The archaic/modern lists were generated from the material presented in (15). We used high-coverage genotypes for three archaic individuals: one Denisovan (58), one Neanderthal from the Denisova cave in Altai mountains (59), and another Neanderthal from Vindija cave, Croatia (60). The data are publicly available at http://cdna.eva.mpg.de/neandertal/Vindija/VCF/, with the human genome version hg19 as reference. High-frequency (HF) differences were defined as positions where more than 90% of present-day humans carry a derived allele, while at least the Denisovan and one Neanderthal carry the ancestral allele. High-frequency changes in archaics were defined as occurring at less than 1% in present-day humans, while at least two archaic individuals carry the derived allele. The HF lists used here were examined as presented in (15), with the exception of the HF lists in regulatory regions, which were extracted from the same dataset but not presented as such in the original paper.

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