A molecular and bioinformatic investigation into the phylogenetic relationships and life cycles of amoeboid protists

Eukaryotic organisms that cannot be classified as animals, land plants, or fungi are termed protists. Despite the fact that protists represent the majority of eukaryotic diversity, these organisms have received relatively little attention from biological researchers beyond morphological characterization. Reasons that likely contributed to their neglect include their mostly microscopic nature, that only a few lineages are the causative agents of human disease, that laboratory cultivation can be challenging, and that species concepts for the majority of protists was vague in many lineages. Initial attempts to resolve relationships among eukaryotes produced the five kingdoms model. This model suggested protists were an evolutionary assemblage separate from the animals, plants, and fungi. Molecular systematics provided a more accurate view of relationships amongst eukaryotic taxa. Results from molecular phylogenetic studies demonstrated that protists were a polyphyletic group made of many assemblages, and that more complex lineages such as plants and animals were nested within these assemblages. This new evolutionary framework brought increased attention to protists. The application of molecular biology, especially genomic and transcriptomic sequencing to protists has allowed researchers to generate meaningful data on poorly understood lineages rapidly. Applying these techniques to understudied amoeboid protists, I demonstrated the presence of a complex life cycle in a well-studied group of opportunistic pathogens and their close relatives that was not previously known, as well as characterized new diversity within the group. I made methodological advances in the field of molecular systematics through development of a novel ortholog collection algorithm that I have included in a phylogenomic package capable of resolving ancient (\u3e100 million years) divergences in the tree of eukaryotes. I used the algorithm to build the packages accompanying manually curated database of 240 homologs from 304 eukaryotic taxa. Using the newly developed software and manually curated gene set has yielded the most complete and highly resolved tree of eukaryotes to date. Finally, I used developmental transcriptomics to demonstrate the amoeba Copromyxa protea evolved a means of simple cooperative multicellularity independently from other more well studied multicellular lineages