Fig. 1

The fate of introgressed archaic haplotypes in the modern human genome. a Simplified demographic model of human populations. The size of the branches reflects effective population sizes (Ne), and a red arrow indicates Neanderthal introgression. Numbers indicate the relative position of the ancestral and present-day populations on the tree. b Haplotype structures and trajectory of archaic ancestry at three different regions that harbor distinct type of genetic variants (deleterious additive, deleterious recessive, beneficial). For ancestry trajectories, horizontal dotted line indicates the initial introgression frequency, green arrow represents the onset of selection for the beneficial allele. For haplotype structures, haplotypes are represented as columns. Neutral alleles are shown in blue, deleterious alleles in red (additive) or orange (recessive), and beneficial alleles in green