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Title: Diversity of South American ambrosia beetles (Curculionidae : Scolytinae: Xyleborini) and their fungal partners
Creator: Osborn, Rachel Kathryn
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Ambrosia beetles from the tribe Xyleborini (Coleoptera: Curculionidae: Scolytinae) small, haplodiploid beetles that farm nutritional fungi on the walls of tunnels they excavate in the xylem of dead or nearly dead trees. These biological traits make them successful participants in worldwide wooded ecosystems and facilitate their human-mediated invasion beyond their native ranges. A minority of these introduced species are classified as pests because of the physical damage they cause to their...
Show moreAmbrosia beetles from the tribe Xyleborini (Coleoptera: Curculionidae: Scolytinae) small, haplodiploid beetles that farm nutritional fungi on the walls of tunnels they excavate in the xylem of dead or nearly dead trees. These biological traits make them successful participants in worldwide wooded ecosystems and facilitate their human-mediated invasion beyond their native ranges. A minority of these introduced species are classified as pests because of the physical damage they cause to their plant hosts, or because they vector pathogenic fungi that infect ornamental, lumber, and forest trees. Most of the current knowledge on the diversity of xyleborine beetles and their fungi centers around species found in North America, Asia, and Europe. Little is known about the ambrosia partnerships in the Neotropics, which is concerning because South America is a strong trading partner with the US and the potential for new invasive Xyleborini to be imported from this area is significant. Continuing forest damage caused by invasive Xyleborini/fungi inspires robust research efforts to describe these symbionts and document their biological traits. Considerable efforts are required to enhance such endeavors in underrepresented regions such as South America and Africa. To increase understanding of the South American Xyleborini and their associated fungi, I compiled current knowledge of their historical and contemporary taxonomic records, biological records, and ecological studies. I also completed surveys throughout Ecuador to collect beetles and fungi. Molecular analysis of fungi isolated from Ecuadorian beetles reveals that several Coptoborus species associate with Fusarium fungi, including the ambrosia Fusarium Clade (AFC) that has previously been recovered from Euwallacea spp. and Xyleborus ferrugineus in Central America, Florida, California, Israel, and Asia. Examination of the morphology of some South American xyleborine specimens previously classified as Coptoborus spp. suggests a high similarity to Xyleborus spp. from Africa. Phylogenetic analysis of these South American and African beetles as well as morphological assessment of additional specimens necessitates the designation of a new genus Xenoxylebora gen. nov. containing species endemic to both continents. This unusual distribution demonstrates the ability of these ambrosia beetles to survive long-distance trans-oceanic dispersal.
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Title: MECHANISMS UNDERLYING DESICCATION RESISTANCE IN DROSOPHILA SPECIES
Creator: Wang, Zinan
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Adaptation to various and extreme environments is key to long-term species persistence. Reducing water loss is important for organisms adapting to different terrestrial environments. In Drosophila fruit flies and other terrestrial insects, their small body size and large surface areas to volume ratios make them vulnerable to desiccation stress. Their ability to prevent water loss is crucial for their survival. Previous studies have suggested that cuticular water loss accounts for the majority...
