Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Alu elements are approximately 300 base pair (bp) primate specific non- autonomous retrotransposons. Alu elements, a short interspersed element (SINE), account for high copy numbers in all primate genomes. Numerous Alu element subfamilies have undergone varying degrees of activity and amplification within primates. Identification of these subfamilies has proved to be very informative in elucidating phylogenies and as phylogenomic markers. Squirrel monkeys, genus Saimiri, are one of the most well-known neotropical primates and the second most commonly used laboratory monkey. Squirrel monkey species diverged approximately 1.5 million years ago and are native to South America. Despite being well-known, there are many questions still unanswered regarding the evolutionary dynamics of the squirrel monkey and its genome. We computationally examined Saimiri lineage specific Alu element insertions. We determined the Alu subfamily amplification within the lineage is consistent with both the modified master gene model (a subfamily will accumulate copies for a certain time period and then become inactive) and with the stealth model (subfamilies with low retrotranspositional activity over extended periods of time with occasional short lived hyperactive copies) of Alu evolution. Forty-six new lineage specific subfamilies and 51 possible species indicative markers were reported within Saimiri lineage of New World Monkeys.

Baboons, genus Papio, are Old World Monkeys (OWMs) that reside in distinct regions but with overlapping hybrid zones. There are six species of baboons that are part of most recent studies, including: yellow baboon (P. cynocephalus), olive baboon (P. anubis), hamadryas baboon (P. hamadryas), guinea baboon (P. papio), chacma baboon (P. ursinus), and the kinda baboon (P. kindae). Recent studies have explored Alu element dynamics within baboons and determined there is extensive amplification within the lineage. We computationally examined the genome of the olive baboon (P. anubis) and identified 129 active Alu subfamilies in Papio baboons, with 127 of these subfamilies being baboon specific.



Committee Chair

Batzer, Mark