Utilization of Phylogenetic Analysis Methods to Understand Deep Phylogeny

This thesis describes two analyses conducted to learn more about the early evolution of life and characteristics of the last universal common ancestor (LUCA). In chapter one, tree metric analysis methods were employed to determine if protein families identified in a previous analysis should be attributed to LUCA. It was found that many of the protein families identified by the previous analysis were likely the result of methodological errors, and either should not be attributed to LUCA or do not represent the full scope of diversity within the given protein family. Chapter two presents data from an ATP synthase catalytic subunit phylogenetic analysis conducted in RAxML, including representation from several novel lineages of archaea including the ASGARD and DPANN groups. Using methods such as Dayhoff recoding to reduce compositional bias in the sequences, the positions of these novel lineages were examined critically. This called into question results garnered from previous analyses using other genes for phylogenetic reconstruction. By including representation of Eukaryotic sequences, this analysis enabled a re-evaluation of their evolutionary origins, and their relationship to the novel lineages in the ASGARD group in particular