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Title: Understanding the role of standing genetic variation in functional genetics and compensatory evolution
Creator: Chari, Sudarshan R.
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Conventionally the phenotypic outcome of a mutation is considered to be due to a specific DNA lesion. But it has long been known that mutational effects can be conditional on environment (GxE) and genetic background (GxG). Thus it is standard practice to perform experiments by controlling for rearing environment and using co-isogenic strains. Though such a controlled approach has been very successful in enabling many discoveries, by not considering conditional effects our understanding of...
Show moreConventionally the phenotypic outcome of a mutation is considered to be due to a specific DNA lesion. But it has long been known that mutational effects can be conditional on environment (GxE) and genetic background (GxG). Thus it is standard practice to perform experiments by controlling for rearing environment and using co-isogenic strains. Though such a controlled approach has been very successful in enabling many discoveries, by not considering conditional effects our understanding of biological systems is incomplete. My research utilized conditionality in terms of genetic background and standing genetic variation therein to understand whether mutational interactions can themselves be background dependent. I demonstrated that a majority of mutational interactions identified via a dominant modifier screen are background dependent. Extending this idea of contingency in terms of standing genetic variation to the phenomenon of compensatory evolution in the presence of deleterious mutations, I demonstrated that natural populations of Drosophila melanogaster possess standing genetic variation for compensatory alleles to ameliorate even severe phenotypic defects. I further demonstrated that, despite considerable standing variation to ameliorate the focal phenotype perturbed by the mutation, natural selection exploits alternative evolutionary trajectories to recover fitness. Additionally this model system also allowed me to understand that loss of sexual signaling can be compensated by modulating behavioural and life history traits.
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Title: The role of evolutionary history and niche differentiation in structuring species co-occurrence in New Zealand Pittosporum (Pittosporaceae)
Creator: Nolting, Kristen Marie
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Understanding the processes that shape the spatial distribution of species, and their co-existence in communities, remains one of the biggest challenges that ecologists face today. Investigations of co-existence typically treat species as independent entities, thereby ignoring their shared evolutionary history, niche preferences and functional similarity. This limits the ability of ecologists to make strong inferences regarding co-existence mechanisms. It is more useful to employ a...
Show moreUnderstanding the processes that shape the spatial distribution of species, and their co-existence in communities, remains one of the biggest challenges that ecologists face today. Investigations of co-existence typically treat species as independent entities, thereby ignoring their shared evolutionary history, niche preferences and functional similarity. This limits the ability of ecologists to make strong inferences regarding co-existence mechanisms. It is more useful to employ a pluralistic approach that integrates phylogenetic information and species-specific environmental and trait associations. In this study I evaluated the role of evolutionary history and environmental and functional trait differentiation in predicting species co-occurrence in the New Zealand plant genus Pittosporum. I hypothesized that co-occurring species would be more distantly related than non co-occurring species, given that closely related species are likely to be more ecologically similar as a result of their shared ancestry, and thus competitive interactions would preclude them from co-occurring. Similarly, I predicted that co-occurring species would be more divergent in their functional traits to enable co-existence. I found that co-occurring species were no different than non co-occurring species with respect to their phylogenetic dissimilarity, that co-occurring species had higher environmental niche overlap than non co-occurring species, and that for most traits measured there was no difference in trait dissimilarity among co-occurring and non co-occurring species. Approximate maximum vessel length and leaf nitrogen content, however, showed convergence among co-occurring species.
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Title: The evolutionary origins of memory use in navigation
Creator: Grabowski, Laura M.
Date: 2009
Collection: Electronic Theses & Dissertations

Title: Teaching and learning with digital evolution : factors influencing implementation and student outcomes
Creator: Lark, Amy M.
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Science literacy for all Americans has been the rallying cry of science education in the United States for decades. Regardless, Americans continue to fall short when it comes to keeping pace with other developed nations on international science education assessments. To combat this problem, recent national reforms have reinvigorated the discussion of what and how we should teach science, advocating for the integration of disciplinary core ideas, crosscutting concepts, and science practices....
