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Title: Species pluralism
Creator: Holmes, John Alan
Date: 2000
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: Understanding the role of standing genetic variation in functional genetics and compensatory evolution
Creator: Chari, Sudarshan R.
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Conventionally the phenotypic outcome of a mutation is considered to be due to a specific DNA lesion. But it has long been known that mutational effects can be conditional on environment (GxE) and genetic background (GxG). Thus it is standard practice to perform experiments by controlling for rearing environment and using co-isogenic strains. Though such a controlled approach has been very successful in enabling many discoveries, by not considering conditional effects our understanding of...
Show moreConventionally the phenotypic outcome of a mutation is considered to be due to a specific DNA lesion. But it has long been known that mutational effects can be conditional on environment (GxE) and genetic background (GxG). Thus it is standard practice to perform experiments by controlling for rearing environment and using co-isogenic strains. Though such a controlled approach has been very successful in enabling many discoveries, by not considering conditional effects our understanding of biological systems is incomplete. My research utilized conditionality in terms of genetic background and standing genetic variation therein to understand whether mutational interactions can themselves be background dependent. I demonstrated that a majority of mutational interactions identified via a dominant modifier screen are background dependent. Extending this idea of contingency in terms of standing genetic variation to the phenomenon of compensatory evolution in the presence of deleterious mutations, I demonstrated that natural populations of Drosophila melanogaster possess standing genetic variation for compensatory alleles to ameliorate even severe phenotypic defects. I further demonstrated that, despite considerable standing variation to ameliorate the focal phenotype perturbed by the mutation, natural selection exploits alternative evolutionary trajectories to recover fitness. Additionally this model system also allowed me to understand that loss of sexual signaling can be compensated by modulating behavioural and life history traits.
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Title: 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: Evolution of cooperation in the light of information theory
Creator: Mirmomeni, Masoud
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Cooperation is ubiquitous in different biological levels and is necessary for evolution to shape the life and create new forms of organization. Genes cooperate in controlling cells; cells efficiently collaborate together to produce cohesive multi-cellular organisms; members of insect colonies and animal clans cooperate in protecting the colony and providing food. Cooperation means that members of a group bear a cost, c, for another individuals to earn a benefit, b. While cooperators of the...
Show moreCooperation is ubiquitous in different biological levels and is necessary for evolution to shape the life and create new forms of organization. Genes cooperate in controlling cells; cells efficiently collaborate together to produce cohesive multi-cellular organisms; members of insect colonies and animal clans cooperate in protecting the colony and providing food. Cooperation means that members of a group bear a cost, c, for another individuals to earn a benefit, b. While cooperators of the group help others by paying a cost, defectors receive the benefits of this altruistic behavior without providing any service in return to the group. To address this dilemma, here we use a game theoretic approach to model and study evolutionary dynamics that can lead to unselfish behavior. Evolutionary game theory is an approach to study frequency-dependent systems. In evolutionary games the fitness of individuals depends on the relative abundance of the various types in the population. We explore different strategies and different games such as iterated games between players with conditional strategies, multi player games, and iterated games between fully stochastic strategies in noisy environments to find the necessity conditions that lead to cooperation. Interestingly, we see that in all of these games communication is the key factor for maintaining cooperation among selfish individuals. We show that communication and information exchange is necessary for the emergence of costly altruism, and to maintain cooperation in the group there should be minimum rate of communication between individuals. We quantify this minimum amount of information exchange, which is necessary for individuals to exhibit cooperative behavior, by defining a noisy communication channel between them in iterated stochastic games and measuring the communication rate (in bits) during the break down of cooperation.
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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: Microbial diversity and metabolic potential of the serpentinite subsurface environment
Creator: Twing, Katrina Irene
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Serpentinization is the hydrous alteration of mafic rocks to form serpentine minerals and magnetite. The reactions of this alteration result in elevated pH of the surrounding fluids, abiotic generation of H2, CH4 (and other organic molecules), and depletion of dissolved inorganic carbon. Thus, serpentinization has implications for the origin of life on Earth and possibly Mars and other planetary bodies with water. The microbial diversity of continental serpentinite systems consistently shows...
