Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Retrotransposons are an active family of mobile elements within primate genomes and the Short INterspersed Element (SINE) Alu is the most abundant member. These non-autonomous elements are responsible for introducing genomic diversity on an intra- and inter- species level that is useful in studies of forensic identity, population genetics, and evolutionary biology. In a computational survey of the human sex chromosomes, 344 recently integrated Alu elements were detected and subjected to empirical testing by polymerase chain reaction to determine presence/absence polymorphism. Sixteen elements were found to be polymorphic on the X chromosome, and only one polymorphic element on the Y chromosome (previously termed YAP, Y chromosome Alu Polymorphism), across four geographically diverse populations. In line with previous research using other types of genetic markers, these results indicate a low Alu-associated diversity level on the human sex chromosomes, presumably due to reduced recombination rates and lower effective population sizes on the sex chromosomes. Alu elements often contribute to genomic instability via insertional and recombinational mutagenesis. Recently, a novel mechanism of retrotransposon-associated genomic instability was discovered, termed retrotransposition-mediated deletion. A computational search within the draft human and chimpanzee genomes found evidence of 33 retrotransposition-mediated deletion events that have eliminated approximately 9,000 nucleotides of genomic DNA. During the course of primate evolution, Alu retrotransposition may have contributed to over 3000 deletion events, eliminating approximately 900,000 bp of DNA in the process. Potential mechanisms for the creation of Alu retrotransposition-mediated deletions include L1 endonuclease-dependent retrotransposition, L1 endonuclease-independent retrotransposition, internal priming on DNA breaks, and promiscuous target primed reverse transcription (pTPRT). Approximately 0.27% of all human disease mutations are attributable to the activity of Long INterspersed Element (LINE) L1, Alu and SVA (SINE-R/VNTR/Alu) retrotransposons within our genomes. Although researchers in the field of human genetics have discovered many mutational mechanisms for retrotransposable elements, including retrotranspositional insertion, recombination, retrotransposition-mediated and gene conversion-mediated deletion, in addition to 3' transduction, their individual contribution to genetic variation within humans is still being resolved.



Document Availability at the Time of Submission

Release the entire work immediately for access worldwide.

Committee Chair

Mark Batzer