Lavanya Rishishwar Thesis Defense

Monday, November 7th, 2016 Thesis Advisor: Dr. King Jordan, School of Biological Sciences Committee Members: Dr. John McDonald, School of Biological Sciences Dr. Greg Gibson, School of Biological Sciences Dr. Soojin Yi, School of Biological Sciences Dr. Leonardo Mariño-Ramírez, National Center for Biotechnology Information, National Institute of Health Abstract: Transposable element (TE) activity has had a major impact on the human genome; more than two-thirds of the sequence is derived from TE insertions. Several families of human TEs - primarily Alu, L1 and SVA - continue to actively transpose, thereby generating insertion polymorphisms between individuals. Until very recently, it has not been possible to characterize the genetic variation generated by the activity of these TE families at the scale of whole genomes for multiple individuals within and between human populations. For this reason, the impact of recent TE activity on human evolution has yet to be fully appreciated. My dissertation research leverages novel technologies in data science to investigate the role that recent TE activity has played in shaping human population genetic variation. Specifically, my dissertation addresses three problems: 1) evaluation of the computational techniques used to characterize human polymorphic TE insertion sites from whole genome, next-generation sequence data, 2) characterization of the population genomic variation of human polymorphic TEs and evaluation of their effectiveness as markers of human genetic ancestry and admixture, and 3) analysis of the effects that natural selection (negative and positive) has exerted on human polymorphic TE insertions. I close by presenting a broad prospectus on the implications of genome-scale analyses of human polymorphic TE insertions for population and clinical genetic studies. The results reported in this dissertation represent the dawn of the population genomics era for human TEs.