Theses and Dissertations from UMD

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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM

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Subject: search.filters.subject.Evolution & development

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    Sex and the Evolution of a Double Hermaphrodite
    (2023) Ficklin, John Alexander; Haag, Eric S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The Kryptolebias marmoratus species complex contains the only known self-fertile hermaphroditic vertebrates. There are three species in this clade and all three live in the mangrove forests across the tropical Americas. All three have individuals with both testis and ovarian tissue in their gonads with two using self-fertility as their main mode of reproduction, and all three have apparent different sex determination and sexual modes. In this dissertation, I explore aspects of sex in these species. K. marmoratus is the androdiecious and self-fertile member of the species complex with sequential hermaphroditism. In this species, the control of sex change from hermaphrodite to male is poorly understood. Individuals that were believed to be genetically identical could be raised in the same environment and change sex at drastically different times or not at all. Small fluctuations and variance in the hormonal profiles of individuals was thought to be a potential cause and while androgen dosing can lead to masculinization of both the gonad and the soma, it was not enough to maintain a permanent transition like what is seen in nature. In K. ocellatus, the obligate outcrosser of the K. marmoratus species complex, it was believed that they were using genetic sex determination to differentiate between males and the females that had hermaphroditic gonads. While we found strong evidence against heteromorphic sex chromosomes, all tests for homomorphic sex chromosomes came back inconclusive due to apparent K. hermaphroditus DNA contaminating the dataset. K. hermaphroditus, the self-fertile hermaphrodite species with exceptionally rare males, appears to be extending its range further and further south and/or hybridizing with K. ocellatus at rates previously underappreciated. The hermaphrodites of the Kryptolebias genus still hold many evolutionary and physiological secrets but can potentially be revolutionary to the understanding of vertebrate sexual development and evolution.
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    Evolutionary history and consequences of gene flow in bearded manakins
    (2023) Bennett, Kevin Faulkner Philipson; Braun, Michael J; Wilkinson, Gerald S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Recent advances in DNA sequencing have revolutionized evolutionary biology by allowing for genome-scale studies of non-model organisms. We can now readily connect genotype with phenotype, i.e., identify the genetic basis of particular traits, a key goal in the study of evolution. In addition, genome-scale sequence analysis has shifted our understanding of the frequency and magnitude of gene flow in nature. Once viewed as important only for its role preventing divergence, the common view now is that in many taxa gene flow occurs among many lineages in the early stages of divergence. My dissertation focuses on gene flow in bearded manakins (genus Manacus), which are notable for their intense tandem courtship display, high degree of reproductive skew among males, and bright male plumage. In western Panama, yellow-collared M. vitellinus and white-collared M. candei interbreed in a narrow hybrid zone. Male vitellinus secondary sexual traits, including the yellow collar, have introgressed roughly 50 km west across the hybrid zone into candei populations and then stalled at the east bank of the Río Changuinola, the region’s largest river. Evidence from studies of male-male interaction and female choice implicate positive sexual selection for yellow collars as a driver of introgression. For thirty years since this situation was first described in detail, several key issues have remained unresolved, including why introgression has not continued across the river and what gene or genes are responsible for yellow coloration. In the first chapter, I reviewed the current state of knowledge of the Manacus hybrid zone system and proposed new hypotheses for some of the patterns exhibited by these populations. In the second chapter, I used reduced-representation genome sequencing to investigate whether reduced gene flow across the Río Changuinola alone can explain stalled trait introgression. I found that, although advantageous plumage traits have not introgressed far beyond the river, substantial gene flow is occurring, implicating an additional selective force or forces in preventing trait introgression. In the third chapter, I used whole-genome sequencing of all major Manacus lineages, including unpigmented M. manacus and pigmented M. aurantiacus, to explore the evolution and genetic basis of collar coloration. I identified the carotenoid metabolism gene beta-carotene oxygenase 2 (BCO2) as responsible for collar color differences between vitellinus and candei and uncovered evidence of past introgression introducing aurantiacus BCO2 alleles into vitellinus. I argue that gene flow is likely to be a more common mechanism than previously appreciated for spreading sexual traits among species.