Show moreAdaptation to various and extreme environments is key to long-term species persistence. Reducing water loss is important for organisms adapting to different terrestrial environments. In Drosophila fruit flies and other terrestrial insects, their small body size and large surface areas to volume ratios make them vulnerable to desiccation stress. Their ability to prevent water loss is crucial for their survival. Previous studies have suggested that cuticular water loss accounts for the majority of water loss in insects and hypothesized that differences in cuticular hydrocarbon (CHC) content accounted for differences in desiccation resistance between mesic and desert species. However, the specific association between different CHC components and desiccation has not been established, and the genetic mechanisms underlying the evolution of these CHC components that confer high desiccation resistance have not been elucidated. This dissertation investigated how the evolution of CHCs in insects affected desiccation resistance and elucidates the genetic mechanisms underlying their evolution. With a comprehensive association study of desiccation resistance and CHCs in 46 Drosophila species and 4 species in closely-related genera, the analyses showed that mbCHC chain lengths were important predictors of desiccation resistance and longer mbCHCs contributed to higher desiccation resistance. This dissertation further investigated the genetic and molecular mechanisms underlying longer chain mbCHCs and higher desiccation resistance in a desert Drosophila species, Drosophila mojavensis. A fatty acyl-CoA elongase gene, mElo (methyl-branched CHC Elongase), was identified in Drosophila species for the elongation of mbCHCs. Overexpression experiments in D. melanogaster demonstrated that coding changes in mElo from D. mojavensis lead to longer mbCHCs and higher desiccation resistance. Further experiments using CRISPR-Cas9 to knock out mElo from D. mojavensis showed that knockout of this gene decreased the production of the longest mbCHCs and significantly reduced desiccation resistance at their ecological-relevant temperature. Results from this dissertation elucidate the molecular and evolutionary mechanisms that enable species to reduce water loss and maintain water balance as our planet gets warmer and more arid in the next few decades.
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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: 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: 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: The Evolutionary Origins of Cognition : Understanding the early evolution of biological control systems and general intelligence
Creator: Carvalho Pontes, Anselmo
Date: 2021
Collection: Electronic Theses & Dissertations
Description: In the last century, we have made great strides towards understanding natural cognition and recreating it artificially. However, most cognitive research is still guided by an inadequate theoretical framework that equates cognition to a computer system executing a data processing task. Cognition, whether natural or artificial, is not a data processing system; it is a control system.At cognition's core is a value system that allows it to evaluate current conditions and decide among two or more...
Show moreIn the last century, we have made great strides towards understanding natural cognition and recreating it artificially. However, most cognitive research is still guided by an inadequate theoretical framework that equates cognition to a computer system executing a data processing task. Cognition, whether natural or artificial, is not a data processing system; it is a control system.At cognition's core is a value system that allows it to evaluate current conditions and decide among two or more courses of action. Memory, learning, planning, and deliberation, rather than being essential cognitive abilities, are features that evolved over time to support the primary task of deciding “what to do next”. I used digital evolution to recreate the early stages in the evolution of natural cognition, including the ability to learn. Interestingly, I found cognition evolves in a predictable manner, with more complex abilities evolving in stages, by building upon previous simpler ones. I initially investigated the evolution of dynamic foraging behaviors among the first animals known to have a central nervous system, Ediacaran microbial mat miners. I then followed this up by evolving more complex forms of learning. I soon encountered practical limitations of the current methods, including exponential demand of computational resources and genetic representations that were not conducive to further scaling. This type of complexity barrier has been a recurrent issue in digital evolution. Nature, however, is not limited in the same ways; through evolution, it has created a language to express robust, modular, and flexible control systems of arbitrary complexity and apparently open-ended evolvability. The essential features of this language can be captured in a digital evolution platform. As an early demonstration of this, I evolved biologically plausible regulatory systems for virtual cyanobacteria. These systems regulate the cells' growth, photosynthesis and replication given the daily light cycle, the cell's energy reserves, and levels of stress. Although simple, this experimental system displays dynamics and decision-making mechanisms akin to biology, with promising potential for open-ended evolution of cognition towards general intelligence.
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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: 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: 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: 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: 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: 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: 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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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: 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: Evolution and evolvability in changing environments
Creator: Canino-Koning, Rosangela
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "The specific meaning of the term 'evolvability' is heavily debated, but most definitions can be summarized as: the potential of populations and genomes to produce adaptive variation and complex structures in response to mutation and selection. Changing environments are thought to play a significant role in shaping and promoting evolvability through alternating selective pressures. In this dissertation, I will discuss my recent research on the interplay between changing environments,...
