Lengths of IBD Segments that Match the Neandertal Genome

Figure 24A shows the density of the lengths of all IBD segments (human genome) vs. the density of the lengths of IBD segments that match the Neandertal genome. The human IBD segment lengths density has a peak at 24,200 bp (41 kya), while the lengths distribution of IBD segments with the Neandertal genome (the part of the IBD segment that matches the Neandertal genome) has a global peak at 18,000 bp (75 kya) and a smaller peak at 43,000 bp (43 kya). Figure 24B shows densities of lengths of IBD segments that match the Neandertal genome and are enriched in a particular population. The peak of the lengths distribution for IBD segments that are shared by Africans is at 17,000 bp (79 kya). Asians have a density peak at 25,800 bp (59 kya) and Europeans have a peak at 24,000 bp (62 kya). Both the densities of lengths of IBD segments that are private to Europeans and that are private to Asians and match the Neandertal genome have a peak around 42,000 bp (44 kya). The density peak for Africans is clearly separated from the density peaks for Europeans and Asians which match each other. This hints to introgression from the Neandertals into anatomically modern humans that were the ancestors of Europeans and Asians after these humans left Africa. The higher density of short IBD segments which are prominent in Africans in the range 5,000-15,000 bp (220-87 kya) hint at old DNA segments that humans share with the Neandertal genome.

Figure 24: Panel A (click image to enlarge): Density of the lengths of all IBD segments vs. the lengths of IBD segments that match the Neandertal genome. The dashed lines indicate the peaks of densities at 18,000 bp and 24,200 bp as well as the smaller peak at 43,000 bp. Panel B (click image to enlarge): Densities of lengths of IBD segments that match the Neandertal genome and are enriched in a particular population. The dashed lines indicate the density peaks at 17,000 bp for Africans, 25,800 bp for Asians, and 24,000 bp for Europeans. Further a smaller peak for both Europeans and Asians is visible at 42,000 bp.

Next we consider IBD segments that are private to a population. Figure 25A shows densities of lengths of IBD segments that match the Neandertal genome and are private to a population. The peaks are at 15,500 bp (84.5 kya) for Africans, at 19,500 bp (71 kya) for all humans, at 22,800 bp (64 kya) for Europeans, and at 23,800 bp (62 kya) for Asians. The densities of Asians and Europeans agree very well to each other. The peak close to 43,000 bp is no longer visible and seems to have been caused by IBD segments that are shared between Asians and Europeans. Therefore, we are interested in IBD segments that match the Neandertal genome and that are private to Africans and those which are not observed in Africans. Figure 25B shows densities of lengths of IBD segments that match the Neandertal genome and are private to Africans vs. IBD segments that are not observed in Africans. The peak for Africans is at 17,000 bp (79 kya), while IBD segments that are not observed in Africans have a global lengths density peak at 23,800 (62,000 years) and a smaller peak at 21,000 bp (68 kya). Interestingly, the peak near 43,000 bp (43 kya) is again visible. Thus, this peak is from IBD segments that are shared between Europeans and Asians. Most prominently, non-African IBD segments that match the Neandertal genome are enriched in the range 40,000-55,000 bp (45-38 kya).

Figure 25: Panel A (click image to enlarge): Densities of lengths of IBD segments that match the Neandertal genome and are private to a population. The peaks are at 15,500 bp for Africans, 19,500 bp for all humans, 22,800 bp for Europeans, and 23,800 bp for Asians. Panel B (click image to enlarge): Densities of lengths of IBD segments that match the Neandertal genome and are private to Africans vs. IBD segments that are not observed in Africans. The peak for Africans is at 17,000 bp, while IBD segments that are not observed in Africans have a global lengths density peak at 23,800 and a smaller peak at 21,000 bp. The peak near 43,000 bp is again visible. Most prominently, non-African IBD segments that match the Neandertal genome are enriched in the range 40,000-55,000 bp (blue density).