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    The genomics of species divergence in drosophila
    (2023) Carpinteyro Ponce, Javier; Machado, Carlos A; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    How do new species arise and diverge? Has been a fundamental question in evolutionary biology. The process of species divergence can be studied at many different levels of biological organization. However, it is until the recent advancements of genome sequencing technologies that genome-wide signatures of species divergence have started to unveil the complex genomic landscape of speciation. In this dissertation we investigate the landscape of genomic divergence using a classic pair of Drosophila species. We generated four new high quality genome assemblies for Drosophila pseudoobscura and D. persimilis to explore the genomic differences at three different levels. We first characterized the structural variation landscape between D. pseudoobscura and D. persimilis and stablished its association with transposable elements and tested how intrinsic genomic factors, such as recombination, influence the accumulation ofstructural variation associated with transposable elements in both species. With a combination of high-quality genome assemblies and a comprehensive population genomics data set, we also explored how the contribution of recombination rate and introgression promote sequence divergence with the potential of forming species barriers. Moreover, we investigated how gene co-expression networks potentially rewiring between species contribute to the divergence landscape between D. pseudoobscura and D. persimilis. Our work highlights the complex landscape of species divergence occurring at multiple levels of organization. Moreover, the integration of potential species drivers identified at different scales shed lights on the molecular mechanisms involved in speciation.
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    MECHANISMS OF SEXUAL MODE EVOLUTION IN CAENORHABDITIS ELEGANS
    (2022) Skelly, Lauren E; Haag, Eric S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    ABSTRACT Title of dissertation: MECHANISMS OF SEXUAL MODE EVOLUTION IN CAENORHABDITIS ELEGANS Lauren Skelly, Doctor of Philosophy, 2022 Dissertation directed by: Professor Eric S. Haag, Department of Biology The evolution of phenotypic novelties is a broad biological phenomenon, and how organisms evolve new traits is dependent on the molecular mechanisms that underlie those traits. Transcriptional regulation is often the focus of phenotype evolution, but post-transcriptional mechanisms such as mRNA splicing, stability, and translational control are also important components. Germ cells are particularly influenced by post-transcriptional mechanisms and are therefore a good system to study how these mechanisms lead to phenotypic novelties. This topic can be studied especially well in model systems that contain closely related species with recently evolved traits, such as self-fertility in Caenorhabditis elegans hermaphrodites. C. elegans hermaphrodites are essentially XX females that evolved the ability to produce sperm in an ovary. There are many known components necessary for sperm development, including a protein-protein-mRNA complex consisting of GLD-1, FOG-2 and tra-2. GLD-1 and FOG-2 dimerize and bind the 3’ UTR of tra-2 mRNA to repress its activity during spermatogenesis. In this work, I show FOG-2 directly interacts with TRA-2 protein, leading to the model that FOG-2 targets TRA-2 protein for degradation during its translation allowing sperm to form. I also show the expression pattern of tra-2 mRNA in the germline, and that GLD-1 binding on the 3’ UTR does not influence its localization. Another method for the study of novel traits is through hybridization of closely related species. In this work, I attempt to hybridize two closely related species of Caenorhabditis, another self-fertile species C. briggsae and an outcrossing species C. nigoni, to map the genetic loci underlying self-fertility. These hybrid crosses are unable to map genetic loci because males are inviable. These results agree with previous studies. This work contributes to the study of phenotypic evolution by adding an underlying molecular mechanism to Caenorhabditis sex determination.
