Browsing by Subject "Evolution"
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Item Open Access A Computational Synthesis of Genes, Behavior, and Evolution Provides Insights into the Molecular Basis of Vocal Learning(2012) Pfenning, Andreas RVocal learning is the ability modify vocal output based on auditory input and is the basis of human speech acquisition. It is shared by few distantly related bird and mammal orders, and is thus very likely to be an example of convergent evolution, having evolved independently in multiple lineages. This complex behavior is presumed to require networks of regulated genes to develop the necessary neural circuits for learning and maintaining vocalizations. Deciphering these networks has been limited by the lack of high throughput genomic tools in vocal learning avian species and the lack of a solid computational framework to understand the relationship between gene expression and behavior. This dissertation provides new insights into the evolution and mechanisms of vocal learning by taking a top-down, systems biology approach to understanding gene expression regulation across avian and mammalian species. First, I worked with colleagues to develop a zebra finch Agilent oligonucleotide microarray, including developing programs for more accurate annotation of oligonucleotides and genes. I then used these arrays and tools in multiple collaborative, but related projects, to measure transcriptome expression data in vocal learning and non-learning avian species, under a number of behavioral paradigms, with a focus on song production. To make sense of the avian microarray data, I compiled microarray data from other sources, including expression analyses across over 900 human brain regions generated by Allen Brain Institute. To compare these data sets, I developed and performed a variety of computational analyses including clustering, linear models, gene set enrichment analysis, motif discovery, and phylogenetic inference, providing a novel framework to study the gene regulatory networks associated with a complex behavior. Using the developed framework, we are able to better understand vocal learning at different levels: how the brain regions for vocal learning evolved and how those brain regions function during the production of learned vocalizations. At the evolutionary level, we identified genes with unique expression patterns in the brains of vocal learning birds and humans. Interesting candidates include genes related to formation of neural connections, in particular the SLIT/ROBO axon guidance pathway. This algorithm also allowed us to identify the analogous regions that are a part of vocal learning circuit across species, providing the first quantitative evidence relating the human vocal learning circuit to the avian vocal learning circuit. With the avian song system verified as a model for human speech at the molecular level, we conducted an experiment to better understand what is happening in those brain regions during singing by profiling gene expression in a time course as birds are producing song. Surprisingly, an overwhelming majority of the gene expression identified was strongly enriched in a particular region. We also found a tight coupling between the behavioral function of a particular region and the gene expression pattern. To gain insight into the mechanisms of this gene regulation, we conducted a genomic scan of transcription factor binding sites in zebra finch. Many transcription factor binding sites were enriched in the promoters of genes with a particular temporal patterns, several of which had already been hypothesized to play a role in the neural system. Using this data set of gene expression profiles and transcription factor binding sites along with separate experiments conducted in mouse, we were able uncover evidence that the transcription factor CARF plays a role in neuron homeostasis. These results have broadened our understanding of the molecular basis of vocal learning at multiple levels. Overall, this dissertation outlines a novel way of approaching the study of the relationship between genes and behavior.
Item Open Access A Mechanical Analysis of Suspensory Locomotion in Primates and Other Mammals(2016) Granatosky, Michael ConstantineFor primates, and other arboreal mammals, adopting suspensory locomotion represents one of the strategies an animal can use to prevent toppling off a thin support during arboreal movement and foraging. While numerous studies have reported the incidence of suspensory locomotion in a broad phylogenetic sample of mammals, little research has explored what mechanical transitions must occur in order for an animal to successfully adopt suspensory locomotion. Additionally, many primate species are capable of adopting a highly specialized form of suspensory locomotion referred to as arm-swinging, but few scenarios have been posited to explain how arm-swinging initially evolved. This study takes a comparative experimental approach to explore the mechanics of below branch quadrupedal locomotion in primates and other mammals to determine whether above and below branch quadrupedal locomotion represent neuromuscular mirrors of each other, and whether the patterns below branch quadrupedal locomotion are similar across taxa. Also, this study explores whether the nature of the flexible coupling between the forelimb and hindlimb observed in primates is a uniquely primate feature, and investigates the possibility that this mechanism could be responsible for the evolution of arm-swinging.
To address these research goals, kinetic, kinematic, and spatiotemporal gait variables were collected from five species of primate (Cebus capucinus, Daubentonia madagascariensis, Lemur catta, Propithecus coquereli, and Varecia variegata) walking quadrupedally above and below branches. Data from these primate species were compared to data collected from three species of non-primate mammals (Choloepus didactylus, Pteropus vampyrus, and Desmodus rotundus) and to three species of arm-swinging primate (Hylobates moloch, Ateles fusciceps, and Pygathrix nemaeus) to determine how varying forms of suspensory locomotion relate to each other and across taxa.
