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Title: Adaptation and specialization in biological and digital organisms
Creator: Ostrowski, Elizabeth Anne
Date: 2005
Collection: Electronic Theses & Dissertations

Title: Bloom syndrome as a human mutator mutation
Creator: Warren, Stephen Theodore
Date: 1981
Collection: Electronic Theses & Dissertations

Title: Characterization of the sequence and substrate reactivity of dihydroneopterin aldolase and its site-directed mutants by tandem mass spectrometry
Creator: Scherperel, Gwynyth
Date: 2006
Collection: Electronic Theses & Dissertations

Title: Characterization of ultraviolet light-induced diphtheria toxin-resistant mutations in normal and xeroderma pigmentosum human fibroblasts
Creator: Glover, Thomas Warren
Date: 1979
Collection: Electronic Theses & Dissertations

Title: Chemical and plastome-mutator mutagenesis of Oenothera
Creator: Baldwin, Susan
Date: 1995
Collection: Electronic Theses & Dissertations

Title: Consequences of ecological specialization in long-term evolving populations of Escherichia coli
Creator: Cooper, Vaughn Scott
Date: 2000
Collection: Electronic Theses & Dissertations

Title: Detection of boscalid resistance and the H272R mutation in the SDHB gene of Blumeriella jaapii
Creator: Outwater, Cory Alan
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Cherry leaf spot (CLS), caused by the fungus Blumeriella jaapii, is a major disease of tart cherry (Prunus cerasus) trees, leading to early defoliation which results in poor fruit quality, reduced fruit set, and tree death. Pristine, a commonly-utilized fungicide for CLS management in Michigan, is a premix of boscalid, a succinate dehydrogenase inhibitor, and pyraclostrobin, a quinone outside inhibitor. Reduced efficacy of Pristine for CLS control observed in...
Show moreCherry leaf spot (CLS), caused by the fungus Blumeriella jaapii, is a major disease of tart cherry (Prunus cerasus) trees, leading to early defoliation which results in poor fruit quality, reduced fruit set, and tree death. Pristine, a commonly-utilized fungicide for CLS management in Michigan, is a premix of boscalid, a succinate dehydrogenase inhibitor, and pyraclostrobin, a quinone outside inhibitor. Reduced efficacy of Pristine for CLS control observed in field trials and commercial orchards highlighted the importance of resistance monitoring. A total of 1,288 isolates from commercial orchards and 111 isolates from non-treated trees were collected in 2010 and 2011 and assayed on boscalid-amended media at concentrations of 0, 0.1, 0.5, 1, 2.5, 5, 10, and 25 g ml-1. The minimum inhibitory concentration (MIC) of boscalid was determined after incubation at 23 oC for 14 days. Isolates from non-treated trees had MIC values ranging from 0.1 to 0.5 μg ml-1 while isolates from commercial orchards ranged from 0.1 to > 25 μg ml-1 . Isolates with MIC values of > 25 μg ml-1 were considered resistant and comprised 22% and 35% of isolates in 2010 and 2011 respectively. Sequencing of the SDHB gene of resistant isolates led to the detection of the amino acid mutation H272R known to confer boscalid resistance. The occurrence of the H272R mutation in Michigan populations of B. jaapii is correlated with the reduction in sensitivity to boscalid observed in commercial orchards.
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Title: Dynamics of mutation and selection in asexual populations
Creator: Gerrish, Philip J. (Philip John)
Date: 1998
Collection: Electronic Theses & Dissertations

Title: Evidence from mutation spectra that the UV hypermutability of xeroderma pigmentosum variant cells reflects abnormal, error-prone replication on a template containing photoproducts
Creator: Wang, Yi-Ching
Date: 1993
Collection: Electronic Theses & Dissertations

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: Functional analysis of cytoplasmic [gamma]-actin mutations causing non-syndromic, progressive autosomal dominant hearing loss
Creator: Korrapati, Soumya
Date: 2009
Collection: Electronic Theses & Dissertations

Title: Glucocorticoid receptor gene mutations associate with glucocorticoid-responsive leukocyte and production traits in cattle
Creator: Jacob, Jennifer Brigitte
Date: 2003
Collection: Electronic Theses & Dissertations

Title: Isolation and characterization of symbiotically defective mutant strains of Rhizobium trifolii and Rhizobium meliloti
Creator: Gardiol, Alicia E.
Date: 1985
Collection: Electronic Theses & Dissertations

