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Title
The causes and effects of genital hypoallometry in Drosophila
Creator
Dreyer, Austin P.
Date
2014
Collection
Electronic Theses & Dissertations
Description
The study of size covariation between traits has a long history of describing morphological variation. For over a century, scientists have recognized variation in the proportional size of traits, and have searched to explain the patterns from an evolutionary perspective. Research on the scaling relationships between traits, called allometries, has established the interaction of traits within an organism plays a crucial role in the adaptation of species to their environment. The evolutionary...
Show moreThe study of size covariation between traits has a long history of describing morphological variation. For over a century, scientists have recognized variation in the proportional size of traits, and have searched to explain the patterns from an evolutionary perspective. Research on the scaling relationships between traits, called allometries, has established the interaction of traits within an organism plays a crucial role in the adaptation of species to their environment. The evolutionary forces that give rise to changes in the proportional size of traits have been more difficult to elucidate. Using the model organism, Drosophila melanogaster, I have focused my research on the scaling of male genitalia in relation to overall body size to explore proximate and ultimate causes of allometries in general. Most traits scale at or near a 1:1 ratio to overall body size, called isometry. In contrast, the male genitalia of many groups scale hypoallometrically to body size, remaining a constant size across a range of body sizes. Determining the factors that drive the atypical allometric relationship of the male genitalia promises to reveal principles of size control across all traits. To investigate the developmental mechanisms underlying genital hypoallometry, I first compared the effects of genetic variation on genital traits (hypoallometric) to somatic traits (isometric). Previous research has shown that genital traits are less sensitive to environmental variation than somatic traits and here I demonstrate that genital traits are also less sensitive to variation in genetic factors that affect trait size. I also showed that genitalia have low levels of developmental stability than somatic traits, measured as the response in trait size to stochastic developmental errors. Next, I used targeted gene expression of insulin-signaling genes in developing genital tissues of Drosophila to allometrically engineer male flies with extreme genital sizes. Females were exposed to males with different genital sizes, and demonstrated a preference for copulating, and fertilizing progeny, with males that had larger genitalia. To expand the scope of these results, a stochastic mathematical model of allometry evolution was designed that incorporated the developmental regulation of size. Results of simulated allometry evolution showed that the underlying factors controlling final trait size largely determine how scaling relationships respond to selection and evolve. Collectively, my dissertation represents a significant step forward in our understanding of trait size regulation between covarying traits. Additionally, my research demonstrates the novel use of Drosophila melanogaster to modify existing levels of trait variation to test selection hypotheses. Scaling relationships between traits are an important component of morphological evolution that we can continue learning about only via multifaceted research as demonstrated here.
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Title
The evolution of complexity and robustness in small populations
Creator
LaBar, Thomas
Date
2018
Collection
Electronic Theses & Dissertations
Description
"A central goal of evolutionary biology is to understand a population's evolutionary trajectory from fundamental population-level characteristics. The mathematical framework of population genetics provides the tools to make these predictions. And while population genetics provides a well-studied framework to understand how adaptation and neutral evolution quantitatively alter population fitness, less attention has been paid to using population genetics to predict qualitative evolutionary...
Show more"A central goal of evolutionary biology is to understand a population's evolutionary trajectory from fundamental population-level characteristics. The mathematical framework of population genetics provides the tools to make these predictions. And while population genetics provides a well-studied framework to understand how adaptation and neutral evolution quantitatively alter population fitness, less attention has been paid to using population genetics to predict qualitative evolutionary outcomes. For instance, do different populations evolve alternative genetic mechanisms to encode similar phenotypic traits, and if so, which processes lead to these differences? This dissertation investigates the role of population size in altering the qualitative outcome of evolution. It is difficult to experimentally investigate qualitative evolutionary outcomes, especially in small populations, due to the time required for novel evolutionary features to appear. To get around this constraint, I use digital experimental evolution. While digital evolution experiments lack aspects of biological realism, in some regards they are the only methodology that can approach the complexity of biological systems while maintaining the ease of analysis present in mathematical models. Digital evolution experiments can never prove that certain evolutionary trajectories occur in biological populations, but they can suggest hypotheses to test in more realistic model systems. First, I explore the role of population size in determining the evolution of both genomic and phenotypic complexity. Previous hypotheses have argued that small population size may lead to increases in complexity and I test aspects of those hypotheses here. Second, I introduce the novel concept of 'drift robustness' and argue that drift robustness is a strong factor in the evolution of small populations. Finally, I end with a project on the role of genome size in enhancing the extinction risk of small populations. I conclude with a broader discussion of the consequences of this research, some limitations of the results, and some ideas for future research."--Page ii.
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Title
Identifying the genetic basis of attenuation in Marek's disease virus via experimental evolution
Creator
Hildebrandt, Evin
Date
2014
Collection
Electronic Theses & Dissertations
Description
Marek's disease virus (MDV), an oncogenic alphaherpesvirus of chickens, causes up to $2 billion in loses a year due to Marek's disease (MD). Therefore control of this economically important disease is critical. The primary method to control MD is vaccination. Attenuated, or weakened, strains of MDV have been generated via repeated in vitro serial passage to generate avirulent MDV strains that have been used as successful MD vaccines. Despite introduction of several vaccines since the 1970's,...
