Sub-Saharan Africans show U-shaped conditional site frequency spectra indicating archaic introgression. Archaic population split before Neanderthal-modern human divergence. Introgression occurred 0-124,000 years ago. Admixture fraction is 2-19% across Yoruba, Esan, Gambian, Mende. Yoruba genomes contain 482 megabases of archaic sequence. Mende genomes contain 502 megabases of archaic sequence. About 6.6-7% of Yoruba and Mende genomes are putatively archaic. Archaic segments more diverged than from Neanderthals, Denisovans, or Pygmies. TMRCA of archaic segments 1.23-1.69 times older than non-archaic. 33 loci in Yoruba and 37 in Mende have archaic segments at ≥50% frequency. High-frequency archaic genes include NF1 tumor suppressor, MTFR2 mitochondrial respiration, HSD17B2 hormone regulation. NF1, KCNIP4, TRPS1 show prior selection signals in Yoruba. Demographic models without archaic introgression fail to fit data. Ghost archaic effective population size 22,000-28,000. Archaics likely persisted in Africa until recently.
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