Date of Award


First Advisor

Bill Dunbar

Second Advisor

Tom Coote

Third Advisor

Erin McMullin


In this thesis, phylogenies (evolutionary histories, represented by trees) of both genes and species are examined, specifically in the ways they intersect. Incomplete lineage sorting is used as a window into the broader issue of the history of species trees. In the first part, gene histories are examined. Then, species tree methods including concatenation and multi-species coalescent methods are discussed and analyzed. This is done through a close reading of some of the most important works in the field. In addition, an experiment on simulated data was run to test the performance of a variety of species tree methods, and the results are reported. The main comparison was between concatenation, summary statistics, and SVDquartets. All methods performed comparably well. The thesis concludes with a discussion of how each method interprets the data, leading to a finding that SVDquartets is the most legitimate species tree reconstruction method.