Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Alu mobile elements are much more than “junk DNA”. Inherent properties such as high copy number, small ~300 bp size, and their nearly homoplasy-free nature make these elements particularly useful in resolving primate phylogenies. In addition, shared sequence features and identity with the Alu element allow for discovery of new SINE retrotransposons, such as the Platyrrhine-limited Platy-1 element. Building on previous research of subfamily analysis, the Platy-1 and Alu elements can be used not only to explore the controversial New World monkey (NWM) phylogeny, but also the mode and tempo of their amplification in different primate genera and species.

Chapter 2 explores the amplification of the NWM-limited Platy-1 element. While a large expansion of Platy-1 elements was observed in the marmoset genome, the same cannot be said for the capuchin monkey, squirrel monkey and owl monkey genomes. Of these three genomes, only the owl monkey genome contained evidence of Platy-1 mobilization as shown by the presence of polymorphic (for insertion presence/absence) Platy-1 insertions, low percent divergence values, and the emergence of two new Platy-1 subfamilies. However, there were too few phylogenetically informative Platy-1 insertions to resolve the controversial Cebidae NWM phylogeny.

Chapter 3 characterizes the use of the polyDetect pipeline mapping short sequence reads to a reference genome for detecting shared Alu elements that could resolve the NWM phylogeny. However, the short homology provided by the reads was not enough to accurately predict shared Alu insertions of these four NWM genera that have diverged by ~20 million years.

Chapter 4 explores not only using longer stretches of identity/homology in the hope of accurately detecting shared Alu insertions, but also analyzes Alu subfamily evolution to resolve the Cebidae NWM phylogeny. A largely congruent network analysis and Bayesian phylogenetic tree were generated as well as Alu alignments, all suggesting that the branching pattern of marmoset, owl monkey, squirrel monkey and capuchin monkey starts with marmoset as the most basal of these four Cebidae NWMs, with owl monkey as a sister outgroup to the sister group of squirrel monkey and capuchin monkey.

Committee Chair

Batzer, Mark