Kelleher, Erin S.2019-09-152019-09-15August 2012019-08August 201Portions of this document appear in: Zhang, Shuo, and Erin S. Kelleher. "Targeted identification of TE insertions in a Drosophila genome through hemi-specific PCR." Mobile DNA 8, no. 1 (2017): 10.https://hdl.handle.net/10657/4697Transposable elements (TEs) are ubiquitous and selfish genetic entities whose mobilization poses a significant threat to their host. In the germline of metazoan, the Piwi-interacting RNAs (piRNAs) derived from TE-enriched loci (called piRNA clusters) regulate TE activity in a sequence specific manner. However, the emergence and dynamics of piRNA-mediated repressor alleles to an invading TE remain elusive. P-element, a DNA transposon that recently invaded the D. melanogaster genome around 1950, provides a unique opportunity to study the evolution of host repression. In this dissertation, I first adapted a targeted sequencing strategy and developed a computational pipeline to annotate P-element insertions in a sequenced Drosophila melanogaster genome. My approach precisely determined P-element insertion breakpoints and found new P-element insertions, which were undetected by previously methods. Next, I modified the pipeline to annotate P-element insertions in the Drosophila melanogaster genetic reference panel (DGRP), a panel composed of 205 fully sequenced inbred lines. I found over 90% of DGRP genomes have P-elements in ancestral piRNA clusters that are active prior to the P-element invasion. This indicates de novo mutation, in which P-elements transpose into pre-existing piRNA clusters, is the predominant mechanism for the origin of repressor alleles. Moreover, I detected no fewer than 84 independent P-element insertions in ancestral piRNA clusters. Finally, I observed that P-element insertions in piRNA clusters segregate at significant higher frequency than P-elements outside of piRNA clusters, suggesting that cluster P-elements confer a selective advantage. Taken together, my results revealed a striking example of polygenic adaptation, in which a plethora of de novo beneficial P-element insertions into multiple piRNA clusters, fueled the evolution of a ubiquitous repressive phenotype in <60 years.application/pdfengThe author of this work is the copyright owner. UH Libraries and the Texas Digital Library have their permission to store and provide access to this work. UH Libraries has secured permission to reproduce any and all previously published materials contained in the work. Further transmission, reproduction, or presentation of this work is prohibited except with permission of the author(s).Transposable elementP-elementPiRNADe novo mutationPolygenic adaptation2019-09-15Thesisborn digital