. While gene-centrism is certainly parsimonious, its explanations fall short of describing two patterns of evolutionary and social phenomena: the evolution of sex and the evolution of social altruism. I review and analyze current theories on the evolution of sex. I then introduce the conflict presented to gene-centric evolution by social phenomena such as altruism and caste sterility in eusocial insects. I review gene-centric models of inclusive fitness and kin selection proposed by Hamilton and Maynard Smith. Based their assumptions, that relatedness should be equal between sterile workers and reproductives, I present several empirical examples that conflict with their models. Following that, I introduce a unique system of genetic caste determination (GCD) observed in hybrid populations of two sister-species of seed harvester ants, Pogonomyrmex rugosus and Pogonomyrmex barbatus. I review the evidence for GCD in those species, followed by a critique of the current gene-centric models used to explain it. In chapter two I present my own theoretical model that is both simple and extricable in nature to explain the origin, evolution, and maintenance of GCD in Pogonomyrmex. Furthermore, I use that model to fill in the gaps left behind by the contributing authors of the other GCD models. As both populations in my study system formed from inter-specific hybridization, I review modern discussions of heterosis (also called hybrid vigor) and use those to help explain the ecological competitiveness of GCD. I empirically address the inbreeding depression the lineages of GCD must overcome in order to remain ecologically stable, demonstrating that as a result of their unique system of caste determination, GCD lineages have elevated recombination frequencies. I summarize and conclude with an argument for why GCD evolved under selective mechanisms which cannot be considered gene-centric, providing evidence that natural selection can effectively operate on non-heritable genotypes appearing in groups and other social contexts. / Dissertation/Thesis / M.S. Biology 2012

abstract: How fast is evolution? In this dissertation I document a profound change that occurred around the middle of the 20th century in the way that ecologists conceptualized the temporal and spatial scales of adaptive evolution, through the lens of British plant ecologist Anthony David Bradshaw (1926–2008). In the early 1960s, one prominent ecologist distinguished what he called “ecological time”—around ten generations—from “evolutionary time”— around half of a million years. For most ecologists working in the first half of the 20th century, evolution by natural selection was indeed a slow and plodding process, tangible in its products but not in its processes, and inconsequential for explaining most ecological phenomena. During the 1960s, however, many ecologists began to see evolution as potentially rapid and observable. Natural selection moved from the distant past—a remote explanans for both extant biological diversity and paleontological phenomena—to a measurable, quantifiable mechanism molding populations in real time. The idea that adaptive evolution could be rapid and highly localized was a significant enabling condition for the emergence of ecological genetics in the second half of the 20th century. Most of what historians know about that conceptual shift and the rise of ecological genetics centers on the work of Oxford zoologist E. B. Ford and his students on polymorphism in Lepidotera, especially industrial melanism in Biston betularia. I argue that ecological genetics in Britain was not the brainchild of an infamous patriarch (Ford), but rather the outgrowth of a long tradition of pastureland research at plant breeding stations in Scotland and Wales, part of a discipline known as “genecology” or “experimental taxonomy.” Bradshaw’s investigative activities between 1948 and 1968 were an outgrowth of the specific brand of plant genecology practiced at the Welsh and Scottish Plant Breeding stations. Bradshaw generated evidence that plant populations with negligible reproductive isolation—separated by just a few meters—could diverge and adapt to contrasting environmental conditions in just a few generations. In Bradshaw’s research one can observe the crystallization of a new concept of rapid adaptive evolution, and the methodological and conceptual transformation of genecology into ecological genetics. / Dissertation/Thesis / Doctoral Dissertation Biology 2015

