Doctor of Philosophy, The Ohio State University, 2018, Evolution, Ecology and Organismal Biology

Most broadly, this study aimed to develop a better understanding of how organisms evolve novel functions and traits, and examine how seemingly complex adaptive trait syndromes can convergently evolve. As an ideal example of this, the carnivorous plants were chosen. This polyphyletic grouping contains taxa derived from multiple independent evolutionary origins, in at least five plant orders, and has resulted in striking convergence of niche and morphology. First, a database study was performed, with the goal of understanding the evolutionary trends that impact carnivorous plants as a whole. Using carnivorous and non-carnivorous plant genomes available from GenBank. An a priori list of Gene Ontology-coded functions implicated in plant carnivory by earlier studies was constructed via literature review. Experimental and control samples were tested for statistical overrepresentation of these functions. It was found that, while some functions were significant in some taxa, there was no overall shared signal of plant carnivory, with each taxon presumably having selected for a different subset of these functions. Next, analyses were performed that targeted Sarracenia alata specifically. A reference genome for S. alata was assembled using PacBio, Illumina, and BioNano data and annotated using MAKER-P with additional preliminary database filtration. From these, it was found that Sarracenia alata possesses significant and substantial overrepresentation of genes with functions associated with plant carnivory, at odds with the hypothesis that the plant primarily relies on symbioses. Finally, pitcher fluid was collected from S. alata in the field. RNA was extracted from the fluid, sequenced via Illumina, and assembled with Trinity. Sequences were sorted into host plant and microbiome based on BLAST match to the S. alata reference genome. It was found that, while S. alata contributes two-thirds of the transcripts, these encode no digestive enzymes and a very limited set o (open full item for complete abstract)

Committee: Bryan Carstens Ph.D. (Advisor); Marymegan Daly Ph.D. (Committee Member); Zakee Sabree Ph.D. (Committee Member); Andrea Wolfe Ph.D. (Committee Member) Subjects: Bioinformatics; Biology; Botany

Doctor of Philosophy, The Ohio State University, 2016, Evolution, Ecology and Organismal Biology

Interactions among species are driving forces behind the formation, structure, and persistence of ecological communities. The nature of species interactions that characterize communities, however, has long been debated by ecologists, varying from communities as fluid entities to communities as evolving units. For species with obligate interactions (e.g., host and parasite, plant and pollinator), we might expect these ecologically dependent associations to be reflected in a shared evolutionary history, yet relatively few studies have demonstrated this process in nature. To address this central tenet in ecology and evolutionary biology, my research explores co-diversification in the Sarracenia alata pitcher plant system. Sarracenia alata (family Sarraceniaceae) is a carnivorous pitcher plant distributed along the Gulf Coast of the American southeast, bisected by the Mississippi River. Leaves of this plant are tube-shaped and filled with fluid, adapted for the capture and digestion of prey items. The breakdown of prey provides inorganic compounds to the plant, necessary in the nutrient-poor habitats where these plants are found. In addition to prey capture, the plant's modified leaves harbor a unique biota of associated organisms (i.e., inquilines)—diverse species that share ecological relationships and often provide important services (e.g., secrete digestive enzymes) for the plant. My dissertation tests coevolution theory, exploring how a host plant may influence the population genetic structure of associated species. Shared structure would suggest stable ecological relationships through evolutionary time, and would provide evidence that ecologically interacting lineages can evolve as a unit. I first analyzed DNA sampled directly from the pitcher fluid to identify microorganisms contained within the community (Chapter 2). My results recover a diverse set of taxa found within the pitcher fluid, and demonstrate that roughly half of the small eukaryotes (e.g., fungi, (open full item for complete abstract)

Committee: Bryan Carstens (Advisor); Laura Kubatko (Committee Member); John Freudenstein (Committee Member) Subjects: Biology