Show moreSerpentinization is the hydrous alteration of mafic rocks to form serpentine minerals and magnetite. The reactions of this alteration result in elevated pH of the surrounding fluids, abiotic generation of H2, CH4 (and other organic molecules), and depletion of dissolved inorganic carbon. Thus, serpentinization has implications for the origin of life on Earth and possibly Mars and other planetary bodies with water. The microbial diversity of continental serpentinite systems consistently shows communities that are dominated by two major taxa – microaerophilic Betaproteobacteria and anaerobic Clostridia. Previous studies relied on few samples collected from natural springs or seeps, meaning that the flow path of fluids from the subsurface process of serpentinization was unknown. The Coast Range Ophiolite Microbial Observatory (CROMO), a set of wells drilled into the actively serpentinizing subsurface environment in northern California, was established in northern California to gain a better understanding of the habitability and microbial functions within the serpentinite subsurface environment. This dissertation represents a culmination of microbiological investigations into the serpentinite subsurface environment at CROMO to identify the microbial inhabitants of subsurface fluids, rocks, and in situ colonization experiments using molecular methods and high-throughput sequencing. The CROMO wells represent a broad range of geochemical gradients and pH and the concentrations of carbon monoxide and methane have the strongest correlation with microbial community composition. The most extremely high pH wells were inhabited exclusively by a single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia, while more moderate pH wells exhibited greater diversity. Genes involved in the metabolism of hydrogen, carbon monoxide, and carbon fixation were abundant in the extreme pH fluids, while genes for metabolizing methane were exclusively in the moderate pH wells. The subsurface environment is an amalgamation of fluids and rocks, and as such, studying fluids alone only gives half the story. CROMO represents the first drill campaign into the continental serpentinite environment and the microbial diversity of serpentinite cores to a depth of 45 meters below surface suggests that specific geological features harbor different microbial communities. Archaea, previously undetected at CROMO, dominated cores containing magnetite-bearing serpentine, while bacteria were more abundant in layers containing clay particles. Additionally, organisms involved in the cycling of nitrogen and methane were found associated with core materials, indicating core-associated communities may have strong biogeochemical roles within the serpentinite subsurface environment. Given that microbial communities appear to vary with geological composition and that serpentinite fluids are a challenging habitat for life, depleted in inorganic carbon and electron acceptors, microbe-mineral interactions within the serpentinite subsurface environment through the use of in situ colonization devices to see if communities were able to utilize inorganic carbon in calcite or ferric iron as a terminal electron acceptor from magnetite. In the highest pH well, calcite led to an increased abundance of Clostridia and Deinococcus, while magnetite led to an increase in diversity, including Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, suggesting further that mineralogical composition of solids within the subsurface impact community composition. The data discussed here further our understanding of life associated with serpentinite fluids and minerals within the subsurface environment.
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Title: Coexistence in temporally variable environments : eco-evolutionary perspectives
Creator: Kremer, Colin T.
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Ecological systems are rarely constant through time. The abundances of predators & prey and competitors & mutualists fluctuate, driven by biotic interactions and underlying variation in precipitation, nutrients, and temperature. This reality challenges our ability to study ecology and disentangle its underlying mechanisms, both empirically and theoretically. Temporal variation is more than just a nuisance: it contributes to creating and maintaining the diversity of ecological communities, as...
Show moreEcological systems are rarely constant through time. The abundances of predators & prey and competitors & mutualists fluctuate, driven by biotic interactions and underlying variation in precipitation, nutrients, and temperature. This reality challenges our ability to study ecology and disentangle its underlying mechanisms, both empirically and theoretically. Temporal variation is more than just a nuisance: it contributes to creating and maintaining the diversity of ecological communities, as changing environmental conditions favor different species at different times. Tradeoffs limit the ability of individual species to perform optimally in every situation; as a consequence, times that are the best for some species are likely to be the worst for others. Temporal variation can also drive evolution by imposing selective pressures on the traits that allow species to succeed under particular conditions. Together, the interaction of ecological and evolutionary processes influences how many species can coexist and their identity and traits. To better understand the diversity, composition, and function of communities, I adopt a synthetic, eco-evolutionary approach to studying coexistence in temporally variable environments. I seek to understand how evolution modifies the functioning of ecological communities and under what conditions this is possible. My work includes both theoretical investigations, applying mathematical tools and approximations to the dissection, analysis, and interpretation of models, and efforts to create models that generate testable predictions.