abstract: Early weaning, slow somatic and dental growth, and late age at reproduction are all part of a suite of energetic trade-offs that have shaped human evolution. A similar suite of energetic trade-offs has shaped the evolution of the indriid-palaeopropithecid clade, though members of this clade exhibit extremely fast dental development and nearly vestigial deciduous teeth. The development and functional occlusion of the primary postcanine dentition (i.e., deciduous premolars and molars) coincides with several life history parameters in great apes and indriids. This dissertation explored great ape dental macrowear, molar development in indriids, and molar size in lemurs with a broader goal of improving reconstructions of life history profiles in extinct primates. To this aim, macrowear and dental development were analyzed in apes and lemurs, respectively. Occlusal casts (six great ape species; N=278) were scanned to track mandibular fourth deciduous premolar (dp4) macrowear. Utilizing dental topographic analyses, changes in occlusal gradient and terrain were quantified. A subset of the great ape data (four species; n=199) was analyzed to test if differences in dp4 wear correlate with age at weaning. Using dental histology, molar development was reconstructed for Indri indri (n=1) and Avahi laniger (n=1). Life history and molar size data were collected from the literature. The results of this dissertation demonstrate that most great apes exhibited evidence of topographic maintenance, suggesting dp4s wear in a manner that maintain functional efficiency during growth and development; however, the manner in which maintenance is achieved (e.g., preservation of relief or complexity) is species specific. Dp4 macrowear is not correlated with age at weaning in great apes and is probably unreliable to reconstruct age at weaning in hominins. The pace of molar development in members of the indriid- palaeopropithecid clade did not correlate with body or brain size, an association present in several other primates. Associations of molar size with age at weaning suggest that expanding other developmental models (e.g., the inhibitory cascade) to life history is worth consideration. The broad variation in macrowear, dental development, and size highlights how the primary dentition may correlate with different life history parameters depending on the species and ecological setting, an important consideration when using teeth to reconstruct life history profiles. / Dissertation/Thesis / Doctoral Dissertation Anthropology 2016

abstract: At the interface of developmental biology and evolutionary biology, the very criteria of scientific knowledge are up for grabs. A central issue is the status of evolutionary genetics models, which some argue cannot coherently be used with complex gene regulatory network (GRN) models to explain the same evolutionary phenomena. Despite those claims, many researchers use evolutionary genetics models jointly with GRN models to study evolutionary phenomena. How do those researchers deploy those two kinds of models so that they are consistent and compatible with each other? To address that question, this dissertation closely examines, dissects, and compares two recent research projects in which researchers jointly use the two kinds of models. To identify, select, reconstruct, describe, and compare those cases, I use methods from the empirical social sciences, such as digital corpus analysis, content analysis, and structured case analysis. From those analyses, I infer three primary conclusions about projects of the kind studied. First, they employ an implicit concept of gene that enables the joint use of both kinds of models. Second, they pursue more epistemic aims besides mechanistic explanation of phenomena. Third, they don’t work to create and export broad synthesized theories. Rather, they focus on phenomena too complex to be understood by a common general theory, they distinguish parts of the phenomena, and they apply models from different theories to the different parts. For such projects, seemingly incompatible models are synthesized largely through mediated representations of complex phenomena. The dissertation closes by proposing how developmental evolution, a field traditionally focused on macroevolution, might fruitfully expand its research agenda to include projects that study microevolution. / Dissertation/Thesis / Doctoral Dissertation Biology 2017

abstract: For most of human history hunting has been the primary economic activity of men. Hunted animals are valued for their food energy and nutrients, however, hunting is associated with a high risk of failure. Additionally, large animals cannot be consumed entirely by the nuclear family, so much of the harvest may be shared to others. This has led some researchers to ask why men hunt large and difficult game. The “costly signaling” and “show-off” hypotheses propose that large prey are hunted because the difficulty of finding and killing them is a reliable costly signal of the phenotypic quality of the hunter. These hypotheses were tested using original interview data from Aché (hunter gatherer; n=52, age range 50-76, 46% female) and Tsimané (horticulturalist; n=40, age range 15-77, 45% female) informants. Ranking tasks and paired comparison tasks were used to determine the association between the costs of killing an animal and its value as a signal of hunter phenotypic quality for attracting mates and allies. Additional tasks compared individual large animals to groups of smaller animals to determine whether assessments of hunters’ phenotypes and preferred status were more impacted by the signal value of the species or by the weight and number of animals killed. Aché informants perceived hunters who killed larger or harder to kill animals as having greater provisioning ability, strength, fighting ability, and disease susceptibility, and preferred them as mates and allies. Tsimané informants held a similar preference for hunters who killed large game, but not for hunters targeting hard to kill species. When total biomass harvested was controlled, both populations considered harvesting more animals in a given time period to be a better signal of preferred phenotypes than killing a single large and impressive species. Male and female informants both preferred hunters who consistently brought back small game over hunters who sometimes killed large animals and sometimes killed nothing. No evidence was found that hunters should forgo overall food return rates in order to signal phenotypic qualities by specializing on large game. Nutrient provisioning rather than costly phenotypic signaling was the strategy preferred by potential mates and allies. / Dissertation/Thesis / Doctoral Dissertation Anthropology 2019

