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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: 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: 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: Contextual influences on undergraduate biology students' reasoning and representations of evolutionary concepts
Creator: de Lima, Joelyn
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Context is the background or the settings of an event or idea. It is only when events or ideas are considered within the context in which they occur that they can be fully understood. In education, the application of knowledge communicated in one context to a different one is a central feature of learning. However, knowledge transfer can be affected by multiple factors including contexts used. Context plays a vital role in both shaping students’ learning and in eliciting their knowledge....
Show moreContext is the background or the settings of an event or idea. It is only when events or ideas are considered within the context in which they occur that they can be fully understood. In education, the application of knowledge communicated in one context to a different one is a central feature of learning. However, knowledge transfer can be affected by multiple factors including contexts used. Context plays a vital role in both shaping students’ learning and in eliciting their knowledge. Therefore, understanding how context can help or hinder learning and how context impacts knowledge assessment is important for improving science learning outcomes.For my dissertation, I studied contextual influences on the ways students reason and represent their knowledge. My studies explored two types of contexts: surface features of prompts provided to students (e.g., organism used) and the mode of response requested (e.g., written narratives vs constructed models). I analysed the effect of prompt surface features on the content of students’ written responses and on the architecture of models they constructed to explain evolution by natural selection. I also analysed the effect of mode on the content and level of scientific plausibility of students’ responses. In addition, I explored the association between instruction and prior achievement and susceptibility to contextual influences.My results indicate that prompt contextual features and mode of response are eliciting differences in the content of students’ representations. Contextual susceptibility decreased with instruction and higher prior academic achievement. This could indicate that they are novice learners and have a fragile understanding of either the subject matter (evolution), the alternative representation that was required (constructing models), or of both the subject matter and the representation. Incorporating multiple contexts and modes of assessment has potential to generate a more holistic view of students’ understanding and may promote greater transfer by requiring students to think and reason across contexts.
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Title: Digital Evolution in Experimental Phylogenetics and Evolution Education
Creator: Kohn, Cory
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The creation and evaluation of known evolutionary histories and the implementation of student investigatory experiences on evolution are difficult endeavors that have only recently been feasible. The research presented in this dissertation is related in their shared use of digital evolution with Avidians as a model study system, both to conduct science research in experimental phylogenetics and to conduct education research in curricular intervention to aid student understanding.I first...
Show moreThe creation and evaluation of known evolutionary histories and the implementation of student investigatory experiences on evolution are difficult endeavors that have only recently been feasible. The research presented in this dissertation is related in their shared use of digital evolution with Avidians as a model study system, both to conduct science research in experimental phylogenetics and to conduct education research in curricular intervention to aid student understanding.I first present background discussions on the Avidian digital evolution study system—as implemented in Avida and Avida-ED—and its favorable use in experimental phylogenetics and biology education owing to its greater biological realism than computational simulations, and greater utility and generality than biological systems. Prior work on conducting experimental evolution for use in phylogenetics and work on developing undergraduate lab curricula using experimental evolution are also reviewed. I establish digital evolution as an effective method for phylogenetic inference validation by demonstrating that results from a known Avidian evolutionary history are concordant, under similar conditions, to established biological experimental phylogenetics work. I then further demonstrate the greater utility and generality of digital evolution over biological systems by experimentally testing how phylogenetic accuracy may be reduced by complex evolutionary processes operating singly or in combination, including absolute and relative degrees of evolutionary change between lineages (i.e., inferred branch lengths), recombination, and natural selection. These results include that directional selection aids phylogenetic inference, while stabilizing selection impedes it. By evaluating clade accuracy and clade resolvability across treatments, I evaluate measures of tree support and its presentation in the form of consensus topologies and I offer several general recommendations for systematists. Using a larger and more biologically realistic experimental