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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: Evolution of laboratory and natural populations of Escherichia coli
Creator: Maddamsetti, Rohan
Date: 2016
Collection: Electronic Theses & Dissertations
Description: My dissertation spans two dichotomies: evolution in the laboratory versus evolution in nature, and asexual versus sexual evolutionary dynamics. In Chapter 1 I describe asexual evolutionary dynamics in one population of Lenski’s long-term evolution experiment with Escherichia coli. I describe cohorts of mutations that sweep to fixation together as characteristic of clonal interference dynamics. I also describe an ecological interaction that evolved and then went extinct after thousands of...
Show moreMy dissertation spans two dichotomies: evolution in the laboratory versus evolution in nature, and asexual versus sexual evolutionary dynamics. In Chapter 1 I describe asexual evolutionary dynamics in one population of Lenski’s long-term evolution experiment with Escherichia coli. I describe cohorts of mutations that sweep to fixation together as characteristic of clonal interference dynamics. I also describe an ecological interaction that evolved and then went extinct after thousands of generations, and discuss how such interactions affect cohorts of mutations. In Chapter 2 I report that conserved core genes tend to be targets of selection in the long-term experiment. In Chapter 3, I investigate the surprising observation that synonymous genetic diversity is not uniform across the genomes of natural E. coli isolates. This observation is surprising because in clonal organisms with a constant point mutation rate, synonymous diversity should be constant across the genome. I use patterns of synonymous mutations in the long-term experiment to argue that genome-wide variation in the mutation rate does not adequately explain patterns of synonymous genetic diversity. In Chapter 4, I propose that recombination and gene flow could account for genome-wide variation in synonymous genetic diversity. In Chapter 5, I analyze E. coli genomes isolated from an evolution experiment with recombination in which E. coli K-12 with known growth defects could donate genetic material to recipient populations founded by long-term experiment clones. The degree of recombination varied dramatically across sequenced clones. The strongest predictor of successful transfer was proximity to the oriT origin of transfer in the K-12 donors. Donor alleles close to oriT replaced their recipient counterparts at a high rate, and in many of those cases, known beneficial mutations in the recipients were replaced by donor alleles.
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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: 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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Title: Evolution of distributed behavior
Creator: Knoester, David B.
Date: 2011
Collection: Electronic Theses & Dissertations
Description: In this dissertation, we describe a study in the evolution of distributed behavior, where evolutionary algorithms are used to discover behaviors for distributed computing systems. We define distributed behavior as that in which groups of individuals must both cooperate in working towards a common goal and coordinate their activities in a harmonious fashion. As such, communication among individuals is necessarily a key component of distributed behavior, and we have identified three classes of...
Show moreIn this dissertation, we describe a study in the evolution of distributed behavior, where evolutionary algorithms are used to discover behaviors for distributed computing systems. We define distributed behavior as that in which groups of individuals must both cooperate in working towards a common goal and coordinate their activities in a harmonious fashion. As such, communication among individuals is necessarily a key component of distributed behavior, and we have identified three classes of distributed behavior that require communication: data-driven behaviors, where semantically meaningful data is transmitted between individuals; temporal behaviors, which are based on the relative timing of individuals' actions; and structural behaviors, which are responsible for maintaining the underlying communication network connecting individuals. Our results demonstrate that evolutionary algorithms can discover groups of individuals that exhibit each of these different classes of distributed behavior, and that these behaviors can be discovered both in isolation (e.g., evolving a purely data-driven algorithm) and in concert (e.g., evolving an algorithm that includes both data-driven and structural behaviors). As part of this research, we show that evolutionary algorithms can discover novel heuristics for distributed computing, and hint at a new class of distributed algorithm enabled by such studies.The majority of this research was conducted with the Avida platform for digital evolution, a system that has been proven to aid researchers in understanding the biological process of evolution by natural selection. For this reason, the results presented in this dissertation provide the foundation for future studies that examine how distributed behaviors evolved in nature. The close relationship between evolutionary biology and evolutionary algorithms thus aids our study of evolving algorithms for the next generation of distributed computing systems.
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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: Genome evolution of Campylobacter jejuni during experimental adaptation
Creator: Jerome, John Paul
Date: 2012
Collection: Electronic Theses & Dissertations
Description: Campylobacter jejuni is a leading cause of foodborne bacterial enteritis in humans. An important reservoir for C. jejuni is in chickens, but it has been shown to colonize a large host range. Passage through a mouse model of campylobacteriosis resulted in a hypervirulent phenotype in mice for C. jejuni strain NCTC11168. After analyzing the wild-type and mouse-adapted variants by phenotype assays, expression microarray, pulse-field gel...
