Patterns of Archaic Hominin DNA in Modern Human Genomes

Thesis (Ph.D.)--University of Washington, 2015In this dissertation I describe the development of a method for identifying introgressed archaic haplotypes. I then present the application of this method to several populations. In 15 African hunter-gatherer genomes, I identify signatures of introgression from an unknown archaic hominin with an apparent divergence time with modern humans that is similar to the divergence time of Neanderthals. In a sample of 379 European and 279 East Asian genomes, I identify on average 1/4 of each individual's introgressed Neanderthal sequence, composing a total of 600Mb of the Neanderthal genome. I use characteristics of this sequence to estimate demographic parameters, including ancestral effective population size (Ne), and the complexity of the introgression event. I also present signatures of both purifying selection against Neanderthal sequence in modern humans, and selection for other, beneficial Neanderthal alleles. In a separate analysis, I show that the inferred parameters of the introgression event are not influenced by differing efficiency of selection between Europeans and East Asians, and explore alternative models for the complexity of the introgression event. In a sample of 35 Melanesian individuals from Papua New Guinea, I identify both Neanderthal and Denisovan introgression, and use this map of archaic introgression to identify regions of the genome that are depleted of archaic sequence from two independent introgression events, implying the presence of non-random forces such as selection in the creation of such regions