From the data collected in this study it is evident the specialized gait characteristics present during above branch quadrupedal locomotion in primates are not observed when walking below branches. Instead, gait mechanics closely replicate the characteristic walking patterns of non-primate mammals, with the exception that primates demonstrate an altered limb loading pattern during below branch quadrupedal locomotion, in which the forelimb becomes the primary propulsive and weight-bearing limb; a pattern similar to what is observed during arm-swinging. It is likely that below branch quadrupedal locomotion represents a “mechanical release” from the challenges of moving on top of thin arboreal supports. Additionally, it is possible, that arm-swinging could have evolved from an anatomically-generalized arboreal primate that began to forage and locomote below branches. During these suspensory bouts, weight would have been shifted away from the hindlimbs towards forelimbs, and as the frequency of these boats increased the reliance of the forelimb as the sole form of weight support would have also increased. This form of functional decoupling may have released the hindlimbs from their weight-bearing role during suspensory locomotion, and eventually arm-swinging would have replaced below branch quadrupedal locomotion as the primary mode of suspensory locomotion observed in some primate species. This study provides the first experimental evidence supporting the hypothetical link between below branch quadrupedal locomotion and arm-swinging in primates.
Item Open Access Adaptive Motivations Drive Concern for Common Good Resources(2019) Bowie, Aleah CHumans universally demonstrate intrinsically motivated prosocial behavior towards kin, non-kin ingroup members, and strangers. However, humans struggle to extend the same prosocial behavior to more abstract concepts like future-others and non-human species. The Adaptive Motivation Hypothesis posits that humans evolved intrinsic motivations to act prosocially towards more tangible social partners like those within an individual’s ingroup, but prosocial behavior towards more distant and abstract partners is constrained by ecological certainty. Prosocial behavior towards these more abstract concepts is more variable and more likely motivated by extrinsic reward. This dissertation aims to examine the development of motivations for prosocial behavior towards these more abstract concepts. My studies rely on common goods games as a proxy for examining behavior towards abstract recipients of prosocial behavior. Common goods are any resource like forests or fisheries that are non-excludable to a population, but rivalrous. In-demand common goods require cooperation of humans to ensure sustainable use in order to avoid depletion. Chapter One examined how children in three populations that differed in ecological certainty behaved in a common goods game where they were asked to contribute portions of their personal endowment to the maintenance of a forest. Participants were either provided a high extrinsic motivation, a low extrinsic motivation, or no extrinsic motivation for contributing to the maintenance of the common good. Results show that overall, children of all ages were more motivated to contribute to abstract recipients when extrinsic motivation is high. However, noticeable variation in behavior between populations was driven by ecological and cultural differences. Chapter Two examined whether aggregated extrinsic rewards increased contributions to common goods in a sample of children aged six to fourteen. Results suggest that both information about personal loss and delay in an acquiring resource together dramatically increase children’s contributions to common goods within both experimental and real-world contexts. Chapter Three explores whether making a typically abstract social partner more tangible increases an individual’s prosocial behavior towards said partner. Results for Chapter Three, conducted with a population in the Democratic Republic of the Congo, find that increasingly the tangibility of an abstract population marginally increases prosocial behavior in children but not in adults. Together, the results of these studies have implications improved understanding of the development of prosocial motivations in school age children, as well as applications to understanding motivations for socially conscious behavior in the face of environmental and conservation dilemmas.
Item Open Access Advances in Bayesian Modeling of Protein Structure Evolution(2018) Larson, GaryThis thesis contributes to a statistical modeling framework for protein sequence and structure evolution. An existing Bayesian model for protein structure evolution is extended in two unique ways. Each of these model extensions addresses an important limitation which has not yet been satisfactorily addressed in the wider literature. These extensions are followed by work regarding inherent statistical bias in models for sequence evolution.
Most available models for protein structure evolution do not model interdependence between the backbone sites of the protein, yet the assumption that the sites evolve independently is known to be false. I argue that ignoring such dependence leads to biased estimation of evolutionary distance between proteins. To mitigate this bias, I express an existing Bayesian model in a generalized form and introduce site-dependence via the generalized model. In the process, I show that the effect of protein structure information on the measure of evolutionary distance can be suppressed by the model formulation, and I further modify the model to help mitigate this problem. In addition to the statistical model itself, I provide computational details and computer code. I modify a well-known bioinformatics algorithm in order to preserve efficient computation under this model. The modified algorithm can be easily understood and used by practitioners familiar with the original algorithm. My approach to modeling dependence is computationally tractable and interpretable with little additional computational burden over the model on which it is based.
The second model expansion allows for evolutionary inference on protein pairs having structural discrepancies attributable to backbone flexion. Thus, the model expansion exposes flexible protein structures to the capabilities of Bayesian protein structure alignment and phylogenetics. Unlike most of the few existing methods that deal with flexible protein structures, our Bayesian flexible alignment model requires no prior knowledge of the presence or absence of flexion points in the protein structure, and uncertainty measures are available for the alignment and other parameters of interest. The model can detect subtle flexion while not overfitting non-flexible protein pairs, and is demonstrated to improve phylogenetic inference in a simulated data setting and in a difficult-to-align set of proteins. The flexible model is a unique addition to the small but growing set of tools available for analysis of flexible protein structure. The ability to perform inference on flexible proteins in a Bayesian framework is likely to be of immediate interest to the structural phylogenetics community.
