Extended Data Fig. 5: Counts of young and old archaic alleles present in modern populations and shared by archaic reference genomes.

a, Recall that ‘young’ introgression calls are SNPs that appear in Call Set 2 generated by Sankararaman, et al. while ‘old’ calls appear in Call Set 1 for at least one archaic species but not in either set of young calls. In every modern human population, we find that 20-30% of old introgressed SNPs are shared with both the Altai Neandertal and Altai Denisovan, suggesting they likely predate the divergence of Neandertals and Denisovans or are at least old enough to have passed between the two species by gene flow. b, In contrast, only 10-20% of young introgressed SNPs are present in both archaic reference genomes. Over 45% of young Neandertal alleles are shared with the Altai Neandertal but not the Altai Denisovan; conversely, over 45% of young Denisovan alleles are shared with only the Denisovan reference. Compared to the sets of young Neandertal and Denisovan alleles, old Neandertal and Denisovan alleles look more similar to each other in their archaic reference sharing profiles: each contains 10-25% Neandertal-specific alleles and 2-10% Denisovan-specific alleles. These patterns support our hypothesis that the old calls are indeed older than the young calls. c, This panel shows the numbers of introgressed SNPs classified as young versus old within each population. Each SNP set is further subdivided into SNPs that appear in the Neandertal call set only, the Denisovan call set only, or the intersection of both call sets.