design, I systematically examine a few of the complex processes that are hypothesized to affect phylogenetic accuracy—natural selection, recombination, and deviations from the model of evolution. By analyzing the substitutions that occurred and calculating selection coefficients for derived alleles throughout their evolutionary trajectories to fixation, I show that molecular evolution in these experiments is complex and proceeding largely as would be expected for biological populations. Using these data to construct empirical substitution models, I demonstrate that phylogenetic inference is incredibly robust to significant molecular evolution model deviations. I show that neutral evolution in the presence of always-occurring population processes, such as clonal or Hill-Robertson interference and lineage sorting, result in reduced clade support, and that selection and especially recombination, including their joint occurrence, restore this otherwise-reduced phylogenetic accuracy. Finally, this work demonstrates that inferred branch lengths are often quite inaccurate despite clade support being accurate. While phylogenetic inference methods performed relatively well in both theoretically facile and challenging molecular evolution scenarios, their accuracy in clade support might be a remarkable case of being right for misguided reasons, since branch length inference were largely inaccurate, and drastically different models of evolution made little difference. This work highlights the need for further research that evaluates phylogenetic methods under experimental conditions and suggests that digital evolution has a role here. Finally, I examine student understanding of the importance of biological variation in the context of a course featuring a digital evolution lab. I first describe the Avida-ED lab curriculum and its fulfillment of calls for reform in education. Then I describe the specific education context and other course features that aim to address student conceptualization of variation. I present a modified published assessment on transformational and variational understanding and findings regarding student understanding of variation within an evolution education progression. Finally, I offer suggestions on incorporating course material to engage student understanding of variation.
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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: 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: Do latex and resin canals spur plant diversification? : re-examining a classic example of escape and radiate coevolution
Creator: Foisy, Michael
Date: 2020
Collection: Electronic Theses & Dissertations
Description: The association between increased lineage diversification rates and the evolution of latex and resin canals is widely cited as a paradigmatic example of Ehrlich and Raven's 'escape-and-radiate' hypothesis of co-evolution. However, it has been nearly three decades since these plant defenses have been examined as key innovations, and updates to phylogenetic comparative methods, plant molecular systematics, and phenotypic data warrant a reassessment of this classic finding. I gathered data on...
Show moreThe association between increased lineage diversification rates and the evolution of latex and resin canals is widely cited as a paradigmatic example of Ehrlich and Raven's 'escape-and-radiate' hypothesis of co-evolution. However, it has been nearly three decades since these plant defenses have been examined as key innovations, and updates to phylogenetic comparative methods, plant molecular systematics, and phenotypic data warrant a reassessment of this classic finding. I gathered data on latex and resin canals across 345 families and 986 genera of vascular plants and conducted a multi-scale test of the association between these traits and lineage diversification rates. At a broad scale (across clades), I used sister-clade comparisons to test whether 28 canal-bearing clades had higher net diversification rates than their canal-lacking sister clades. At a finer scale (within clades), I used ancestral state reconstructions and phylogenetic models of lineage diversification rates to examine the relationship between trait evolution and the timing of diversification rate shifts in two better-characterized clades - Araceae and Papaveraceae. At both scales of analyses, I found poor support for the predicted relationship between diversification and the evolution of latex and resin canals. This re-examination reveals that there is no longer strong evidence for latex or resin canals as general, consistently replicable drivers of species diversity across plants. However, I could not rule out a relationship in all groups, and therefore argue that theoretical and empirical work aimed at understanding ecological factors that condition 'escape-and-radiate' dynamics will allow for more nuanced tests of the hypothesis in the future.
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Title: Developing Reverse Genetic Tools in Weakly Electric Fish : Investigating Electric Organ in vivo scn4aa Function Through CRISPR Knockouts and Morpholino Knockdowns
Creator: Constantinou, Savvas James
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The ability to determine gene function allows research to progress at one of the finest scales in biology and is a goal in electric fish research. Reverse genetics allows researchers to determine gene function and would aid the electric fish community in beginning to answer some of the broadest and most complicated questions in biology such as linking genotype to phenotype and understanding the processes that lead to biological diversity. In this dissertation, I describe the development of...