Show moreMarek's disease virus (MDV), an oncogenic alphaherpesvirus of chickens, causes up to $2 billion in loses a year due to Marek's disease (MD). Therefore control of this economically important disease is critical. The primary method to control MD is vaccination. Attenuated, or weakened, strains of MDV have been generated via repeated in vitro serial passage to generate avirulent MDV strains that have been used as successful MD vaccines. Despite introduction of several vaccines since the 1970's, more virulent strains of MDV have evolved to break vaccinal protection. Therefore, development of new MD vaccines is necessary. To address this concern, we sought to better understand the molecular basis of attenuation in MDV to provide information that may assist in the rationale design of MD vaccines. Three attenuated replicates of a virulent MDV were serially passed in vitro for over 100 passages. DNA and RNA from attenuated viruses were deep sequenced using Illumina next-generation sequencers to identify changes in DNA sequence or expression following attenuation. Top candidate mutations identified via sequencing were used to generate seven recombinant viruses using red-mediated recombineering for mutations within UL42, UL46, UL5, two involving LORF2 and two mutations within ICP4. These recombinant viruses were tested in vivo to determine the impact of these mutations on MD incidence, in vivo replication and horizontal transmission. Point mutations within UL42, UL46, LORF2-Promoter and ICP4 did not cause observable phenotypic changes compared to the parental virus. A single point mutation within LORF2-Intron and a double mutant involving ICP4 both resulting in 100% MD in challenged birds but failed to transmit horizontally to uninfected contact birds. Finally, a point mutation within UL5 reduced MD incidence by over 90%, significantly reduced in vivo replication, and eliminated horizontal transmission. Further characterization of this UL5 point mutation determined that it increased in vitro replication in growth curves, yet head-to-head competition of the Mut UL5 virus versus parental virus showed the parental virus outcompeted the mutant virus. Furthermore, serial passage of Mut UL5 in vivo did not result in increased in MD incidence, in vivo replication or result in reversion or compensatory mutations to UL5 after passage through birds. Trials testing vaccinal protection of the Mut UL5 virus showed the virus provided partial protection against challenge with virulent MDV, yet did not exceed protection achieved through use of traditional vaccines. Therefore, use of this point mutation in combination with other candidate mutations was tested. Addition of the UL5 mutation with Delta Meq, a candidate vaccine with high protection and replication but also induces bursal-thymic atrophy (BTA), resulted in a recombinant virus that replicated at low levels and did not cause BTA, yet reduced levels of vaccinal protection, indicating an intricate relationship between replication levels, BTA and vaccinal protection. This study shows that a variety of genes are mutated during attenuation, and particularly mutations within DNA replication genes, such as UL5, appear to play an important role in attenuation. We also determined that experimental evolution is a process that not only can identify mutations involved in attenuation, but also offer protection as a vaccine to provide information for further development of MD vaccines.
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Title
Digital sex : causes and consequences of recombination
Creator
Misevic, Dusan
Date
2006
Collection
Electronic Theses & Dissertations
Title
Genomic analysis of pathogen evolution : virulence gene acquisition and genetic erosion in Escherichia coli
Creator
Nelson, Adam Michael
Date
2008
Collection
Electronic Theses & Dissertations
Title
The evolutionary ecology of senescence in Daphnia
Creator
Dudycha, Jeffry L.
Date
2000
Collection
Electronic Theses & Dissertations
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
Gene content evolution In plant genomes : studies of whole genome duplication, intergenic transcription and expression evolution In Brassicaceae and Poaceae species
Creator
Moghe, Gaurav Dilip
Date
2013
Collection
Electronic Theses & Dissertations
Description
Phenomena that create new genes and influence their diversification are important contributors to evolutionary novelty in living organisms. My research has focused on addressing the following questions regarding such phenomena in plants. First, what are the patterns of evolution of duplicate genes derived via whole genome duplication (WGD)? Second, do transcripts originating from intergenic regions constitute novel genes? Third, how do expression patterns of orthologous genes evolve in plants...
Show morePhenomena that create new genes and influence their diversification are important contributors to evolutionary novelty in living organisms. My research has focused on addressing the following questions regarding such phenomena in plants. First, what are the patterns of evolution of duplicate genes derived via whole genome duplication (WGD)? Second, do transcripts originating from intergenic regions constitute novel genes? Third, how do expression patterns of orthologous genes evolve in plants? I have addressed these questions using comparative genomic and transcriptomic analyses of species in the Brassicaceae and Poaceae families. To understand the evolution of WGD derived duplicate genes, we sequenced and annotated the genome of wild radish (Raphanus raphanistrum), a Brassicaceae species which experienced a whole genome triplication (WGT) event ~24-29 million years ago. Through comparative genomic analyses of sequenced Brassicaceae species, I found that most WGT duplicate genes were lost over time. Duplicates that are still retained were found to undergo sequence and expression level divergence. Interestingly, while duplicate copies tend to diverge in expression level, one of the copies tends to maintain its original expression state in the tissue studied. Furthermore, duplicates that are retained in extant species tend to have higher expression levels, broader expression breadth, higher network connectivity and tend to be involved in functions such as transcription factor activity, stress response and development. Functional diversification of such duplicates can assist in evolution of novel characters in plants post WGD. To understand the nature of intergenic transcription, I analyzed multiple transcriptome datasets in Arabidopsis thaliana as well as in species of the Poaceae family. My results suggest that plant genomes do not show any evidence of pervasive intergenic transcription. Although thousands of intergenic transcripts can be found in each species, most of these transcripts have low breadths of expression, tend not to be conserved within or between species and show a significant bias in being located very close to genes or in open chromatin regions. My results suggest that most intergenic transcripts may be associated with transcription of the neighboring genes or may be produced as a result of noisy transcription. Properties of intergenic transcripts identified in my research will be useful in distinguishing functionally relevant transcripts from noise. To understand expression evolution, I analyzed patterns of evolution of orthologous genes between Poaceae species and found that sequence divergence is strongly associated with level and breadth of expression, and very weakly with expression divergence. Both sequence and expression evolution were found to be constrained for genes involved in core biological processes such as metabolism, transcription, photosynthesis and transport. Overall, the results of this research are broadly applicable to the field of gene annotation and increase our understanding of evolution of gene content in plant genomes.
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