Theses and Dissertations Collection

Sequence data exist for about 1/5 of plant species, and so we are at risk of losing many branches of the tree of life before they are placed into an evolutionary context. This neces- sitates phylogeny estimation of understudied, rare, and threatened taxa; forcing researchers to utilize historical collections. Reduced representation sequencing approaches allow rapid generation of tens of thousands of loci, however, these methods are primarily employed with high-quality specimen. We resolve intraspecific relationships, but not interspecific relation- ships in Chloropyron, a genus of rare flowering plants, using historical collections, due to high rates of missing data. We characterize the behavior of two commonly used quartet-based species tree methods when rates of missing data are high to assess accuracy of species tree estimation using reduced representation libraries from historical collections. Finally, we elu- cidate sampling, sequencing, and species tree estimation schemes to better utilize historical samples for phylogenetics.