Doctor of Philosophy (PhD)


Biological Sciences

Document Type



The rapidly increasing amount of sequence data has brought about a new appreciation for the tremendous influence mobile elements have had in shaping eukaryotic genomes. Despite their ubiquity, however, the factors governing the proliferation of mobile elements—or, in some cases, the lack of proliferation—across diverse taxa remain poorly understood. Analysis of Alu activity in humans and chimpanzees since their divergence indicates a two-fold increase in human Alu activity compared to that of the chimpanzee. This human retrotransposition increase is accompanied by a roughly two-fold higher level of chimpanzee Alu diversity. We prepose a model, wherein smaller effective population sizes in humans brought about a shift in host-element dynamic, ultimately leading to increased Alu activity in humans. We also survey Alu-associated diversity on the human sex chromosomes in order to examine whether Alu elements behave similarly to genetic marker systems. Our results suggest that, comparable to other genetic systems, Alu elements exhibit reduced diversity on the sex chromosomes. Our data provide no evidence for retrotransposon targeted biology influencing Alu insertion frequencies. We go on to synthesize several recent advances in the mobile element field and propose a novel hypothesis concerning how retrotransposon lineages manage to largely lie below the radar of population-level negative selection.



Document Availability at the Time of Submission

Release the entire work immediately for access worldwide.

Committee Chair

Mark Batzer