Finally, I present work related to the study of bias in site-independent models for sequence evolution. In the case of binary sequences, I discuss strategies for theoretical proof of bias and provide various details to that end, including detailing efforts undertaken to produce a site-dependent sequence model with similar properties to the site-dependent structural model introduced in an earlier chapter. I highlight the challenges of theoretical proof for this bias and include miscellaneous related work of general interest to researchers studying dependent sequence models.
Item Open Access An evolutionary genomics approach towards understanding Plasmodium vivax in central Africa(2022) Gartner, ValerieIncreased attention has recently been placed on understanding the natural variation of the malaria parasite Plasmodium vivax across the globe, as in 2020 alone, P. vivax caused an estimated 4.5 million malaria cases and lead to over 600,000 deaths around the world. P. vivax infections in central Africa have been of particular interest, as humans in Sub-Saharan Africa frequently possess a P. vivax resistance allele known as the Duffy-negative phenotype that is believed to prevent infection in these individuals. However, new reports of asymptomatic and symptomatic infections in Duffy-negative individuals in Africa raise the possibility that P. vivax is evolving to evade host resistance.Whole genome sequencing has become more common as a means of understanding the population diversity of P. vivax. However, there is still a scarcity of information about P. vivax in central Africa. In this dissertation, I analyze whole genome sequencing data from a new P. vivax sample collected from the Democratic Republic of the Congo in central Africa. By studying P. vivax from central Africa, we can begin to understand the evolutionary history of the pathogen in this part of the world as it relates to the global context of this pathogen. I also investigate the relationship of P. vivax in the DRC with a potential animal reservoir of a closely related species, P. vivax-like, in non-human primates in this region. Due to the scarcity of P. vivax samples in central Africa, I also investigated methods with which to best make use of whole genome sequencing data, particularly in generating phylogenetic trees. While many studies of P. vivax genetic diversity employ whole genome variation data in order to study evolutionary relationships of P. vivax populations, in this dissertation I make use of the P. vivax apicoplast, a non-photosynthetic plastid organelle genome. The apicoplast genome is five times longer than the mitochondrial genome and does not undergo recombination, making it a valuable locus for studying P. vivax evolutionary history using phylogenetic trees.
Item Open Access Bayesian Structural Phylogenetics(2013) Challis, ChristopherThis thesis concerns the use of protein structure to improve phylogenetic inference. There has been growing interest in phylogenetics as the number of available DNA and protein sequences continues to grow rapidly and demand from other scientific fields increases. It is now well understood that phylogenies should be inferred jointly with alignment through use of stochastic evolutionary models. It has not been possible, however, to incorporate protein structure in this framework. Protein structure is more strongly conserved than sequence over long distances, so an important source of information, particularly for alignment, has been left out of analyses.
I present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model and mutations follow a standard substitution matrix, while backbone atoms diffuse in three-dimensional space according to an Ornstein-Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables pairwise evolutionary distance estimation on time scales not previously attainable with sequence evolution models. Ideally inference should not be performed in a pairwise fashion between proteins, but in a fully Bayesian setting simultaneously estimating the phylogenetic tree, alignment, and model parameters. I extend the initial pairwise model to this framework and explore model variants which improve agreement between sequence and structure information. The model also allows for estimation of heterogeneous rates of structural evolution throughout the tree, identifying groups of proteins structurally evolving at different speeds. In order to explore the posterior over topologies by Markov chain Monte Carlo sampling, I also introduce novel topology + alignment proposals which greatly improve mixing of the underlying Markov chain. I show that the inclusion of structural information reduces both alignment and topology uncertainty. The software is available as plugin to the package StatAlign.
Finally, I also examine limits on statistical inference of phylogeny through sequence information models. These limits arise due to the `cutoff phenomenon,' a term from probability which describes processes which remain far from their equilibrium distribution for some period of time before swiftly transitioning to stationarity. Evolutionary sequence models all exhibit a cutoff; I show how to find the cutoff for specific models and sequences and relate the cutoff explicitly to increased uncertainty in inference of evolutionary distances. I give theoretical results for symmetric models, and demonstrate with simulations that these results apply to more realistic and widespread models as well. This analysis also highlights several drawbacks to common default priors for phylogenetic analysis, I and suggest a more useful class of priors.