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    What makes a successful invader? Population genomics and adaptation to novel environments in the invasive Japanese white-eye (Zosterops japonicus)
    (2021) Venkatraman, Madhvi; Gruner, Daniel S; Fleischer, Robert C; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Invasive species face many obstacles when colonizing new habitats. Yet, many overcome these hurdles and successfully establish populations. Therefore, understanding how invasive species cope with novel stressors while colonizing new environments is a fundamental goal of evolutionary biology. Additionally, broadening our understanding of how birds adapt to novel environments can help us predict how species will respond to habitat degradation and stressors resulting from climate change in the future. Here, we focus on the Japanese white-eye (Zosterops japonicus), an East Asian bird that was introduced into Hawaii in the early 1900s and is now the most abundant land bird in the archipelago. First, we sequenced and assembled a high-quality Z. japonicus genome and compared genome annotation pipelines. We found that AUGUSTUS was more conservative with gene predictions when compared to BRAKER2, but the final number of annotated gene models was similar between the two workflows. Additionally, we found that while adding more data did not significantly change the number of annotated genes using AUGUSTUS, using BRAKER2 the number increased substantially. Next, we compared whole genomes of Z. japonicus individuals from both their native and introduced ranges to characterize genetic diversity and population history and divergence and to identify genes potentially under selection between the two populations. We saw evidence of mixed ancestry in the introduced population, supported by drastically different demographic histories in Hawaii. This suggests that admixture could have contributed to increased genetic diversity in the introduced population and therefore to overall invasion success. Lastly, we conducted one-, three-, and six-week one-way transplants of individuals from near sea level to 2,790m, with individuals kept at sea level as controls, and later a six-week reciprocal transplant from high to low elevation and vice versa. We assessed morphological and physiological traits as well as gene expression using RNA-seq on heart and lung tissues. We found strong evidence for phenotypic plasticity in hematological and cardiac response to hypoxia and cold stress and some evidence of maladaptive plasticity in pulmonary circulation. We identified two genes potentially under divergent selection in the high elevation population that could be indicative of early-stage genotypic specialization in response to hypoxia and cold stress. Our results suggest that the population of Z. japonicus on Mauna Kea is able to persist at high elevation because of ancestral plasticity, which also could have contributed to its remarkable success as an invasive species.
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    INTERNAL AND EXTERNAL ENVIRONMENTAL REGULATION OF OPSIN EXPRESSION IN AFRICAN CICHLIDS
    (2021) Yourick, Miranda Rose; Carleton, Karen L; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Evolutionary biology has long sought to understand the evolution of adaptive phenotypes. While purely genetic factors are often emphasized, environmental influences also significantly contribute to phenotypic variation. In this dissertation, we investigate the environmental regulation of visual sensitivity in cichlids. Cichlid fishes exhibit a diversity of color vision facilitated by differential expression of opsin proteins, including light-induced phenotypic plasticity which was known to occur during development. To determine whether cichlids retain plasticity into adulthood, adult fish were moved between different light environments. Adult fish not only exhibited plasticity of opsin expression, but it was rapid, reversible, and shifted in a direction that would maximize light input to the retina. In order to observe the effect of diurnal variation of light on opsin cycles, we collected retinae from a continuous 25 hour time-series. This enabled us to develop guidelines for qRT-PCR normalization and determined that opsins were most highly expressed in the late afternoon. Opsins also cycled together, suggesting some common diurnally-sensitive regulatory mechanism. Given that there are species differences in plasticity, we sought to determine genetic loci that were affected by light. To determine how quantitative trait loci (QTL) changed between light environments, we raised all generations of a previously studied hybrid cross in a new light environment. One QTL was significant in both environments, indicating it is universally important for opsin expression. However, another QTL was only significant in one light environment, indicating it may be environmentally-sensitive. We propose a possible candidate gene for this locus. Plasticity is prevalent during development, with thyroid hormone (TH) being a common cue for developmental changes. Previous studies have found TH causes opsin expression shifts from short- to long-wavelength sensitivity as organisms age. To see its effect on species of cichlids with different developmental opsin progressions, we treated fish with TH. Interestingly, TH shifted fish to longer-wavelength sensitivities regardless of species. We also uncovered a possible interaction between TH and light-induced plasticity. Characterization of environmental influences on vision will continue to enhance our understanding of the evolution of visual diversity in these incredible fishes.
