Miller, John JamesDinoflagellates and haptophytes are both prominent members of the marine phytoplankton and are considered chromalveolates. The interactions of the parasitic dinoflagellate Amoebophrya with its host dinoflagellate Akashiwo sanguinea were studied using cell biological techniques. The free-swimming dinospore stage of Amoebophrya has two flagella, trichocyts, striated strips, condensed chromatin resembling heterochromatin, and electron dense bodies. When entering the host cytoplasm and again when entering the host nucleus, the electron dense bodies appear in a tube of microtubules close to the surface of the host or its nucleus. Host entry is inhibited by cytochalasin D implying a role for microfilament polymerization in the entry process. While in the host cytoplasm, Amoebophrya appears to be separated from the host cytoplasm by two membranes. After entering the host nucleus, the parasite grows and undergoes mitosis forming a multinucleated trophont. The mastigocoel is an internal cavity that contains flagella and becomes the outside of the parasite after it leaves the host. This study indicates that the mastigocoel forms as a result of vesicle fusion. Eventually, Amoebophrya fills the host nucleus and takes on a beehive appearance. The beehive stage contains numerous trichocyts and striated strips. The level of chromatin condensation in intracellular trophonts is highly variable. It then exits its host as a multinucleated vermiform shaped creature, which then splits up into individual infective dinospores. A phylogenomic pipeline was designed to analyze the genome and evolutionary history of the haptophyte Emiliania huxleyi. It appears to have genes linking it to three lineages: heterokonts, green algae, and red algae. Genes with shared phylogenetic affinities appear to fit into limited functional categories and be physically localized in the genome. The phylogenetic affinities of E. huxleyi with the green algae may be an artifact of the much greater number of sequenced genomes from the Viridiplantae (=plants+ green algae) when compared to the rhodophytes. The evolutionary history of E. huxleyi is still unclear although they do seem to be similar in many ways to heterokonts and are generally believed to have red algae derived plastids.DissertationBiology, BioinformaticsBiology, ParasitologyBiology, MorphologyAmoebophryaEmilianiagenomephylogenomicsultrastructure