Item Open Access Behavioral Measures and Ecological Correlates of Vision in Poeciliid Fishes(2022) Solie, SarahUnderstanding how animals see the world and how visual systems have evolved to meet the needs of particular animals are major goals of visual ecology research. The Poeciliidae are a diverse family of Neotropical freshwater fishes and are excellent models for visual ecology research given longstanding interest in visual signaling in this group. However, despite extensive research investigating the form and function of visual signals in the poeciliids, there remains a surprising paucity of research regarding poeciliid visual system function and evolution. To address this gap, my dissertation research sought to investigate: (1) how Trinidadian guppies (Poecilia reticulata) perceive visual stimuli that vary in spatial detail and contrast, (2) correlates of eye size and eye investment across P. reticulata populations that experience different threats from predation and, (3) visual signaling correlates of eye size across the family Poeciliidae.
The first chapter of this dissertation introduces the questions and the study system. In Chapter 2, I examine the ability of Trinidadian guppies (Poecilia reticulata) to perceive visual stimuli that vary in spatial frequency and contrast. Male P. reticulata bear complex body patterning made up of patches that vary in color, contrast, and size, and these visual signals that are known to be important in mate choice. However, the extent to which conspecifics are able to resolve the details of these patterns has historically been overlooked. I used an optomotor assay to measure the behavioral responses of eight individual P. reticulata (N = 4 males; 4 females) to rotating achromatic stimuli. Unsurprisingly, I found that P. reticulata are better able to perceive stimuli as they increase in contrast and decrease in spatial frequency. Moreover, I found that female P. reticulata may outperform males on optomotor tasks.
In Chapter 3, I investigate how predation environment contributes to eye size variation in P. reticulata. Eye size is an important predictor of visual abilities, and it varies widely across taxa. Moreover, eye size is known to be correlated with numerous ecological factors including habitat complexity, light availability, and predation risk. However, less is known about how differences in ecological parameters across populations influence variation in eye size within species. I measured the eye diameter and standard length of 45 females and 307 males from 21 populations of known geographic origin and predation environment. I found that eye diameter was correlated with predation environment after controlling for standard length, with fish from low-predation environments having eyes that are 5.5% - 7.9% larger in diameter than those from high-predation environments. I also found that sexual dimorphism in eye diameter appears to be driven by sexual dimorphism in standard length, as there was no significant effect of sex on eye diameter after accounting for standard length.
Finally, in Chapter 4 I examine variation in eye size across the Poeciliidae. The poeciliids are a diverse family of freshwater fishes to which Poecilia reticulata belongs, and the group exhibits substantial variation in the distribution and types of visual signals used in mate choice. I measured eye size and eye investment for 66 species of poeciliids and took a phylogenetic approach to test whether variation in eye morphology was correlated with aspects of visual signaling. I found that the presence of sexually selected visual signals was associated with greater eye investment and, in particular, that sexual dichromatism was associated with an approximately 6% increase in eye diameter investment compared to species without sexual dichromatism.
Item Open Access Cell and extracellular matrix growth theory and its implications for tumorigenesis.(Bio Systems, 2021-03) Sauer, TJ; Samei, E; Bejan, ACells associated with an abnormal (cancerous) growth exchange flows, morph freely and grow hand-in-glove with their immediate environment, the extracellular matrix (ECM). The cell structure experiences two mass flows in counterflow. Flowing into the structure are nutrients and flowing out is refuse from the metabolically active biomass within. The physical effect of the evolution of the cell and extracellular structure is more flow and mixing in that space, that is, more mixing than in the absence of a biological growth in that space. The objective of the present theory is to predict the increase in the size of the cell cluster as a function of its structure, and also to predict the critical cluster sizes that mark the transitions from one distinct cluster configuration to the next. This amounts to predicting the timing and the main features of the transitions from single cell to clusters with two, four, eight and more cells, including larger clusters with cells organized on its outer surface. The predicted evolution of the size and configuration of the cell cluster is validated successfully by comparison with measurements from several independent studies of cancerous and non-cancerous growth patterns.Item Open Access Complexity by Subtraction(Evolutionary Biology, 2013) McShea, DW; Hordijk, WThe eye and brain: standard thinking is that these devices are both complex and functional. They are complex in the sense of having many different types of parts, and functional in the sense of having capacities that promote survival and reproduction. Standard thinking says that the evolution of complex functionality proceeds by the addition of new parts, and that this build-up of complexity is driven by selection, by the functional advantages of complex design. The standard thinking could be right, even in general. But alternatives have not been much discussed or investigated, and the possibility remains open that other routes may not only exist but may be the norm. Our purpose here is to introduce a new route to functional complexity, a route in which complexity starts high, rising perhaps on account of the spontaneous tendency for parts to differentiate. Then, driven by selection for effective and efficient function, complexity decreases over time. Eventually, the result is a system that is highly functional and retains considerable residual complexity, enough to impress us. We try to raise this alternative route to the level of plausibility as a general mechanism in evolution by describing two cases, one from a computational model and one from the history of life. © 2013 Springer Science+Business Media New York.Item Open Access Created and Evolved: Describing a nuanced theological anthropology for the contemporary church through the writings of Gregory of Nyssa and Charles Darwin(2023) Nielsen, William JohnThe following thesis addresses an issue in ways of knowing that is both commonand destructive in the contemporary American context. Specifically, the issue of misunderstood anthropologies is posited to be an unnecessary destructive force against American churches already in decline. This damage is caused by wooden and polarizing theological and evolutionary anthropologies that underlie the basis of how many define themselves. This project endeavors to show that theological and evolutionary anthropologies are not necessarily adversarial. To this end, the theological anthropology of Gregory of Nyssa as described in On the Making of Man (de Hominis Opificio) and the evolutionary anthropology as described by Charles Darwin in The Descent of Man are defined and compared. These seminal yet still authoritative works are shown to be making different statements about humanity’s coming into being, more so than confrontational ones. The lack of mutual exclusivity between these two anthropologies is heightened by a number of interesting points of connection between them, such as reason being the definitive characteristics of humanity as well as the notion that humanity is continually becoming a more good creature. These ideas will serve to remove barriers of belief for many, all the while providing for a more holistic view of the origins of humanity and thus humanity’s place in the world.
