Title: Inferring the structure of archaic admixture in present-day humans

Abstract:

Analysis of the genomes of archaic hominins, such as Neandertals and Denisovans, has revealed that these groups have contributed to the genetic variation of modern human populations. Characterizing these admixture events and their impact on the structure and function of human genomes is an important problem in human population genomics. To systematically understand the structure of archaic admixture, we need to infer archaic local ancestry i.e., a labeling of each region of an individual genome as tracing its ancestry to an archaic population. To this end, we have developed a discriminative statistical model for inferring archaic local ancestry. We applied this model to infer maps of Neandertal as well as Denisovan local ancestry in diverse populations of present-day humans. Analyses of these maps document fine-scale variation in archaic ancestries across populations (including elevated Denisovan ancestry in populations in east and south Asia) as well as along the genome (driven partly by the action of selection on archaic alleles) and illustrate the impact of archaic admixture on human biology.