Two Accounts of History A Phylogenetic Approach to Reconstructing Gene Trees and Species Trees or Ninety-Five Theses on Species A Tree-tise

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