Show moreScience literacy for all Americans has been the rallying cry of science education in the United States for decades. Regardless, Americans continue to fall short when it comes to keeping pace with other developed nations on international science education assessments. To combat this problem, recent national reforms have reinvigorated the discussion of what and how we should teach science, advocating for the integration of disciplinary core ideas, crosscutting concepts, and science practices. In the biological sciences, teaching the core idea of evolution in ways consistent with reforms is fraught with challenges. Not only is it difficult to observe biological evolution in action, it is nearly impossible to engage students in authentic science practices in the context of evolution. One way to overcome these challenges is through the use of evolving populations of digital organisms.Avida-ED is digital evolution software for education that allows for the integration of science practice and content related to evolution. The purpose of this study was to investigate the effects of Avida-ED on teaching and learning evolution and the nature of science. To accomplish this I conducted a nationwide, multiple-case study, documenting how instructors at various institutions were using Avida-ED in their classrooms, factors influencing implementation decisions, and effects on student outcomes. I found that all of the participating instructors held views on teaching and learning that were well aligned with reform-based pedagogy, and although instructors used Avida-ED in a variety of ways, all adopted learner-centered pedagogical strategies that focused on the use of inquiry. After implementation, all of the instructors indicated that Avida-ED had allowed them to teach evolution and the nature of science in ways consistent with their personal teaching philosophies. In terms of assessment outcomes, students in lower-division courses significantly improved both their understanding and acceptance of evolution after using Avida-ED, and learning of content was positively associated with increased acceptance. Although student learning outcomes and instructor familiarity with Avida-ED were not associated with student affective response to the program, instructor familiarity was highly influential with regard to both how Avida-ED was implemented and student affective response, particularly student interest, enjoyment, and self-efficacy. The results of this dissertation provide strong evidence suggesting that Avida-ED is a promising tool for teaching and learning about evolution in reform-based ways, and suggest that improving instructor pedagogical content knowledge with regard to research-based tools like Avida-ED may be implicated in generating student interest in STEM.
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Title: Species pluralism
Creator: Holmes, John Alan
Date: 2000
Collection: Electronic Theses & Dissertations

Title: Social Modulation of Individual Decision-Making in Foraging Bumblebees : Mechanisms and Evolution
Creator: Incorvaia, Darren
Date: 2021
Collection: Electronic Theses & Dissertations
Description: How and why animals choose to do what they do at any given moment is one of the fundamental questions in animal behavior. For social animals, influences on decision-making can come from both personal and social sources, and in eusocial insects like ants, bees, and wasps, the reliance on social information is taken to the extreme. Foraging bumblebees offer the perfect model in which to examine the social influences on individual decision-making because they are presented with extensive...
Show moreHow and why animals choose to do what they do at any given moment is one of the fundamental questions in animal behavior. For social animals, influences on decision-making can come from both personal and social sources, and in eusocial insects like ants, bees, and wasps, the reliance on social information is taken to the extreme. Foraging bumblebees offer the perfect model in which to examine the social influences on individual decision-making because they are presented with extensive personal and social information, and when foraging they are solely focused on the task at hand. Chapter 1 reviews information use by foraging bumblebees, setting the stage for the subsequent data chapters. Chapter 2 examines how the motivation for bumblebees to feed from a known feeder is modified by the nutritive state of the colony, such that individuals in colonies with full food stores show lower motivation to feed. In addition to this behavioral result, a biochemical analysis reveals that lipid levels may be involved in the mechanism underlying this social effect. Eusocial insects are famous for collective behaviors, such as the swarming behavior of honeybees, the foraging trails of termites, and the bridge-building of ants. While the collective foraging strategy of other eusocial insects has been well-studied, it has not received attention in bumblebees. In Chapter 3 I use a behavioral experiment to reveal that bumblebees use a strategy of informed individual initiative to collectively ensure they are foraging from the best resources in the environment. In this strategy, individual bees adjust their reward expectations based on the quality of nectar stored in the nest. I followed up this experiment with a computational model to reveal that this strategy is adaptive, as it results in higher fitness than does individual search alone. This strategy is markedly different from the spatial communication of the dance language used by honeybees, who are close relatives of bumblebees. This prompted me to extend the computational model to examine the selective pressures that shape foraging strategies in social insects, including the honeybee dance language and bumblebee strategy of informed individual initiative. In Chapter 4, I present the results of simulations of this extended model, demonstrating that, although resource density influences fitness for both the dance language and informed individual initiative, colony size only matters for the dance language. This suggests that the large colony sizes of honeybees may have been important for the dance language to evolve, whereas a similar spatial communication system would not be adaptive in bumblebees, which have smaller colony sizes. Taken all together, the results in this dissertation explore how individual decision-making is shaped by the social environment in bumblebees, and the potential selective pressures that led to these behavioral strategies over evolutionary time. Bumblebees are important pollinators in both agricultural and natural ecosystems, but many species are facing declines; a more thorough understanding of their behavior is imperative to help us conserve them as the planet continues to change due to climate change and other anthropogenic influences.
