Detecting archaic introgression without archaic reference genomes

Abstract

15 Human populations out of Africa have experienced at least two bouts of introgression from 16 archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both 17 these introgressions. Here we present a new approach to detect segments of individual genomes 18 of archaic origin without using an archaic reference genome. The approach is based on a hidden 19 Markov model that identifies genomic regions with a high density of single nucleotide variants 20 (SNVs) not seen in unadmixed populations. We show using simulations that this provides a 21 powerful approach to identifying segments of archaic introgression with a small rate of false 22 detection. Furthermore our approach is able to accurately infer admixture proportions and 23 divergence time of human and archaic populations. 24 We apply the model to detect archaic introgression in 89 Papuans and show how the identified 25 segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan 26 admixture than previous studies and directly find a shift in size distribution of fragments of 27 Neanderthal and Denisovan origin that is compatible with a difference in admixture time. 28 Furthermore, we identify small amounts of Denisova ancestry in West Eurasians, South East Asians 29 and South Asians. 2 bioRxiv preprint doi: https://doi.org/10.1101/283606; this version posted March 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 30