Title: Kinds and spectra of mutations formed when a shuttle vector containing adducts of benzo [a] pyrene-7,8-diol-9,10-epoxide or 1-nitrosopyrene replicates in mammalian cells
Creator: Yang, Jia-Ling
Date: 1988
Collection: Electronic Theses & Dissertations

Title: Mechanisms of adaptation and speciation : an experimental study using artificial life
Creator: Anderson, Carlos Jesus
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Detailed experimental studies in evolutionary biology are sometimes difficult--even with model organisms. Theoretical models alleviate some of these difficulties and often provide clean results, but they cannot always capture the complexity of dynamic evolutionary processes. Artificial life systems are tools that fall somewhere between model organisms and theoretical models that have been successfully used to study evolutionary biology. These systems simulate simple organisms that replicate,...
Show moreDetailed experimental studies in evolutionary biology are sometimes difficult--even with model organisms. Theoretical models alleviate some of these difficulties and often provide clean results, but they cannot always capture the complexity of dynamic evolutionary processes. Artificial life systems are tools that fall somewhere between model organisms and theoretical models that have been successfully used to study evolutionary biology. These systems simulate simple organisms that replicate, acquire random mutations, and reproduce differentially; as a consequence, they evolve naturally (i.e., evolution itself is not simulated). Here I use the software Avida to study several open questions on the genetic mechanisms of adaptation and speciation.In Chapter 1 (p. 13), I investigated whether beneficial alleles during adaptation came from new mutations or standing genetic variation--alleles already present in the population. I found that most beneficial alleles came from standing genetic variation, but new mutations were necessary for long-term evolution. I also found that adaptation from standing genetic variation was faster than from new mutations. Finally, I found that recombination brought together beneficial combinations of alleles from standing genetic variation.In Chapter 2 (p. 31), I investigated the probability of compensatory adaptation vs. reversion. Compensatory adaptation is the fixation of mutations that ameliorate the effects of deleterious mutations while the original deleterious mutations remain fixed. I found that compensatory adaptation was very common, but the window of opportunity for reversion was increased when the initial fitness of the population was high, the population size was large, and the mutation rate was high. The reason that the window of opportunity for reversion was constrained was that negative epistatic interactions with compensatory mutations prevented the revertant from being beneficial to the population.In Chapter 3 (p. 58), I showed experimentally that compensatory adaptation can lead to reproductive isolation (specifically, postzygotic isolation). In addition, I found that the strength of this isolation was independent of the effect size of the original deleterious mutations. Finally, I found that both deleterious and compensatory mutations contribute equally to reproductive isolation.Reproductive isolation between populations often evolves as a byproduct of independent adaptation to new environments, but the selective pressures of these environments may be divergent (`ecological speciation') or uniform (`mutation-order speciation'). In Chapter 4 (p. 75), I compared directly the strength of postzygotic isolation generated by ecological and mutation-order processes with and without migration. I found that ecological speciation generally formed stronger isolation than mutation-order speciation and that mutation-order speciation was more sensitive to migration than ecological speciation.Under the Dobzhansky-Muller model of speciation, hybrid inviability or sterility results from the evolution of genetic incompatibilities (DMIs) between species-specific alleles. This model predicts that the number of pairwise DMIs between species should increase quadratically through time, but the few tests of this `snowball effect' have had conflicting results. In Chapter 5 (p. 101), I show that pairwise DMIs accumulated quadratically, supporting the snowball effect. I found that more complex genetic interactions involved alleles that rescued pairwise incompatibilities, explaining the discrepancy between the expected accumulations of DMIs and observation.
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Title: Mechanisms of adaptation in Oryza and Arabidopsis
Creator: Grillo, Michael A.
Date: 2013
Collection: Electronic Theses & Dissertations
Description: 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: Novel studies of spontaneous mutation : measurements of fitness in the field and gene expression in the lab
Creator: Roles, Angela Jennifer
Date: 2007
Collection: Electronic Theses & Dissertations

Title: On the beneficial effects of deleterious mutations
Creator: Covert, Arthur W.
Date: 2010
Collection: Electronic Theses & Dissertations

Title: On the evolution of mutation bias in digital organisms
Creator: Rupp, Matthew
Date: 2011
Collection: Electronic Theses & Dissertations
Description: 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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Title: Part I, Studies on the hamster ribonucleotide reductase genes : Part II, Construction of mutations in the chicken adult alpha globin genes
Creator: Bates, Paul F.
Date: 1985
Collection: Electronic Theses & Dissertations

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