Item Open Access Culture From Infrahumans to Humans: Essays in the Philosophy of Biology(2007-05-07T19:07:23Z) Ramsey, Grant AaronIt has become increasingly common to explain the behavior of animals—from sperm whales to songbirds—in terms of culture. But what is animal culture, what is its relationship to other biological concepts and to human culture, and what impact does culture have on a species’ evolution and ecology? My dissertation is an attempt to answer these questions. After an introductory chapter, the dissertation begins (Chapter 2) with a proposal for a novel concept of culture and a critique of the existing ways in which culture has been characterized. These characterizations include views from cultural anthropology as well as attempts to apply the concept of culture to animals. The existing concepts are problematic in a number of ways, such as a priori excluding infrahumans from being candidates for possessing culture, or mistaking what culture is for its measure. In this chapter I offer a way to understand culture that avoids these and other problems. With a concept of culture in hand, the next chapter of my dissertation (Chapter 3) examines and criticizes one key way of understanding the concept of culture, meme theory. In Chapter 4 I turn to the question of how cultural systems can arise in nature, how they can be adaptive, and how the evolution and ecology of species is impacted by the possession of a cultural system. In order to answer these questions I introduce a general constraint on cultural systems—what I am calling the Fundamental Constraint—that has to be satisfied in order for cultural systems to be adaptive. In the final chapter I develop a concept of innovation and draw out the conceptual and empirical implications of this concept.Item Open Access Designer Science: A History of Intelligent Design in America(2021) Howell, Christopher WilliamDesigner Science: A History of Intelligent Design in America undertakes the first full-length historical overview of the intelligent design movement (ID), a popular and influential antievolutionary ideology prominent at the turn of the 21st century. To date, on one hand, full length treatments of ID have been primarily polemical, consisting of either critical refutations or hagiographic defenses. The scholarly, non-polemical assessments, on the other hand, have folded ID into a larger story of American creationism and in general do not focus on ID on its own. Rather than making ID a small part of a history of creationism or engaging in polemical conflict, this dissertation treats intelligent design it as its own subject.
In contrast to some critics and scholars who have interpreted intelligent design as a sleeker, deceptive, or “stealth” version of creationism, I find that ID is better understood as an evolution of creationist views into a distinct movement and ideology. The differences are especially stark if creationism is understood as young-Earth creationism, from which ID’s worldview was a significant departure. ID was animated less by the Biblical literalism and geological focus of young-Earth creationism and more by theistic metaphysics, the argument from design, and post-WWII intellectual conservatism. Its minimalist theological principles entailed a jettisoning of many of young-Earth creationism’s most important features, and its resultant lowest-common-denominator approach to antievolution (and reluctance to engage in doctrinal disputes) allowed ID to build a broad but shallow political coalition across antievolutionary movements. It was an expansive “big tent” with influence across the spectrum of antievolutionists and conservative political groups, and so creationists of all kinds were welcome (provided they sidelined doctrinal issues). However, ID and its supporters met their Waterloo in 2005, at the Kitzmiller v. Dover trial in Pennsylvania, where ID’s leaders struggled to clearly articulate a scientific vision for the concept and were dealt a disastrous legal defeat. Though ID did not disappear after the Dover trial, it was considerably reduced. Media interest declined, scientists reveled in their victory, and ID’s intellectual leaders responded by doubling down on existing arguments. ID’s general appeal meant that its leaders’ allegations of scientific bias legitimated a narrative of persecution that found great receptivity with its conservative religious supporters. In spite of its public decline, ID’s influence continued to be felt from the cultural margins, and the movement’s transition from an empirical challenge against Darwin to a radical rejection of scientific expertise is an illuminating development in the popular perception of science in the early 21st century. ID had little impact on the way science was practiced in America, but its influence on culture persists.
