March 16, 2018
Human populations out of Africa have experienced at least two bouts of introgression from archaic humans, Neandertal and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on the detection of genomic regions with a high SNV density of SNVs not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a small rate of false detection. Furthermore our approach is able to accurately infer admixture proportions and divergence time of human and archaic populations. We apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neandertal or Denisovan origin. We report more Denisovan admixture than previous studies and directly find a shift in size distribution of fragments of Neandertal and Denisovan origin that is compatible with a difference in admixture time. Furthermore we identify small amounts of Denisova ancestry in West Eurasians, South East Asians and South Asians.