The Distribution of Neanderthal Ancestry Across Populations And Within Genomes

Thesis (Ph.D.)--University of Washington, 2019For many millennia, modern humans overlapped in time and space with archaic humans such as Neanderthals and Denisovans. We now know that modern and archaic humans interbred, and that modern human populations carry some amount of archaic ancestry. The complexities of this admixture history, however, have persisted as outstanding questions in the field of archaic genomics. This dissertation focuses on some of these questions. In the first chapters of this dissertation, I focus on methods for detecting archaic sequence in modern humans and their application to geographically diverse populations. These studies provide insight regarding the distribution of Neanderthal ancestry across populations, and illustrate the complexity of the admixture dynamics between archaic and modern humans. Specifically, they show how pervasive archaic ancestry is across modern populations, being found in every population examined to date. Furthermore, they highlight a role for both Neanderthal-to-human gene flow and human-to-Neanderthal gene flow. These initial chapters also describe the heterogeneous distribution of archaic sequence across the genome, and raise questions about the dynamics and mechanisms by which archaic sequence was retained or lost. The later chapter of this dissertation extensively examines the mechanisms responsible for forming regions significantly depleted of archaic ancestry. By modeling demographic histories of admixture, I show that these regions are possible under neutral processes only through extreme conditions. Altogether, this work elucidates some of the complexities of archaic and modern human admixture and answers several of the outstanding questions in this field. Leveraging the discovery of archaic sequence provides an opportunity to better understand the evolutionary processes that have shaped the modern human genome and led to exceptional human phenotypes