Lengths of IBD Segments that Match the Denisova Genome

Figure 22A shows the density of the lengths of all IBD segments (human genome) vs. the density of the lengths of IBD segments that match the Denisovan genome. The human IBD segment lengths density has a peak at 24,200 bp (41 kya), while the lengths distribution of IBD with the Denisovan genome has a peak at 9,000 bp (131 kya). Clearly, segments of IBD with the Denisovan genome are shorter than among humans (red density above blue at the left hand side). We are interested in how different populations share the Denisovan genome. Figure 22B shows densities of lengths of IBD segments that match the Denisova genome and are enriched by a particular population. For Africans, the density peak is at 8,500 bp (137 kya). Asians have a clear enrichment of IBD lengths in the range 18,000-28,000 bp (75-56 kya). Europeans show three peaks at 18,000 (75 kya), 25,500 (59 kya), and 40,000 (45 kya). This density seems to reveal that there was a gene flow from Denisovans into the Asian genome outside Africa. However, also Europeans show some hints of introgression from the Denisovans after migration out of Africa.

Figure 22: Panel A (click image to enlarge): Density of the lengths of all IBD segments vs. the lengths of IBD segments that match the Denisova genome. The dashed lines indicate the peaks at 9,000 bp for Denisovan and 24,200 bp for human genome. Panel B (click image to enlarge): Densities of lengths of IBD segments that match the Denisova genome and are enriched in a particular population. The dashed lines indicate the density peaks at 8,500 bp for for Africans; 24,400 bp for Asians (range 18,000-28,000 bp); 18,000, 25,500, and 40,000 bp for Europeans.

These peaks can be seen more clearly if only IBD segments are considered that are private to a population. Figure 23A shows densities of lengths of IBD segments that match the Denisova genome and are private to a population. For all populations together, the peak of the lengths density is at 8,500 bp (137 kya); for IBD segments private to Africans, it is at 9,700 (123 kya); for IBD segments private to Europeans, it is at 14,800 (87 kya); and for IBD segments private to Asians, it is at 27,000 (57 kya). The density of IBD lengths that match the Denisova genome and are private to Asians is also high around 40,000 bp (45 kya). Figure 23B shows densities of lengths of IBD segments that match the Denisova genome and are private to Africans vs. IBD segments that are not observed in Africans. The peak for Africans is at 10,000 bp (120 kya), while the density of lengths of IBD segments that are not observed in Africans has peaks at 20,000 (70 kya) and 28,000 bp (56 kya). Africans have older segments probably stemming from common ancestors of Denisovans and humans. For non-African populations, the high densities for longer IBD segments hint at an introgression from Denisovans after migration out of Africa. Parts of the Denisovan or archaic genomes may also have been introduced by Neandertals after migration out of Africa. Neandertals may have re-introduced parts of archaic genomes that were lost in humans or parts of the Denisovan genome stemming from introgression of one hominid group into another.

Figure 23: Panel A (click image to enlarge): Densities of lengths of IBD segments that match the Denisova genome and are private to a population. The peaks are at 8,500 for ll IBD segments matching the Denisova genome, 9,700 for Africans, 14,800 for Europeans, and 27,000 for Asians. Panel B (click image to enlarge): Densities of lengths of IBD segments that match the Denisova genome and are private to Africans vs. IBD segments that are not observed in Africans. The peak for Africans is at 10,000 bp, while IBD segment lengths that are not observed in Africans have peaks at 20,000 and 28,000 bp.