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Date of Award
Campus Access Dissertation
Doctor of Philosophy in Biochemistry and Molecular Biology (PhD)
Administrative Home Department
Department of Biological Sciences
Committee Member 1
Committee Member 2
Committee Member 3
Organisms with novel adaptive traits are excellent research subjects for evolutionary biologists. The trajectory of an adaptive trait, how it arose, what evolutionary forces acted on the trait, and fitness effects of the trait, provide insights in understanding how the trait influences biodiversity in the organisms carrying the trait. One such trait is mycotoxin tolerance.
Many mycophagous Drosophila species from the immigrans-tripunctata radiation have adapted to tolerate high concentrations of mycotoxins, an ability not reported in any other eukaryotes. Although an association between mycophagy and mycotoxin tolerance has been established in many Drosophila species, the genetic mechanisms of the tolerance are unknown. In the second chapter of this dissertation, I attempt to understand the genetic architecture of the mycotoxin tolerance trait. I studied the mycotoxin tolerance in four Drosophila species from four separate clades within the immigrans-tripunctata radiation from two distinct locations: Escanaba and Great Smoky Mountains. I observed interspecific variation among four species, with D. falleni being the most tolerant to mycotoxins, followed by D. recens, D. neotestacea, and D. tripunctata, in that order. I observed quantitative genetic variation, indicating that mycotoxin tolerance is a complex trait. The second chapter provides the foundation for further delineating the genetic mechanisms of the mycotoxin tolerance trait. It has been hypothesized that mycotoxin tolerance is costly because Drosophila species that switch hosts from mushrooms to other food sources lose this trait without any evolutionary lag. In the second chapter, I observed fitness effects of the mycotoxin tolerance trait in two species: D. tripunctata and D. neotestacea.
In the third chapter, I attempted to identify whether mycotoxin tolerance has a fitness cost, adversely affecting larval competitive ability. I observed that the extent of mycotoxin tolerance did not affect larval competitive ability. Chapters 2 and 3 also help to shed light on another evolutionary aspect of mycotoxin tolerance, local adaptation. I observed geographic variation in mycotoxin tolerance, suggesting the influence of local adaptation on the mycotoxin tolerance trait.
In chapter 4, I have analyzed 29 Drosophila genomes to identify the codon usage bias between two subgenera: Sophophora and Drosophila. I found a strong correlation between phylogenetic distance and codon usage bias and observed striking differences in codon preferences between the subgenera Drosophila and Sophophora. Compared to the subgenus Sophophora, species of the subgenus Drosophila showed reduced codon usage bias and a reduced preference specifically for codons ending with C, except for codons with G in the second position. I found that codon usage patterns in all species were influenced by the nucleotides in the codons’ 2nd and 3rd positions rather than the biochemical properties of the amino acids encoded. I detected a concordance between preferred codons and preferred dinucleotides (at positions 2 and 3 of codons). Furthermore, I observed an association between speciation, codon preferences, and dinucleotide preferences. This study provides the foundation to understand how selection acts on dinucleotides to influence codon usage bias.
Kokate, Prajakta P., "QUANTITATIVE GENETIC VARIATION IN MYCOTOXIN TOLERANCE, ASSOCIATED FITNESS COSTS, AND STUDY OF CODON USAGE BIAS IN DROSOPHILA SPECIES.", Campus Access Dissertation, Michigan Technological University, 2021.