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Title: Replaying Life's Virtual Tape : Examining the Role of History in Experiments with Digital Organisms
Creator: Bundy, Jason Nyerere
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Evolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not...
Show moreEvolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not everyone was convinced. Some believed that chance was the primary driver of evolutionary change, while others insisted that natural selection was the most powerful influence. Since then, “replaying life’s tape” has become a core method in experimental evolution for measuring the relative contributions of adaptation, chance, and history. In this dissertation, I focus on the effects associated with history in evolving populations of digital organisms—computer programs that self-replicate, mutate, compete, and evolve in virtual environments. In Chapter 1, I discuss the philosophical significance of Gould’s thought experiment and its influence on experimental methods. I argue that his thought experiment was a challenge to anthropocentric reasoning about natural history that is still popular, particularly outside of the scientific community. In this regard, it was his way of advocating for a “radical” view of evolution. In Chapter 2—Richard Lenski, Charles Ofria, and I describe a two-phase, virtual, “long-term” evolution experiment with digital organisms using the Avida software. In Phase I, we evolved 10 replicate populations, in parallel, from a single genotype for around 65,000 generations. This part of the experiment is similar to the design of Lenski’s E. coli Long-term Evolution Experiment (LTEE). We isolated the dominant genotype from each population around 3,000 generations (shallow history) into Phase I and then again at the end of Phase I (deep history). In Phase II, we evolved 10 populations from each of the genotypes we isolated from Phase I in two new environments, one similar and one dissimilar to the old environment used for Phase I. Following Phase II, we estimated the contributions of adaptation, chance, and history to the evolution of fitness and genome length in each new environment. This unique experimental design allowed us to see how the contributions of adaptation, chance, and history changed as we extended the depth of history from Phase I. We were also able to determine whether the results depended on the extent of environmental change (similar or dissimilar new environment). In Chapter 3, we report an extended analysis of the experiment from the previous chapter to further examine how extensive adaptation to the Phase I environment shaped the evolution of replicates during Phase II. We show how the form of pleiotropy (antagonistic or synergistic) between the old (Phase I) and new (Phase II) habitats was influenced by the depth of history from Phase I (shallow or deep) and the extent of environmental change (similar or dissimilar new environment). In the final chapter Zachary Blount, Richard Lenski, and I describe an exercise we developed using the educational version of Avida (Avida-ED). The exercise features a two-phase, “replaying life’s tape” activity. Students are able to explore how the unique history of founders that we pre-evolved during Phase I influences the acquisition of new functions by descendent populations during Phase II, which the students perform during the activity.
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Title: Phylogeny of Astylopsis Casey (Coleoptera : Cerambycidae) species and patterns of host use
Creator: Camerato, Ellen M.
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Cerambycid (longhorn) beetles are diverse in their morphology and life history traits, but all share the common trait of being larval plant-borers. The larvae bore into and develop inside various plant tissues thus they can potentially cause significant economic and ecological damage, especially when transported to non-native localities. There is little empirical data on cerambycid life history traits that are essential in understanding their ecological and economic effects. Astylopsis Casey ...
Show moreCerambycid (longhorn) beetles are diverse in their morphology and life history traits, but all share the common trait of being larval plant-borers. The larvae bore into and develop inside various plant tissues thus they can potentially cause significant economic and ecological damage, especially when transported to non-native localities. There is little empirical data on cerambycid life history traits that are essential in understanding their ecological and economic effects. Astylopsis Casey (Lamiinae: Acanthocinini) is an eastern North American genus of six species. Host preference varies greatly among the species, including both angiosperms and gymnosperms. I used morphological characters and molecular data to reconstruct phylogenies of Astylopsis to test the hypothesis that host plant use among Astylopsis species is conserved. I constructed phylogenies using partial COI and CAD DNA sequences from Astylopsis species and outgroups using parsimony methods. Astylopsis collaris, A. macula, A. sexguttata, and A. arcuata were monophyletic in both COI and combined gene phylogenies, with the genus also exhibiting monophyly in the combined gene tree. Evidence of host shift from angiosperms to gymnosperms in some species was also observed. These results confirm current taxonomic separations among the four species and their outgroups and provide important host use information. No conclusions could be drawn regarding DNA variation in association with geographic locality. These findings will inform future studies expanding the molecular dataset for Astylopsis with additional genes (arginine kinase, 28S, and EF1-α) and species (Astylopsis perplexa and A. fascipennis).