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    Investigating the Distribution of CRISPR Adaptive Immune Systems Among Prokaryotes
    (2019) Weissman, Jake; Johnson, Philip L.F.; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Just as larger organisms face the constant threat of infection by pathogens, so too do bacteria and archaea. In response, prokaryotes employ a diverse set of strategies to simultaneously cope with their viral and physical environments. Here I explore the ecology and evolution of the CRISPR adaptive immune system, a powerful form of protection against viruses that is the only known example of adaptive immunity in prokaryotes. CRISPR systems are widespread across diverse bacterial and archaeal lineages, suggesting that CRISPR effectively defends against viruses in a broad array of environments. Nevertheless, this defense system is nearly absent in many bacterial groups, and in many environments. I focus on understanding these patterns in CRISPR incidence and the ecological drivers behind them. First, I identify the ecological conditions that favor the adoption of a CRISPR-based defense strategy. I develop a phylogenetically-conscious machine learning approach to build a predictive model of CRISPR incidence using data on over 100 phenotypic traits across over 2600 species and discovered a strong but hitherto-unknown negative interaction between CRISPR and aerobicity. I then consider the multiplicity of CRISPR arrays on a genome, testing whether or not selection favors redundancy in immunity. I use a comparative genomics approach, looking across all prokaryotes to demonstrate that on average, organisms are under selection to maintain more than one CRISPR array. I then explain this surprising result with a theoretical model demonstrating that a trade-off between memory span and learning speed could select for paired “long-term memory” and “short-term memory” CRISPR arrays. Finally, I provide a theoretical examination of the phenomenon of immune loss, specifically in the context of CRISPR immunity. In doing so, I propose an additional mechanism to answer the perennial question: “How do bacteria and bacteriophage coexist stably over long time-spans?” I show that the regular loss of immunity by the bacterial host can produce host-phage coexistence more reliably than other mechanisms, pairing a general model of immunity with an experimental and theoretical case study of CRISPR-based immunity.
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    GENOMIC AND REPRODUCTIVE CONSEQUENCES OF SELF-FERTILITY IN CAENORHABDITIS NEMATODES
    (2019) Yin, Da; Haag, Eric S; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The evolution of a new reproductive strategy is expected to be reflected in an organism's genome and impact mating-related traits. Several species of Caenorhabditis nematodes have evolved the ability to self-fertilize from their outcrossing ancestors. Comparisons of species with different reproductive strategies may therefore reveal consequences of transition to self-fertilization. We compared chromosome-scale genome assemblies for the outcrossing nematode Caenorhabditis nigoni and its recently self-fertile sister species, C. briggsae. C. nigoni genome resembles that of outcrossing relatives but encodes 31% more protein-coding genes than C. briggsae. C. nigoni genes lacking C. briggsae orthologs were disproportionately small and male-biased in expression, including the male secreted short (mss) gene family that encodes sperm surface glycoproteins conserved only in outcrossing species. Sperm of mss-null males of an outcrossing species failed to compete with those of wild-type males, despite having normal fertility in non-competitive situations. Restoration of mss to C. briggsae males was sufficient to enhance sperm competitiveness. These results reveal the pervasive influence of sex on genome content that can be used to identify sperm competition factors. Further I found the fitness of mss+ genotype was influenced by mating system and population subdivision. Specifically, mss+ is sufficient to increase male frequency and depress population growth in genetically homogenous androdioecious populations. Using experimental evolution, I demonstrated that when mss+ and mss-null (i.e. wild-type) genotypes compete, mss+ is positively selected in both mixed-mating and strictly outcrossing situations, though more strongly in the latter. I suggest that the lack of inbreeding depression and the strong subdivision thought to characterize natural Caenorhabditis populations impose selection on sex ratio that makes loss of mss adaptive in self-fertile species.
