Date of Completion

Summer 8-31-2015

Thesis Advisor(s)

Johann Peter Gogarten

Honors Major

Molecular and Cell Biology


Bioinformatics | Computational Biology | Environmental Microbiology and Microbial Ecology | Evolution | Genetics | Genomics | Molecular Biology | Molecular Genetics


In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There have been multiple determinations of where they ought to be placed, and the various research groups have used different methods of phylogenetic reconstruction, gene datasets, and taxonomic samples to study the evolution of these taxa. In the present work, the phylogenetic reconstruction programs PhyML and RAxML were used to gain a clearer picture of what clades within the archaea each of these taxa are most closely related to. This method calculates a likelihood value for every topological possibility for each ultrasmall species on a base tree of archaea. These scores were used to construct a likelihood landscape plot in order to determine ‘hotspots’ in the archaeal tree of life where the ultrasmall organisms show genetic similarity.