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Title: Oceanic salt spray and herbivore pressure contribute to local adaptation of coastal perennial and inland annual ecotypes of the Seep Monkeyflower (Mimulus guttatus)
Creator: Popovic, Damian
Date: 2018
Collection: Electronic Theses & Dissertations
Description: In this study, we used the emergent model system Mimulus guttatus to explore the agents of selection that drive local adaptation across California’s coast-inland moisture gradient. We implemented a field reciprocal transplant experiment within agrofabric exclosures at sites in coastal and inland Sonoma County, California – minimizing the effects of aboveground stressors in an effort to elucidate their role in the evolution of local adaptation in this system. ASTER life-history modeling and...
Show moreIn this study, we used the emergent model system Mimulus guttatus to explore the agents of selection that drive local adaptation across California’s coast-inland moisture gradient. We implemented a field reciprocal transplant experiment within agrofabric exclosures at sites in coastal and inland Sonoma County, California – minimizing the effects of aboveground stressors in an effort to elucidate their role in the evolution of local adaptation in this system. ASTER life-history modeling and generalized linear mixed modeling approaches were used to analyze survival and dry aboveground biomass as fitness proxies. Despite altering no edaphic conditions, we found that among coastal exclosures, inland replicates were significantly more fit than their control counterparts, essentially rescuing inland fitness outside of their native range. Exclosures provided no fitness advantage for either ecotype at the inland site, aside from a moderate but statistically significant increase in biomass among exclosed coastal replicates. While it is unlikely to know all the agents of selection limited by our exclosures, we found that the number of replicates that experienced herbivory were significantly lower across all exclosures at the coast site. An elemental analysis of Sodium (Na) using salt traps installed at each site also demonstrated a reduction in salt exposure within exclosures. It is likely that some combination of aboveground stressors, likely driven primarily by herbivory and/or salt stress, plays a continuing role in the evolution of coastal M. guttatus populations, thus providing a new understanding of how local adaptation is maintained in this model system.
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Title: Microbial diversity and metabolic potential of the serpentinite subsurface environment
Creator: Twing, Katrina Irene
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Serpentinization is the hydrous alteration of mafic rocks to form serpentine minerals and magnetite. The reactions of this alteration result in elevated pH of the surrounding fluids, abiotic generation of H2, CH4 (and other organic molecules), and depletion of dissolved inorganic carbon. Thus, serpentinization has implications for the origin of life on Earth and possibly Mars and other planetary bodies with water. The microbial diversity of continental serpentinite systems consistently shows...
Show moreSerpentinization is the hydrous alteration of mafic rocks to form serpentine minerals and magnetite. The reactions of this alteration result in elevated pH of the surrounding fluids, abiotic generation of H2, CH4 (and other organic molecules), and depletion of dissolved inorganic carbon. Thus, serpentinization has implications for the origin of life on Earth and possibly Mars and other planetary bodies with water. The microbial diversity of continental serpentinite systems consistently shows communities that are dominated by two major taxa – microaerophilic Betaproteobacteria and anaerobic Clostridia. Previous studies relied on few samples collected from natural springs or seeps, meaning that the flow path of fluids from the subsurface process of serpentinization was unknown. The Coast Range Ophiolite Microbial Observatory (CROMO), a set of wells drilled into the actively serpentinizing subsurface environment in northern California, was established in northern California to gain a better understanding of the habitability and microbial functions within the serpentinite subsurface environment. This dissertation represents a culmination of microbiological investigations into the serpentinite subsurface environment at CROMO to identify the microbial inhabitants of subsurface fluids, rocks, and in situ colonization experiments using molecular methods and high-throughput sequencing. The CROMO wells represent a broad range of geochemical gradients and pH and the concentrations of carbon monoxide and methane have the strongest correlation with microbial community composition. The most extremely high pH wells were inhabited exclusively by a single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia, while more moderate pH wells exhibited greater diversity. Genes involved in the metabolism of hydrogen, carbon monoxide, and carbon fixation were abundant in the extreme pH fluids, while genes for metabolizing methane were exclusively in the moderate pH wells. The subsurface environment is an amalgamation of fluids and rocks, and as such, studying fluids alone only gives half the story. CROMO represents the first drill campaign into the continental serpentinite environment and the microbial diversity of serpentinite cores to a depth of 45 meters below surface suggests that specific geological features harbor different microbial communities. Archaea, previously undetected at CROMO, dominated cores containing magnetite-bearing serpentine, while bacteria were more abundant in layers containing clay particles. Additionally, organisms involved in the cycling of nitrogen and methane were found associated with core materials, indicating core-associated communities may have strong biogeochemical roles within the serpentinite subsurface environment. Given that microbial communities appear to vary with geological composition and that serpentinite fluids are a challenging habitat for life, depleted in inorganic carbon and electron acceptors, microbe-mineral interactions within the serpentinite subsurface environment through the use of in situ colonization devices to see if communities were able to utilize inorganic carbon in calcite or ferric iron as a terminal electron acceptor from magnetite. In the highest pH well, calcite led to an increased abundance of Clostridia and Deinococcus, while magnetite led to an increase in diversity, including Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, suggesting further that mineralogical composition of solids within the subsurface impact community composition. The data discussed here further our understanding of life associated with serpentinite fluids and minerals within the subsurface environment.
