ORCID Identifier(s)


Graduation Semester and Year




Document Type


Degree Name

Doctor of Philosophy in Quantitative Biology



First Advisor

Sen Xu


Daphnia have been gaining recognition as a key model system for studies of evolution, ecology, toxicology, and more recently genomics. The defining characteristic of this particular model system is its phenotypic plasticity and its responsiveness to environmental cues. At the same time, the advent of RNA sequencing technology has helped researchers gain new insights on the plasticity of gene expression and its role linking environmental cues with the physiological response mounted by the organism. Although many RNA-seq studies have been conducted in Daphnia, surprisingly no one has recorded the gene expression profile of one of Daphnia’s most famous phenotypic plastic trait: cyclical parthenogenesis (CP). In this dissertation we first developed a program that assists in the visualization of functional gene annotations to better infer the functional significance of interesting subsets of genes (e.g., differentially expressed). Next, we investigated the gene expression profile of cyclical parthenogenesis in whole-tissue Daphnia pulex and Daphnia pulicaria. We found that when compared against the sexual cycle, meiosis and cell-cycle genes were under-regulated during the asexual reproductive cycle while metabolic genes were up-regulated. We suggest that the under regulation of those meiosis and cell cycle genes may be responsible for the origin of parthenogenesis from meiosis. Finally, we catalogued the types of regulatory divergence found between two Daphnia species (D. pulex and D. pulicaria) undergoing ecological speciation. We found cis-only, cis + trans, and cis x trans regulatory divergence had significantly increased in interspecific crosses compared to an intraspecific cross. We hypothesized gene misexpression rates to be higher among interspecific hybrids but found no significant difference between gene misexpression rates of inter- and intraspecific hybrids. Lastly, we found an overrepresentation of misexpressed genes with cis x trans and compensatory regulatory divergence, suggesting that incompatibilities between cis- and trans-elements are responsible for hybrid misexpression.


Transcriptomic, Daphnia, Parthenogenesis, Regulatory divergence, Gene expression, KEGG, Evolution


Biology | Life Sciences


Degree granted by The University of Texas at Arlington

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