We determined lineage-specific derived alleles by comparing the high-quality genomes of Vindija and the Altai Neandertal (8, 20), Denisova 3 (19), and a present-day human from Africa [Mbuti, HGDP00456 (19)]. At sites where one of these individuals was heterozygous, we randomly picked an allele. An allele was regarded as ancestral when it matched at least three of four aligned great ape reference genome assemblies [chimpanzee (panTro4) (21), bonobo (panPan1.1) (22), gorilla (gorGor3) (23), and orangutan (ponAbe2) (24); LASTZ alignments to the human genome GRCh37/hg19 prepared in-house and by the University of California, Santa Cruz, genome browser (31)]. The fourth ape was allowed to carry a third allele or have missing data but not to carry the alternative allele. To avoid errors from ancient DNA damage on HST and Scladina sequences at these positions, we only considered sequences that aligned in forward orientation when the ancestral or derived allele at the position was a G or in reverse orientation when either allele was a C and excluded sequences with a third allele. Only positions passing the published map35_100 filter for Denisova 3, Vindija, and the Altai Neandertal genotypes (20) were retained. A correction for the level of present-day human DNA contamination was applied in this analysis and is described in note S9.

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