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Title: MODELING AND PREDICTION OF GENETIC REDUNDANCY IN ARABIDOPSIS THALIANA AND SACCHAROMYCES CEREVISIAE
Creator: Cusack, Siobhan Anne
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Genetic redundancy is a phenomenon where more than one gene encodes products that perform the same function. This frequently manifests experimentally as a single gene knockout mutant which does not demonstrate a phenotypic change compared to the wild type due to the presence of a paralogous gene performing the same function; a phenotype is only observed when one or more paralogs are knocked out in combination. This presents a challenge in a fundamental goal of genetics, linking genotypes to...
Show moreGenetic redundancy is a phenomenon where more than one gene encodes products that perform the same function. This frequently manifests experimentally as a single gene knockout mutant which does not demonstrate a phenotypic change compared to the wild type due to the presence of a paralogous gene performing the same function; a phenotype is only observed when one or more paralogs are knocked out in combination. This presents a challenge in a fundamental goal of genetics, linking genotypes to phenotypes, especially because it is difficult to determine a priori which gene pairs are redundant. Furthermore, while some factors that are associated with redundant genes have been identified, little is known about factors contributing to long-term maintenance of genetic redundancy. Here, we applied a machine learning approach to predict redundancy among benchmark redundant and nonredundant gene pairs in the model plant Arabidopsis thaliana. Predictions were validated using well-characterized redundant and nonredundant gene pairs. Additionally, we leveraged the availability of fitness and multi-omics data in the budding yeast Saccharomyces cerevisiae to build machine learning models for predicting genetic redundancy and related phenotypic outcomes (single and double mutant fitness) among paralogs, and to identify features important in generating these predictions. Collectively, our models of genetic redundancy provide quantitative assessments of how well existing data allow predictions of fitness and genetic redundancy, shed light on characteristics that may contribute to long-term maintenance of paralogs that are seemingly functionally redundant, and will ultimately allow for more targeted generation of phenotypically informative mutants, advancing functional genomic studies.
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Title: Local adaptation and fitness trade-offs
Creator: Dittmar, Emily Loring
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Adaptation generates and maintains genetic and phenotypic diversity. This is thought to occur due to trade-offs, where adaptation to one environment comes at a cost in another. Although trade-offs are believed to play a prominent role in the generation and maintenance of genetic and phenotypic diversity, the mechanisms by which adaptation leads to trade-offs are not well understood.My research explores the forces that lead to adaptive trade-offs in two systems. First, using a RIL mapping...
Show moreAdaptation generates and maintains genetic and phenotypic diversity. This is thought to occur due to trade-offs, where adaptation to one environment comes at a cost in another. Although trade-offs are believed to play a prominent role in the generation and maintenance of genetic and phenotypic diversity, the mechanisms by which adaptation leads to trade-offs are not well understood.My research explores the forces that lead to adaptive trade-offs in two systems. First, using a RIL mapping population created from natural populations of Arabidopsis thaliana, I studied the genetic basis of flowering time, a putatively adaptive trait and one that differs between the parental populations. I identified flowering time QTL in growth chambers that mimicked the natural temperature and photoperiod variation across the growing season in each native environment and compared the genomic locations of flowering time QTL to those of fitness (total fruit number) QTL from a previous three-year field study.In addition, I studied two populations of Leptosiphon parviflorus, an annual wildflower native to California. At Jasper Ridge biological preserve, populations of L. parviflorus grow on and off serpentine soil in close proximity. Due to its harsh growing conditions, serpentine soil exerts strong selective pressures on plants. Despite the close proximity of study populations (<100 m) and ongoing gene flow, reciprocal transplant studies demonstrate that these populations are locally adapted to their native soil types. To determine the selective agents operating in both habitats and the forces underlying fitness trade-offs, I performed manipulative experiments in the field and greenhouse. Results from these studies show that both soil moisture and competitive interactions are important for mediating fitness differences among the populations, and adaptation to serpentine soil might result in a cost to competitive ability.I also addressed the causes of flowering-time differences in these populations. Field reciprocal-transplant studies and watering manipulations in the greenhouse demonstrate the contribution of both the genotype and the environment to observed flowering-time differences. The plasticity of flowering time in response to soil type appears to be driven by differences in soil moisture. In addition, selection on flowering time was measured in both soil types across four years of study using a set of F5 advanced generation hybrids and found to differ among the habitats. Therefore, both selection and plasticity contribute to flowering-time differences between these populations and thus have likely played an important role in the initiation and/or maintenance of adaptive divergence in this system.Finally, the two populations differ in their flower color, a Mendelian trait. Pollinators do not discriminate among flower colors and are unlikely to exert selection on this trait. Instead, flower color may be related to stress tolerance if the causal gene has pleiotropic effects on other traits. Using a set of Near Isogenic Lines (NILs), I found that the flower color locus has an effect on survival in field soil and fecundity in benign conditions. Ongoing work is aimed at addressing the mechanisms underlying the relationship between flower color and soil adaptation.