Show moreThe ability to determine gene function allows research to progress at one of the finest scales in biology and is a goal in electric fish research. Reverse genetics allows researchers to determine gene function and would aid the electric fish community in beginning to answer some of the broadest and most complicated questions in biology such as linking genotype to phenotype and understanding the processes that lead to biological diversity. In this dissertation, I describe the development of two major reverse genetic tools for use in the electric fish system: CRISPR/Cas9 genome editing and morpholinos. To develop these tools, I also produced protocols for in-vitro breeding, husbandry, and single-cell embryo microinjections. In the first chapter, I describe in-vitro breeding, husbandry, and single-cell embryo microinjections and demonstrate that CRISPR/Cas9 is a promising tool for future electric fish research by targeting nonsense mutations to scn4aa in the mormyrid Brienomyrus brachyistius and gymnotiform Brachyhypopomus gauderio, two independently evolved lineages of weakly electric fish, resulting in a reduction in the electric organ discharge amplitude. In the second chapter, I provide electric fish researchers with a detailed analysis of our many successes and failures applying CRISPR/Cas9 methods to this system and discuss future suggestions on how to best apply them to novel electric fish research. In the third chapter, I describe my efforts to utilize vivo-morpholinos in mormyrid electric fish. While a single early pilot study I performed demonstrated vivo-morpholinos can reduce target gene mRNA levels and cause a phenotypic effect, my efforts to replicate these findings demonstrate inconsistent performance: control vivo-morpholino and scn4aa targeting vivo-morpholino injected fish had indistinguishable effects on electric organ discharge amplitude. Due to additional concerns of toxicity, I suggest morpholinos are not an ideal reverse genetic tool in Brienomyrus brachyistius and should only be utilized for future research with caution.
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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: 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: Factors influencing morphological evolution of the limbs in fossorial mammals (sciuridae and soricidae)
Creator: Swiderski, Donald L.
Date: 1990
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: 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: Assessing the viability of the shifting balance process
Creator: Moore, Francis B.,-G
Date: 1996
Collection: Electronic Theses & Dissertations

Title: Biodiversity of tropical Scolytinae (Coleoptera: Curculionidae)
Creator: Dole, Stephanie Alexandra
Date: 2008
Collection: Electronic Theses & Dissertations

Title: The evolutionary origins of memory use in navigation
Creator: Grabowski, Laura M.
Date: 2009
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: 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: A differential evolution approach to feature selection in genomic prediction
Creator: Whalen, Ian
Date: 2018
Collection: Electronic Theses & Dissertations
Description: The use of genetic markers has become widespread for prediction of genetic merit in agricultural applications and is a beginning to show promise for estimating propensity to disease in human medicine. This process is known as genomic prediction and attempts to model the mapping between an organism's genotype and phenotype. In practice, this process presents a challenging problem. Sequencing and recording phenotypic traits are often expensive and time consuming. This leads to datasets often...
Show moreThe use of genetic markers has become widespread for prediction of genetic merit in agricultural applications and is a beginning to show promise for estimating propensity to disease in human medicine. This process is known as genomic prediction and attempts to model the mapping between an organism's genotype and phenotype. In practice, this process presents a challenging problem. Sequencing and recording phenotypic traits are often expensive and time consuming. This leads to datasets often having many more features than samples. Common models for genomic prediction often fall victim to overfitting due to the curse of dimensionality. In this domain, only a fraction of the markers that are present significantly affect a particular trait. Models that fit to non-informative markers are in effect fitting to statistical noise, leading to a decrease in predictive performance. Therefore, feature selection is desirable to remove markers that do not appear to have a significant effect on the trait being predicted. The method presented here uses differential evolution based search for feature selection. This study will characterize differential evolution's efficacy in feature selection for genomic prediction and present several extensions to the base search algorithm in an attempt to apply domain knowledge to guide the search toward better solutions.
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