Show moreCampylobacter jejuni is a leading cause of foodborne bacterial enteritis in humans. An important reservoir for C. jejuni is in chickens, but it has been shown to colonize a large host range. Passage through a mouse model of campylobacteriosis resulted in a hypervirulent phenotype in mice for C. jejuni strain NCTC11168. After analyzing the wild-type and mouse-adapted variants by phenotype assays, expression microarray, pulse-field gel electrophoresis and whole genome sequencing we discovered that the genetic changes in the mouse-adapted variant were confined to thirteen hypermutable regions of DNA in contingency loci. We also show that specific contingency loci changes occurred in parallel during mouse infection when reisolates from multiple mice were analyzed. Furthermore, a mathematical model that considers contingency loci mutation rates and patterns does not explain the observed changes. Taken together, this is the first experimental evidence that contingency loci play a role in the rapid genetic adaptation of C. jejuni to a host, which results in increased virulence. In contrast to the observed virulence increase by serial host passage, we showed that C. jejuni rapidly loses an essential host colonization determinant during adaptive laboratory evolution. Passage in broth culture selected for flagellar motility deficient C. jejuni cells in parallel for five independently evolved lines. Moreover, the loss of motility occurred by two genetic mechanisms: reversible and irreversible. Reversible loss of motility occurred early during broth adaptation, followed by irreversible motility loss in the majority of cells by the end of the experiment. Whole genome sequencing implicated diverse mutation events that resulted in the loss of gene expression necessary for flagellar biosynthesis. Furthermore, reversible mutations in homopolymeric DNA tracts of adenine/thymine residues, and irreversible types of mutation such as gene deletion, were discovered in the broth-evolved populations. In all evolved lines, an alternative sigma factor necessary for flagellar structural gene expression was removed from the genome. Overall, this dissertation contains the first accounts of C. jejuni experimental evolution. The results provide insight into the biological importance of reversible mutations in homopolymeric DNA tracts, and provide a basis for future studies of C. jejuni evolvability.
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Title: Evolutionarily adaptive mechanisms to biliary atresia in the sea lamprey
Creator: Yeh, Chu-Yin
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Lamprey species appeared over 500 million years and are therefore important evolutionary models for research interests ranging from neuronal signaling, genetics, to organ development. Among this group of jawless vertebrates, the sea lamprey is the largest and most widely distributed. It experiences a drastic life history, which includes a complete metamorphosis. During sea lamprey metamorphosis, the biliary tree and the gallbladder degenerate, in a process referred as biliary atresia. Atresia...
Show moreLamprey species appeared over 500 million years and are therefore important evolutionary models for research interests ranging from neuronal signaling, genetics, to organ development. Among this group of jawless vertebrates, the sea lamprey is the largest and most widely distributed. It experiences a drastic life history, which includes a complete metamorphosis. During sea lamprey metamorphosis, the biliary tree and the gallbladder degenerate, in a process referred as biliary atresia. Atresia of the biliary system occurs as a rare disease in human while it is a programmed developmental event in the sea lamprey. The sea lamprey can be used as a model to study the etiology and the adaptive mechanisms of biliary atresia, and the compensatory and adaptive mechanisms in cholestasis based on its various life events including biliary atresia. In this dissertation, I hypothesized that the sea lamprey had evolved unique mechanisms in both liver and intestine in adaption to biliary atresia. To test this hypothesis, I examined sea lamprey liver throughout metamorphic stages at the levels of morphology, histology, mRNA transcripts, and bile salt composition. My results indicate that the sea lamprey has evolved several possible adaptive mechanisms in coping with its developmental biliary atresia. As expected, the enterohepatic circulation is conserved in this basal vertebrate before its metamorphosis. However, the intestine synthesizes and secretes bile salts during and after metamorphosis, or biliary atresia. It is further elucidated that the metamorphic sea lamprey reversed enterohepatic circulation by in vivo perfusion and ex vivo intestine transport assays. It may be an adaptation to the lack of biliary system. Another adaptive mechanism in coping with the aductular life appeared to be dramatic changes in bile salt composition. Also, the down-regulation of cyp7a1, which encodes the rate limiting enzyme of bile acid synthesis, in liver during lamprey biliary atresia resembles the compensatory mechanism in many cholestatic animal models. All of the findings show that the sea lamprey has evolved to cope with biliary atresia and cholestasis. Understanding these mechanisms can shed light on developing treatment and management for patients suffering from biliary atresia and cholestasis.
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