In order to chart a historical narrative of the movement’s rise, climax, and fall, I have focused primarily on ID’s intellectual history, for it was a movement concerned about the origins and effects of ideas. Supplemental research into the history of American conservatism and populist creationism is incorporated into a fuller picture of ID’s similarities and differences from the antievolutionary movements that came before it, and the latter half of the dissertation focuses on the legal and cultural context of ID in conjunction with its intellectual history. This project aims for a better understanding of what ID was—and what it was not—so as to make sense of its socio-political consequences, which are still being felt in 21st century America.
Item Open Access Determining the size of the male-specific region in the genome of the scuttle fly, Megaselia scalaris, a potential model system for the earliest stages of sex chromosome evolution(2012-09-06) Peneva, Ralitza H.Modern day whole-genome sequencing and the ability to make comparisons across many taxa have significantly advanced the study of sex chromosome evolution. The scuttle fly, Megaselia scalaris, is an appropriate model system for studying sex chromosome evolution exhibits sex chromosomes that are homomorphic in size, containing differences that are difficult to detect even microscopically. Presumably, sex in M. scalaris is determined by the presence or absence of a male-determining region, or sex realizer (M), that transposes among chromosomes at a low rate, essentially creating novel Y-chromosomes out of autosomes. M. scalaris would thus serve as a good model for exploring the primary stages of sex chromosome evolution. However, to serve as such a model, the identity and size of the male-specific region must be identified as a boundary within which to search for the sex realizer. This study focused on elucidating the relative size of the male-specific region in M. scalaris in relation to the genome. I compared previously generated genome sequences from male and female M. scalaris to isolate suggested regions unique to the male sex. Through a systematic approach involving sequencing, primer design, and PCR, I found the M. scalaris genome to be 27% male-specific, a preliminary result suggesting a large size inconsistent with published reports. This size further questions observations pointing to a relatively small male-determining region that transposes, but the male-specific region may be composed of additional elements unique to the male sex that do not ultimately determine sex. This study has refined the boundaries within which the sex realizer (M) of M. scalaris may be located. Future studies are necessary to pinpoint the sex realizer, an important step towards M. scalaris’ use as a model system in sex chromosome evolution.Item Open Access Development and Evolution of the Membracid Pronotum(2023) Kudla, Anna MarieA major goal of biological studies is to understand how complex forms develop and evolve. Each form is the result of molecular developmental patterning, growth, and the accumulation of changes in these processes from internal and external perturbations in ancestral forms. This dissertation uses each of these lenses to investigate the complex forms in the insect family Membracidae, which arises from the pronotum. In most insects, the pronotum is a simple, domed structure just behind the head, but in membracids it has enlarged and elaborated to look like thorns, plant stipules, fungi, and ants, among other shapes. To investigate this diversity, I rely on landmark based geometric morphometrics to quantify pronotal shapes. The specimens I used included those from a laboratory colony, those collected in and around San Jose, Costa Rica, and those from the Smithsonian National Museum of Natural History collection. In Chapter 1, I examined 5th instar morphogenesis to elucidate the timing of developmental events during the transition from juvenile to adult. These findings informed Chapter 2, which revealed developmental mechanisms related to growth led to transcriptional similarity between the pronotum and wings. In Chapter 3, I identified ontogenetic changes in the patterning of membracid pronotal shape compared to that of a closely related outgroup. Finally, in Chapter 4, I used a phylogenetic framework to investigate developmental modules and the co-occurrence of pronotal shape with two life history characteristics.
Item Open Access Developmental Single-Cell RNA Sequencing in the Sea Urchin Species Lytechinus variegatus and Heliocidaris erythrogramma(2022) Massri, AbdullThe process by which a single cell develops into a complex multicellular organism with specified cell types and well-defined cellular roles is not completely understood, and the evolution of that process is even more enigmatic. In sea urchin embryos, cell fate specification and differentiation of cell types occurs through gene regulatory networks, or circuits of nodes or genes that interact with and regulate each other’s DNA elements. However, what remains unclear is how a highly conserved developmental GRN can change over evolutionary time and how that can result in altered embryonic form and function.To begin to understand these processes, we developed methods to compare two relatively simple, yet complex sea urchin embryos with radically different life history strategies, the planktotrophic (conserved) Lytechinus variegatus and lecithotrophic (derived) Heliocidaris erythrogramma. To do this, single cell RNA sequencing methods were developed and adapted for the two species to address to what degree the developmental gene regulatory network genes were present, or altered when compared with the known planktotrophic dGRN. Developmental GRN information and gene signatures were applied to assign cell identities, and were vital to the identification of prospective co-expressed candidate dGRN nodes that could participate in a developmental context. With developmental atlases completed in the two species and dGRN nodes examined in both, we then compared gene signatures and dGRN nodes directly to identify prospective candidate dGRN nodes that could participate in the evolution of specification processes. We identified various novel candidates for dGRN analysis and found that, despite the obvious morphological differences, most of the dGRN circuits were conserved. In particular, we found that general specification events are delayed in Heliocidaris erythrogramma; this delay is especially prominent in the skeletogenic precursors, and the number of cells present is greatly reduced—by a factor of 10. In addition, the order of cell specification events, as shown by gene signatures, developmental sub clustering, and integrated analyses, indicate that pigment cells are among the first cell types to be specified, a finding in sharp contrast to known planktotrophic developers. Lastly, this work creates a unified framework of sea urchin development using a novel integrated model based on 1:1 gene orthologs. The application of single cell RNA-seq is a highly useful technique; when applied to a single developmental time series, it can yield insight into the genes and networks deployed over developmental time. Further, when applied to a second developmental time course, it becomes possible to uncover information about the evolution of development, as this application allows us sharp discernment into the genes and networks deployed over evolutionary time.
