Date of Award
2016
First Advisor
Bill Dunbar
Second Advisor
Tom Coote
Third Advisor
Erin McMullin
Abstract
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.
Recommended Citation
Sadowsky, Nathan, "Two Accounts of History A Phylogenetic Approach to Reconstructing Gene Trees and Species Trees or Ninety-Five Theses on Species A Tree-tise" (2016). Senior Theses. 1057.
https://digitalcommons.bard.edu/sr-theses/1057
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