Show more"The specific meaning of the term 'evolvability' is heavily debated, but most definitions can be summarized as: the potential of populations and genomes to produce adaptive variation and complex structures in response to mutation and selection. Changing environments are thought to play a significant role in shaping and promoting evolvability through alternating selective pressures. In this dissertation, I will discuss my recent research on the interplay between changing environments, evolvability, genetic architecture, and the evolution of horizontal gene transfer (HGT), an information-rich mutagenic function that is ubiquitous in nature. Before delving into my own research, however, I begin in the first chapter by providing a survey of current literature on each of these topics, with emphases on how they are believed to arise, how they affect subsequent evolution, and how they relate to each other. Genetic architecture and population dynamics clearly have a complex interplay in ongoing evolutionary dynamics. Evolutionary history, population diversity, modularity, and task size all play a role in determining the location and characteristics of populations in genotype space, and alter the genotype to phenotype map that permits neutral genetic variation. All of these features contribute to evolvability. In Chapter 2, I demonstrate how changing environments provided a sufficient selective pressure to produce quasi-modular genetic architectures that allow for rapid adaptation to the meta-environment of environmental change. Horizontal gene transfer is a highly regulated, ubiquitous, and ancient mechanism for exchanging genetic material between unrelated organisms. In the third chapter, I explore conditions which may have led to the evolution of horizontal gene transfer through transformation, and identify mechanisms that might support its continued performance. In Chapter 4, I compare the fitness and phenotypic effects of the HGT process against other types of increasingly less information rich mutational operators. I demonstrate that not only is HGT selected for in harsh changing environments, but that other mutagenic instructions that contain less information, or provide lesser fitness benefits are not similarly selected for. In the fifth chapter, I explore the long-term evolutionary potential of populations evolved in changing environments by evolving two different populations, one evolved in a minimal changing environment, and the other in a rich changing environment, and exposing them to a brand new environment. I demonstrate that while populations adapted to harsh changing environments are indeed able to adapt quickly to previously seen environmental changes, that these populations do not fare as well in brand new environments. Rather, benign changing environments perform best in measures of task discovery and exploration. In the final chapter, I conclude with a synthesis of my results, along with implications for the field, as well as identification of some new directions for pursuing my research into changing environments."--Pages ii-iii.
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Title: Balancing convergence and diversity in evolutionary single, multi and many objectives
Creator: Seada, Haitham
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Single objective optimization targets only one solution, that is usually the global optimum. On the other hand, the goal of multiobjective optimization is to represent the whole set of trade-off Pareto-optimal solutions to a problem. For over thirty years, researchers have been developing Evolutionary Multiobjective Optimization (EMO) algorithms for solving multiobjective optimization problems. Unfortunately, each of these algorithms were found to work well on a specific range of objective...
Show more"Single objective optimization targets only one solution, that is usually the global optimum. On the other hand, the goal of multiobjective optimization is to represent the whole set of trade-off Pareto-optimal solutions to a problem. For over thirty years, researchers have been developing Evolutionary Multiobjective Optimization (EMO) algorithms for solving multiobjective optimization problems. Unfortunately, each of these algorithms were found to work well on a specific range of objective dimensionality, i.e. number of objectives. Most researchers overlooked the idea of creating a cross-dimensional algorithm that can adapt its operation from one level of objective dimensionality to the other. One important aspect of creating such algorithm is achieving a careful balance between convergence and diversity. Researchers proposed several techniques aiming at dividing computational resources uniformly between these two goals. However, in many situations, only either of them is difficult to attain. Also for a new problem, it is difficult to tell beforehand if it will be challenging in terms of convergence, diversity or both. In this study, we propose several extensions to a state-of-the-art evolutionary many-objective optimization algorithm - NSGA-III. Our extensions collectively aim at (i) creating a unified optimization algorithm that dynamically adapts itself to single, multi- and many objectives, and (ii) enabling this algorithm to automatically focus on either convergence, diversity or both, according to the problem being considered. Our approach augments the already existing algorithm with a niching-based selection operator. It also utilizes the recently proposed Karush Kuhn Tucker Proximity Measure to identify ill-converged solutions, and finally, uses several combinations of point-to-point single objective local search procedures to remedy these solutions and enhance both convergence and diversity. Our extensions are shown to produce better results than state-of-the-art algorithms over a set of single, multi- and many-objective problems."--Pages ii-iii.
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