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Title: Increasing student comprehension of evolution through laboratory investigations and simulations
Creator: McClintock, Steven W.
Date: 2008
Collection: Electronic Theses & Dissertations

Title: IDENTIFICATION OF LTR RETROTRANSPOSONS, EVALUATION OF GENOME ASSEMBLY, AND MODELING RICE DOMESTICATION
Creator: Ou, Shujun
Date: 2018
Collection: Electronic Theses & Dissertations
Description: The majority of fundamental theories in genetics and evolution were proposed prior to the discovery of DNA as the genetic material in 1952. Those include Darwin’s theory of evolution (1859), Mendelian genetics (1865), Wright and Fisher’s population genetics (1918), and McClintock’s transposition of genetic elements (1951). Nevertheless, the underlining mechanisms of those theories were not fully elucidated till the appearance of DNA sequencing technology. At present, technological advances...
Show moreThe majority of fundamental theories in genetics and evolution were proposed prior to the discovery of DNA as the genetic material in 1952. Those include Darwin’s theory of evolution (1859), Mendelian genetics (1865), Wright and Fisher’s population genetics (1918), and McClintock’s transposition of genetic elements (1951). Nevertheless, the underlining mechanisms of those theories were not fully elucidated till the appearance of DNA sequencing technology. At present, technological advances have minimized the cost for sequencing genomes. The real bottleneck to establish genomic resources is the annotation of genomic sequences. Long Terminal Repeat (LTR) retrotransposon is a major type of transposable genetic elements and dominating plant genomes. We developed a new method called LTR_retriever for accurate annotation of LTR retrotransposons. Further, we studied genome dynamics, genome size variation, and polyploidy origin using LTR retrotransposons. The presence of LTR retrotransposons challenges current sequencing and assembly techniques due to their size and repetitiveness. We proposed an unbiased metric called LTR Assembly Index (LAI) which utilizes the assembled LTR retrotransposons to evaluate continuity of genome assembly. We revealed the massive gain of continuity for assembly sequenced based on long-read techniques over short-read methods, and further proposed a standardized classification system for genome quality based on LAI. With high-quality genomes, we can extend our knowledge about microevolution events using a population of genomes. The domestication history of rice is still unresolved due to its complicated demographic history. We collected, re-mapped, and re-analyzed 3,485 cultivated and wild rice resequencing accessions. With data imputation, a total of 17.7 million high-quality single-nucleotide polymorphisms (SNPs) were identified. Our dataset is highly accurate as verified by cross-platform Affymetrix Microarray data, with a pairwise concordance rate of 99%. Combining phylogeny, PCA, and ADMIXTURE analyses, we present profound diversification among rice ecotypes.
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Title: Genome-wide association study reveals genes associated with mite recruitment phenotypes in the domesticated grapevine (vitis vinifera
Creator: LaPlante, Erika R.
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Plants in the grape genus Vitis have varying densities of trichomes and mite-domatia on their leaves, which facilitate the recruitment, retention, and reproduction of beneficial mites. By increasing the abundance of mites on grape leaves, these phenotypes promote a defense mutualism contributing to the control of grape pests and pathogens. Identification of the genes controlling these phenotypes would inform our understanding of the genetics underlying mite-plant mutualistic interactions and...