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    Proximate and ultimate insights in the evolution of color vision in tropical freshwater fish
    (2019) Escobar Camacho, Daniel; Carleton, Karen L; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Evolutionary biology aims to understand diversity and the different mechanisms shaping this organismal variation. Furthermore, several animals vary greatly in coloration patterns and the adaptive mechanisms they have to optimally perceive visual signals in their light environment. The visual system of fish, due to their extensive variation in spectral sensitivities and their numerous adaptations to the underwater light environment, offers a unique opportunity to disentangle this phenotypic diversity. Throughout this dissertation, I analyze the visual systems of two major groups of Neotropical teleosts: cichlids and characins. Through transcriptome, genome and physiological experiments, I characterized the extant opsin gene complements of their visual system, which is a product of highly dynamic opsin gene evolution, and their color vision, which is based on the expression of at least three spectrally different visual pigments. The diversity of visual pigments found in these fish is the product of several spectral tuning mechanisms, which they use to fine-tune their spectral sensitivities to specific wavelengths. Our results follow the sensitivity hypothesis because the visual sensitivities of cichlids and characins match the available light in Neotropical ecosystems. Furthermore, through behavioral assays complemented with visual modeling, I show that African cichlids possess true color vision, the capacity of discriminating color regardless of brightness. This is followed by behavioral experiments analyzing the limits of their chromatic discrimination and discussing the adaptive significance of color vision and its relevance in the visual ecology of Lake Malawi. This dissertation enhances our understanding of color vision in freshwater fish using molecular and behavioral methods. This work encompasses experiments analyzing the genetic complement of visual pigments, builds knowledge in the evolution of these molecules and their relationship with aquatic environments, and analyzes the color dimensionality of visual systems through behavioral trials. Overall, this dissertation demonstrates the evolution of fish color vision with several methodologies highlighting the importance of an integrative and comparative approach in vision research.
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    GENETIC CONFLICT IN LAKE MALAWI CICHLIDS: B CHROMOSOMES AND SEX DETERMINATION
    (2019) Clark, Frances Elizabeth; Kocher, Thomas D.; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    B chromosomes (Bs) are selfish genetic elements known to manipulate various cellular processes. These manipulations increase their transmission to the next generation, a process known as drive. After the recent discovery of Bs in African cichlid fish, sequence amplification methodologies were used to quantify B chromosome distribution in 7 species of Lake Malawi cichlids. In these species, Bs are limited to females and are haploid in the diploid genome. Considering various possible drive mechanisms, I propose this B chromosome drives by manipulating meiosis I in females. Genetic crosses quantifying B transmission in Metriaclima lombardoi confirmed transmission above Mendelian expectations. The transmission of this B also skews the sex ratio among progeny towards females. M. lombardoi individuals lacking Bs were shown, via a genetic linkage analysis, to have a male heterogametic (XY) sex determination system. A similar linkage analysis of families segregating B chromosomes indicated only the progeny lacking a B were influenced by this XY system. This substantiates the hypothesis that this B is a female sex determiner. Individuals of all 7 species were re-sequenced with short-reads and read coverage across the genome was compared in a coverage ratio analysis that resulted in the detection of 1.37 Mb in the reference genome with copies on the B, shared by all 7 species. Accounting for copy number of each sequence, 12-44 Mb of shared B sequence was identified. Amongst this sequence were 144 loci containing genes and gene fragments. A differential expression analysis found hundreds to thousands of differentially expressed loci between individuals with and without Bs, biased towards decreased expression in B individuals. Transcriptomes were analyzed for B-specific SNPs revealing 53 loci transcribed from the B chromosome and six candidate genes that might contribute to drive. I have described the distribution and behavior of the Lake Malawi cichlid B as well as captured a large portion of its sequence. This, combined with the genomic resources available for cichlids, makes this model system a valuable tool for future studies of the molecular mechanisms of drive, sequence structure and evolution of B chromosomes, and the association between B and sex chromosomes.