<p>The capacity of marine organisms to adapt to natural and anthropogenic stressors is an integral component of ocean health. Harmful algal blooms (HABs), which are one of many growing threats in coastal marine ecosystems, represent a historically present natural stressor that has recently intensified and expanded in geographic distribution partially due to anthropogenic activities. In the Gulf of Mexico, HABs of <italic>Karenia brevis</italic> occur almost annually and produce neurotoxic brevetoxins that have been associated with large-scale mortality events of many marine species, including the common bottlenose dolphin (<italic>Tursiops truncatus</italic>). The factors resulting in large-scale dolphin mortality associated with HABs are not well understood, particularly in regards to the seemingly different impacts of HABs in geographically disjunct dolphin populations. My dissertation investigates a genetic basis for resistance to HABs in bottlenose dolphins in central-west Florida and the Florida Panhandle. I used both genome-wide and candidate gene approaches to analyze genetic variation in dolphins that died putatively due to brevetoxicosis and live dolphins from the same geographic areas that survived HAB events. Using restriction site-associated DNA sequencing, I identified genetic variation that suggested both a common genetic basis for resistance to HABs in bottlenose dolphins across the Gulf coast of Florida and regionally specific resistance. Many candidate genes involved in the immune, nervous, and detoxification systems were found in close genomic proximity to survival-associated polymorphisms throughout the bottlenose dolphin genome. I further investigated two groups of candidate genes, nine voltage-gated sodium channel genes selected because of their putative role in brevetoxin binding and four major histocompatibility complex (MHC) loci selected because of their genomic proximity to a polymorphism exhibiting a strong association with survival. I found little variation in the sodium channel genes and conclude that bottlenose dolphins have not evolved resistance to HABs via mutations in the toxin binding site. The immunologically relevant MHC loci were highly variable and exhibited patterns of genetic differentiation among geographic regions that differed from neutral loci; however, genetic variation at the MHC also could not fully explain variation in survival of bottlenose dolphins exposed to HABs. In my final chapter, I consider the advantages and drawbacks of the genome-wide approach in comparison to a candidate gene approach and, as laid out in my dissertation, I recommend using both complementary approaches in future investigations of adaptation in genome-enabled non-model organisms.</p> / Dissertation

abstract: The immigration process changes personal narratives and professional trajectories and challenges identities and individual beliefs. Yet there is currently limited research on European women immigrants' transitions in the United States. This study examines personal and professional trajectories, in the United States, of Eastern European immigrant (EEI) women with prior educational attainment in their country of origin. This study examines the following issues: personal/social learning, developmental and professional experiences prior to and post migration, and social lives after the women's arrival in the United States. The study discusses the results of in-depth interviews with eight EEI women living in Arizona and California and recounts these women's life stories, gathered through open-ended questions that focused on areas of their personal and professional lives, such as childhood, marriage, immigration, education, family relations, socio-economic status, employment, child- rearing, and other significant life events. These areas impacted the women's creation of personal beliefs and their ability to develop new identities in the United States. The study examines EEI women's identity constructions within their life trajectory narratives. / Dissertation/Thesis / Ph.D. Educational Psychology 2014