Show morePlants in the grape genus Vitis have varying densities of trichomes and mite-domatia on their leaves, which facilitate the recruitment, retention, and reproduction of beneficial mites. By increasing the abundance of mites on grape leaves, these phenotypes promote a defense mutualism contributing to the control of grape pests and pathogens. Identification of the genes controlling these phenotypes would inform our understanding of the genetics underlying mite-plant mutualistic interactions and could lead to breeding domesticated Vitis vinifera L. varieties that are naturally defended against pathogens. Little is known about the genetics underlying mite recruitment phenotypes in Vitis. We conducted a GWAS to determine the genetic architecture of mite recruitment traits in V. vinifera using 399 cultivars from a common garden diversity panel. We investigated eight traits previously established in the literature associated with an increase in beneficial mite abundance. We found single nucleotide polymorphisms (SNPs) significantly associated with each mite recruitment trait investigated. Corresponding gene annotations of SNP genetic coordinates revealed notable gene associations, including a trichome development gene, and a physiological defense response gene, suggesting these genetic regions may have a large impact on mediating mite-plant interactions in this species. Our findings are among the first to investigate which genes underly ecologically important mutualisms between plants and beneficial mites and suggest promising candidate genes for breeding and genetic editing to increase naturally occurring predator-based defenses in grapes.
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Title: Genome evolution of Campylobacter jejuni during experimental adaptation
Creator: Jerome, John Paul
Date: 2012
Collection: Electronic Theses & Dissertations
Description: Campylobacter jejuni is a leading cause of foodborne bacterial enteritis in humans. An important reservoir for C. jejuni is in chickens, but it has been shown to colonize a large host range. Passage through a mouse model of campylobacteriosis resulted in a hypervirulent phenotype in mice for C. jejuni strain NCTC11168. After analyzing the wild-type and mouse-adapted variants by phenotype assays, expression microarray, pulse-field gel...
Show moreCampylobacter jejuni is a leading cause of foodborne bacterial enteritis in humans. An important reservoir for C. jejuni is in chickens, but it has been shown to colonize a large host range. Passage through a mouse model of campylobacteriosis resulted in a hypervirulent phenotype in mice for C. jejuni strain NCTC11168. After analyzing the wild-type and mouse-adapted variants by phenotype assays, expression microarray, pulse-field gel electrophoresis and whole genome sequencing we discovered that the genetic changes in the mouse-adapted variant were confined to thirteen hypermutable regions of DNA in contingency loci. We also show that specific contingency loci changes occurred in parallel during mouse infection when reisolates from multiple mice were analyzed. Furthermore, a mathematical model that considers contingency loci mutation rates and patterns does not explain the observed changes. Taken together, this is the first experimental evidence that contingency loci play a role in the rapid genetic adaptation of C. jejuni to a host, which results in increased virulence. In contrast to the observed virulence increase by serial host passage, we showed that C. jejuni rapidly loses an essential host colonization determinant during adaptive laboratory evolution. Passage in broth culture selected for flagellar motility deficient C. jejuni cells in parallel for five independently evolved lines. Moreover, the loss of motility occurred by two genetic mechanisms: reversible and irreversible. Reversible loss of motility occurred early during broth adaptation, followed by irreversible motility loss in the majority of cells by the end of the experiment. Whole genome sequencing implicated diverse mutation events that resulted in the loss of gene expression necessary for flagellar biosynthesis. Furthermore, reversible mutations in homopolymeric DNA tracts of adenine/thymine residues, and irreversible types of mutation such as gene deletion, were discovered in the broth-evolved populations. In all evolved lines, an alternative sigma factor necessary for flagellar structural gene expression was removed from the genome. Overall, this dissertation contains the first accounts of C. jejuni experimental evolution. The results provide insight into the biological importance of reversible mutations in homopolymeric DNA tracts, and provide a basis for future studies of C. jejuni evolvability.
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Title: Factors influencing morphological evolution of the limbs in fossorial mammals (sciuridae and soricidae)
Creator: Swiderski, Donald L.
Date: 1990
Collection: Electronic Theses & Dissertations

Title: FITNESS EFFECTS OF KINSHIP DEPEND ON ECOLOGICAL CONTEXT IN THE AMERICAN TOAD (ANAXYRUS AMERICANUS)
Creator: Garnett, Sara Christine
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Studies of cooperation often ask how variation in kinship impacts the inclusive fitness payoffs of altruism. Hamilton’s rule defines this as a function of cooperation's costs and benefits, which in principle can vary widely across ecological contexts. In this dissertation, I address how kinship influences fitness, how selection balances fitness costs and benefits, and how the effects of kinship modulate the effects of other aspects of an organism’s environment using the American toad system....