Item Open Access Ecological and Evolutionary Factors Shaping Animal-Bacterial Symbioses: Insights from Insects & Gut Symbionts(2017) Brown, BryanAnimal bacterial symbioses are pervasive and underlie the success of many groups. Here, I study ecological and evolutionary factors that shape interactions between a host and gut associates. In this dissertation, I interrogate interactions between the carpenter ant (Camponotus) and its associated gut microbiota to ask the following questions: What are the resident microbiota of the Camponotine gastrointestinal tract? How does persistent gut association affect rates of molecular evolution in gut symbionts? How are gut microbiota transmitted between social hosts? How does gut community composition and structure vary across host development? What evolutionary factors facilitate adaptation to the gut? How do the genomes of gut associates respond to selective pressures associated with persistent gut habitation? I use a combination of next generation sequencing, anaerobic isolate culturing, computational modeling, and comparative genomics to illustrate evolutionary consequences of persistent host association on the genomes of gut associates. In chapter one, I characterize the gut community of C. chromaiodes and describe two novel lineages in the Acetobacteraceae (AAB). I demonstrate rapid evolutionary rates, deleterious evolution at 16S rRNA, and deep divergence of a monophyletic clade of ant associated AAB. In chapter two, I design a novel molecular tool to prevent amplification of nontarget DNA in 16S based community screens. I then use this tool to characterize the gut microbiota of C. chromaiodes across several developmental stages and incipient colonies. I argue that highly similar bacterial profiles between a colony queen and offspring are indicative of reliable vertical transmission of gut bacteria. In chapter three, I isolate and culture two strains of AAB gut associates from C. chromaiodes, as well as an associate in the Lactobacillaceae, and perform whole genome sequencing. I use comparative genomic analyses to delineate patterns of genomic erosion and rampant horizontal gene transfer on AAB gut isolates that lead to genomes with mosaic metabolic pathways.
Taken together, this dissertation establishes a new model system for assessing evolutionary consequences of symbioses with gut bacteria. These results provide novel insights into the repercussions of bacterial adaptation to a host gut tract. They establish a foundation to interrogate questions unique to persistent extracellular gut symbionts. Finally, they delineate distinct forces shaping the functional capacity of symbiont genomes: gene loss through reductive evolution and gene acquisition via horizontal transfer from diverse community members.
Item Open Access Elucidating the Evolutionary Origin of the Neural Crest(2016-05-05) Nesbitt, WilliamThe evolutionary origin of the neural crest, an embryonic stem cell population unique to vertebrates, has eluded biologists since its discovery. The neural crest is characterized by its epithelial to mesenchymal transition (EMT), migration, and differentiation into stereotyped tissues of the embryo. These processes require an intricate gene regulatory network (GRN) that controls the signaling required for successful neural crest formation and differentiation into target tissue types. It is hypothesized that the neural crest, like other complex tissues, arose from co-option of existing developmental GRNs, but this has not been tested. Here, I will use an invertebrate deuterostome, the sea urchin L. variegatus, to look for ancestrally conserved circuits of the neural crest GRN. I hypothesize that genes operating in the neural crest GRN will be found in cells of the L. variegatus embryo that undergo similar processes to vertebrate neural crest cells (EMT, migration, etc.), namely primary mesenchyme cells (PMCs), secondary mesenchyme cells (SMCs), pigment cells, and neurons. I have cloned orthologs of vertebrate neural crest genes in the developing embryo of L. variegatus including foxd, phb1, musk, elk3, egr/krox20, and csnrp. Using RNA in situ hybridization, I have found that these genes are expressed in the predicted cell types in sea urchin embryos. Double in situs were then performed for musk / pks and foxd / phb1 to demonstrate co-expression of the gene pairs. Both pairs of genes were co-expressed, indicating that they may be part of the same GRNs. If these connections are shared with the neural crest GRN, it will provide evidence that these small GRNs are ancestral to deuterostomes and were co-opted into a single tissue in the vertebrate lineage, which gave rise to the neural crest.Item Open Access Evolutionary Dynamics in an Individual Spatial and a Mean Field Differential Equation Host-Pathogen Model(2013-04-30) Zhang, WilliamWe examine a host-pathogen model in which three types of species exist: empty sites, healthy hosts, and infected hosts. In this model six different transitions can occur: empty sites can be colonized by healthy hosts, healthy hosts can be infected, and infected hosts can either recover or die. We implement this general model in both a spatial context with discrete time and in a homogeneously mixing model in continuous time. We then explore evolution for pairs of parameters, calculating viable regions in the ODE model and and evolutionary vector fields in both