Fig. 4 |. Different landscapes of young and old introgressed archaic variation.

a, We classified introgression calls as old or young based on their presence in call sets 1 and 2 generated by Sankararaman et al.⁷. By design, the old alleles (present in call set 1 but not call set 2) are more often shared between Neandertals and Denisovans, and we hypothesize that many of these alleles arose before the Neandertal/Denisovan divergence, as pictured, or else crossed between the two species via Neandertal/Denisovan gene flow. In contrast, we hypothesize that the young alleles most often arose after Neandertals and Denisovans had begun to diverge. b, Numerical counts of old and young introgressed variants in the SGDP human genomes. Young Denisovan variants are probably rare because the Altai Denisovan was not closely related to the Denisovan population that primarily interbred with humans³⁶. c, We computed the fraction of CRF introgression calls that occur as derived alleles in the Altai Neandertal genome and/or the Altai Denisovan genome. As expected, old variants are two- to fourfold more likely than young variants to occur in both archaic reference genomes (see extended Data Fig. 5a,b for more data on allele sharing between introgression calls and the reference archaic genomes). d, In contrast with the young archaic variation considered elsewhere in this paper, old archaic variation is not measurably depleted from enhancers—even enhancers active in numerous tissues. All error bars span 95% binomial confidence intervals; confidence intervals that do not intersect the dotted line (shown at an odds ratio of 1.0) indicate significant depletion of archaic variants relative to matched controls.