Show moreStudies of cooperation often ask how variation in kinship impacts the inclusive fitness payoffs of altruism. Hamilton’s rule defines this as a function of cooperation's costs and benefits, which in principle can vary widely across ecological contexts. In this dissertation, I address how kinship influences fitness, how selection balances fitness costs and benefits, and how the effects of kinship modulate the effects of other aspects of an organism’s environment using the American toad system. I first asked whether tadpoles use chemical cues to perceive differences in relatedness and whether this variation affects the response of several fitness proxies to environmental cues. I found that tadpole growth rates differed in response to cues of resource and kinship environment. In another experiment, growth rate differed based on cues of relative size, with larger tadpoles outperforming smaller partners. This was affected by kinship, at least for smaller tadpoles, who grew more rapidly with a sibling. This indicates that chemical cues communicate information necessary for tadpoles to perceive aspects of their environment, which interact with relatedness to affect fitness.I then investigated whether relatedness influences growth and development in experimental groups of tadpoles, and whether other factors – such as density and nutrient availability – impact the fitness benefits of grouping with kin. In our experiments, groups composed of full-sib kin reached metamorphosis faster and at a larger size than mixtures of different sib groups. The benefits of these fitness components were significant in more competitive, resource-scarce environments, but negligible in less-competitive, resource-abundant environments. Kinship and resource abundance have an interactive effect on the fitness components we measured. Finally, I assessed tadpole aggregation preferences for kin compared to non-kin in the presence and absence of predator cues. In the presence of predator cues, tadpoles may be more likely to choose kin over non-kin. While increased body mass might result in a tadpole being more likely to avoid conspecifics in the presence of predator cues, we saw that larger tadpoles potentially increased the probability of choosing kin over non-kin. While these results were not significant, indicating that predator avoidance is likely not the primary driver of kin aggregation behavior in this species, they are suggestive of a kin-selected benefit to grouping.Taken together, these results help us understand the contexts in which we might expect relatedness to affect fitness, which could further contribute to our understanding of the evolution of social behavior. This emphasizes that the fitness benefits of kin-directed behavior are not identical in all circumstances, and that the ratio of costs to benefits may drive the evolution of different strategies depending on the environment.
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Title: Evolving Phenotypically Plastic Digital Organisms
Creator: Lalejini, Alexander
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The ability to dynamically respond to cues from the environment is a fundamental feature of most adaptive systems. In biological systems, changes to an organism based on environmental cues is called phenotypic plasticity. Indeed, phenotypic plasticity underlies many of the adaptive traits and developmental patterns found in nature and serves as a key mechanism for responding to spatially or temporally variable environments. Most computer programs require phenotypic plasticity, as they must...
Show moreThe ability to dynamically respond to cues from the environment is a fundamental feature of most adaptive systems. In biological systems, changes to an organism based on environmental cues is called phenotypic plasticity. Indeed, phenotypic plasticity underlies many of the adaptive traits and developmental patterns found in nature and serves as a key mechanism for responding to spatially or temporally variable environments. Most computer programs require phenotypic plasticity, as they must respond dynamically to stimuli such as user input, sensor data, et cetera. As such, phenotypic plasticity also has practical applications in genetic programming, wherein we apply the natural principles of evolution to automatically synthesize computer programs rather than writing them by hand. In this dissertation, I achieve two synergistic aims: (1) I use populations of self-replicating computer programs (digital organisms) to empirically study the conditions under which adaptive phenotypic plasticity evolves and how its evolution shapes subsequent evolutionary outcomes; and (2) I transfer insights from biology to develop novel genetic programming techniques in order to evolve more responsive (i.e., phenotypically plastic) computer programs. First, I illustrate the importance of mutation rate, environmental change, and partially-plastic building blocks for the evolution of adaptive plasticity. Next, I show that adaptive phenotypic plasticity stabilizes populations against environmental change, allowing them to more easily retain novel adaptive traits. Finally, I improve our ability to evolve phenotypically plastic computer programs with three novel genetic programming techniques: (1) SignalGP, which provides mechanisms to control code expression based on environmental cues, (2) tag-based genetic regulation to adjust code expression based on current context, and (3) tag-accessed memory to provide more dynamic mechanisms for storing data.
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Title: Evolutionary dynamics of 3D digital constructs
Creator: Stredwick, Jason Michael
Date: 2005
Collection: Electronic Theses & Dissertations

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