Date of Completion


Embargo Period



Short Branch Attraction, Eukaryogenesis, Fundamental Bipartition of Life, Realm, Ibisii, Bacterii

Major Advisor

Dr. Johann Peter Gogarten

Associate Advisor

Dr. Ken Noll

Associate Advisor

Dr. Paul Lewis

Associate Advisor

Dr. David Benson

Associate Advisor

Dr. Jonathan Klassen

Field of Study

Genetics and Genomics


Doctor of Philosophy

Open Access

Open Access


Short Branch Attraction occurs when BLAST searches are used as surrogate for phylogenetic analysis. This results from branch length heterogeneity. The short branches, not the long, are attracting.

The root of cellular life is on the bacterial branch, meaning the Archaea and eukaryotic nucleocytoplasm form a clade. This split, the realm, is the first in the cellular tree of life. I name the clade containing the Archaea and eukaryotic nucleocytoplasm the Ibisii based on shared characteristics involved in information processing and translation. The Bacteria are members of the other realm, the Bacterii.

Eukaryogenesis is the study of how the Eukarya emerged. The beginning state is represented by the relationship between Eukarya and their closest relative, the Archaea. The ending state is represented by the location of the root within the Eukarya. I use Eukaryal stem branch length (ESBL) to inform on the relationship between Archaea and Eukarya. The long ESBL found shows a great deal of evolution, due to a product of time and rate of evolution. This suggests that Eukarya have not evolved from Archaea, but is inconclusive. I propose a new model for evolution, the Watershed of Life, with data representing two signals: vertical descent and horizontal gene transfer. All known data are consistent with only a watershed in which Archaea are monophyletic and shared genes with the Eukarya. Eukarya can be rooted using paralogs duplicated along the eukaryal stem branch to provide a closer outgroup. Unfortunately, the paralog datasets could not resolve the placement of the root.