Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph
Fig 8
A region with predicted heterozygous Sup→Den introgression.
A ∼170kb region on human chromosome 1 is shown in the UCSC Genome Browser. The first two tracks show the predicted regions and posterior probabilties as in Fig 7, except only the supToDen probabilities are shown. The next track shows the variants observed in this region that are used in the ARGweaver-D analysis, with alternating colors indicating variant alleles. Notice that, outside of the introgressed region, the Denisovan is generally homozygous and shares variants with Africans and Neanderthals; but within the region, the Denisova_2 haplotype has many singleton variants, whereas Denisova_1 continues to share many variants with Neanderthals and Africans. When chimpanzee alignments are available, the non-chimp allele is colored; otherwise the minor allele is colored. No color indicates that a haplotype has the chimpanzee or major allele, or missing data. The final phasing sampled by the ARGweaver-D algorithm was used.