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Title
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Mechanisms of adaptation in Oryza and Arabidopsis
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Creator
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Grillo, Michael A.
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Date
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2013
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Collection
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Electronic Theses & Dissertations
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Description
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Here I present a dissertation aimed at understanding the mechanisms of adaptation in two wild rice species and locally adapted populations of Arabidopsis thaliana. First, I assess the genetic architecture of adaptation in the wild progenitors of cultivated rice, by identifying QTL for a number of putative adaptive traits. Through this work flowering time was revealed as a key adaptation for habitat preference between these species. In the next chapter I attempt to elucidate the genetic basis...
Show moreHere I present a dissertation aimed at understanding the mechanisms of adaptation in two wild rice species and locally adapted populations of Arabidopsis thaliana. First, I assess the genetic architecture of adaptation in the wild progenitors of cultivated rice, by identifying QTL for a number of putative adaptive traits. Through this work flowering time was revealed as a key adaptation for habitat preference between these species. In the next chapter I attempt to elucidate the genetic basis of a major flowering time QTL through fine mapping. I continue my examination of flowering time genetics by examining the genetic basis of flowering time differentiation between locally adapted populations of Arabidopsis thaliana. Finally, I conduct a thorough study of comparative floral biology to identify key traits that control mating system divergence between the wild rice relatives. This work sets the stage for future efforts to understand the genetic basis of mating system evolution.
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Title
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Understanding the role of standing genetic variation in functional genetics and compensatory evolution
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Creator
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Chari, Sudarshan R.
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Date
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2014
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Collection
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Electronic Theses & Dissertations
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Description
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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
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On the evolution of mutation bias in digital organisms
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Creator
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Rupp, Matthew
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Date
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2011
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Collection
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Electronic Theses & Dissertations
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Description
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Mutation is one of the primary drivers of genetic change. In this work I study mutation biases, which are sets of different genetic-state inflow probabilities. Mutation biases have the potential to change the composition of genomes over time, leading to divergent short- and long-term evolutionary outcomes. I use digital organisms, self-replicating computer programs, to explore whether or not mutation biases are capable of altering the long-term adaptive behavior of populations; whether...
Show moreMutation is one of the primary drivers of genetic change. In this work I study mutation biases, which are sets of different genetic-state inflow probabilities. Mutation biases have the potential to change the composition of genomes over time, leading to divergent short- and long-term evolutionary outcomes. I use digital organisms, self-replicating computer programs, to explore whether or not mutation biases are capable of altering the long-term adaptive behavior of populations; whether mutation biases can be competitive traits; and whether mutation biases can evolve. I find that mutation biases can alter the long-term adaptive behavior of mutation bias-obligate populations in terms of both mean fitness and complex trait evolution. I also find that mutation biases can compete against one another under a variety of conditions, meaning mutation bias can selectable over relatively-short periods of time. The competitive success of a mutation bias does not always depend upon the presence of beneficial mutations, implicating an increase in the probability of neutral mutations as a sufficient mechanism for bias selection. Finally, I demonstrate that by giving organisms a mutable mutation bias allele, populations preferentially evolve to possess specific biases over others. Overall, this work shows that mutation bias can act as a selectable trait, influencing the evolution of populations with regard to both their internal-genetic and external environments.
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