models. Our results show that results from the spatial model do not always converge to our ODE model results, that stochasticity in the spatial evolutionary vector field can be used as a measure of the magnitude of evolutionary pressure and as an indicator of non-viable parameters, and that the evolutionary pressures on different parameters are not necessarily independent. For example, a lower transmissibility greatly lowers the magnitude of evolutionary pressure for all parameters associated with transitions from infected hosts.Item Open Access Evolutionary Genetics of Reduced Nectar Production in the Selfing Morning Glory, Ipomoea lacunosa (Convolvulaceae)(2021) Liao, IreneNectar production is one of several traits that are reduced in flowering plants that display the selfing syndrome, a suite of trait reductions often associated with the transition from outcross-fertilization to self-fertilization. However, the evolutionary mechanisms that contribute to reduced nectar has not been explored. In this dissertation, I use a pair of sister morning glories, Ipomoea lacunosa, a highly selfing species that displays the selfing syndrome, and I. cordatotriloba, a mixed mating species, to address the question: how did reduced nectar evolve in the selfing syndrome? Through a combination of approaches from quantitative genetics, population genomics, and transcriptomics, I describe the genetic architecture of nectar production and attempt to identify candidate genes that could lead to reduced nectar production – nectar volume and nectar sugar concentration – in I. lacunosa. QTL analyses indicate that nectar traits are polygenic and evolved independently from floral size traits, likely due to direct selection. Transcriptomic analyses reveal several sets of genes that are unique to each nectar trait, but both nectar volume and nectar sugar concentration also share some genes in common. Finally, through incorporating population genomic analyses, a short list of candidate genes was obtained that may explain how reduced nectar evolved in I. lacunosa and how nectar traits remain diverged between the two morning glory species even in regions of sympatry.
Accurate species descriptions are critical for understanding evolutionary relationships. Ipomoea “austinii” was proposed to be a new species found in the US, but conflicting evidence suggested that it was instead I. grandifolia. By examining cross-compatibility between these individuals and through genetic analyses, I find no cross-incompatibility and no genetic differentiation between I. “austinii” and I. grandifolia, thus suggesting that I. “austinii” should be reclassified as I. grandifolia.
Item Open Access Evolutionary Implications and Genetic Basis of Peroxide Survival in Saccharomyces Cerevisiae(2009) Diezmann, StephanieHydrogen peroxide is used by animals and plants to deter the growth of microbial invaders by inflicting DNA lesions, protein oxidation and lipid membrane modifications. Pathogens protect themselves with enzymes and scavenging proteins. This study investigated population genetic, biochemical and genetic aspects of peroxide survival in Saccharomyces cerevisiae to address its importance for yeast biology and fungal pathogenicity.
Population genetic analyses of DNA sequences from five loci from 103 strains encompassing the known ecological spectrum of S. cerevisiae show that it is a recombining species with three divergent subgroups, which are associated with soil, fruit, and vineyards. Clinical isolates cluster with fruit isolates but are significantly more resistant to peroxide. Clinical isolates are genetically diverse, indicating multiple origins of the pathogenic lifestyle and eliminating the possibility that peroxide resistance is due to shared ancestry rather than it's importance for than its importance in colonizing the host.
Biochemical aspects of peroxide survival were studied in a resistant (high-survival) clinical isolate, a sensitive (low-survival) laboratory strain and their hybrid. Catalase activity and expression levels are indistinguishable among strains. Co-culture assays and growth curve records indicate that a secreted factor improves survival of the laboratory strain and that the phenotypic difference is most pronounced during exponential growth, excluding mechanisms of the General Stress Response effective during stationary phase. Semi-quantitative expression profiles of stress response candidate genes do not differ, suggesting a novel resistance mechanism.
To elucidate the genetic basis of peroxide survival, the hybrid was sporulated and 200 F1 segregants phenotyped and genotyped for oxidative stress candidate genes. Peroxide survival is a dominant quantitative trait and not linked to catalase, peroxidase or superoxide dismutase genes. 1,246 backcross segregants were phenotyped and 93 segregants selectively genotyped using microarrays. A 14-gene locus on chromosome XVI displayed marker-trait association. One gene, RDS2, encodes a zinc cluster protein acting as a regulator of drug sensitivity and contains a non-synonymous polymorphism whose exchange between the parental strains results a 15% decrease in survival in the clinical strain.
This work establishes a novel function for RDS2 in oxidative stress response and demonstrates the effect a quantitative trait nucleotide has on a clinically relevant phenotype.
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