PT  - JOURNAL ARTICLE
AU  - Arun Durvasula
AU  - Sriram Sankararaman
TI  - Recovering signals of ghost archaic admixture in the genomes of present-day Africans
AID  - 10.1101/285734
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 285734
4099  - http://biorxiv.org/content/early/2018/03/21/285734.short
4100  - http://biorxiv.org/content/early/2018/03/21/285734.full
AB  - Analyses of Neanderthal and Denisovan genomes have characterized multiple interbreeding events between archaic and modern human populations. While several studies have suggested the presence of deeply diverged lineages in present-day African populations, we lack methods to precisely characterize these introgression events without access to reference archaic genomes. We present a novel reference-free method that combines diverse population genetic summary statistics to identify segments of archaic ancestry in present-day individuals. Using this method, we find that 7.97 ±0.6% of the genetic ancestry from the West African Yoruba population traces its origin to an unidentified, archaic population (FDR ≤20%). We find several loci that harbor archaic ancestry at elevated frequencies and that the archaic ancestry in the Yoruba is reduced near selectively constrained regions of the genome suggesting that archaic admixture has had a systematic impact on the fitness of modern human populations both within and outside of Africa.