Lengths of IBD Segments that Match Neandertal & Denisova

IBD segments that match the ``Archaic genome'' are IBD segments that match both the Neandertal and the Denisova genome. The archaic genome segments stem either from a genome of archaic hominids which were ancestors of Neandertals and Denisovans or stem from introgression of one hominid group into another. Hammer et al. (34) write

``The observation that populations from many parts of the world, including Africa, show evidence of introgression of archaic variants (6, 16, 19) suggests that genetic exchange between morphologically divergent forms may be a common feature of human evolution.''

Elizabeth Pennisi (35) writes:

``The analyses paint a complex picture of mingling among ancient human groups, Pääbo reported. The data suggest inbreeding in Neandertals, a large Denisovan population, and mixing between Denisovans and an even earlier mystery species.''

Figure 26A shows the density of the lengths of all IBD segments (human genome) vs. the density of the lengths of IBD segments that match the Archaic genome. For the human genome, the global density peak is at 24,200 bp (61 kya). For IBD with the Archaic genome, the global density peak is at 11,200 bp (109 kya), but a smaller peak at 42,000 bp (44 kya) can be observed. Figure 26B shows densities of lengths of IBD segments that match the Archaic genome and are enriched in a particular population. IBD lengths density peaks can be seen at 12,000 bp (103 kya) for most populations, 22,000 bp (65.5 kya) for Europeans, and 24,400 bp (61 kya) for Asians. The global peak for Africans is not separated from the global peaks of non-Africans, as we observed in Neandertal- or Denisova-matching IBD segments. Interestingly, a smaller peak is visible for both Europeans and Asians at 42,000 bp (44 kya). This peak at 42,000 bp has already been observed in Neandertal-matching IBD segments. There may be Neandertal matching IBD segments that do not match the single Denisova genome that has been sequenced, but might match other Denisova genomes. Therefore, some Neandertal matching segments might be also old and would belong to the ``Archaic genome'' matching IBD segments.

Figure 26: Panel A (click image to enlarge): Density of the lengths of all IBD segments vs. the lengths of IBD segments that match the Archaic genome. The dashed lines indicate the peaks of densities at 11,200 bp and 24,200 bp as well as the smaller peak at 42,000 bp. Panel B (click image to enlarge): Densities of lengths of IBD segments that match the Archaic genome and are enriched in a particular population. The dashed lines indicate the density peaks at 12,000 bp for most populations, 22,000 bp for Europeans, and 24,400 bp for Asians. Further, a smaller peak is visible for both Europeans and Asians at 42,000 bp.

Next we consider IBD segments that are private to a population. Figure 27A shows densities of lengths of IBD segments that match the Archaic genome and are private to a population. The peaks are at 13,000 bp (97 kya) for humans (1000 Genomes Project), 13,600 bp (93.5 kya) for Europeans, 19,500 bp (71 kya) for Asians, and 21,000 (68 kya) for Africans. A peak appears at 46,000 bp (42 kya) for IBD segments that are private to Europeans. Figure 27B shows densities of lengths of IBD segments that match the Archaic genome and are private to Africans vs. IBD segments that are not observed in Africans. The peak for Africans is at 22,000 bp (65.5 kya), while lengths of IBD segments that are not observed in Africans have a global peak at 14,700 bp (88 kya). However, Africans have also a peak at 14,300 bp (90 kya), while IBD segments that are not observed in Africans have a peak at 21,000 (68 kya). These peaks match quite well on a global scale. Most prominently, non-African IBD segments that match the Archaic genome are enriched in the range 33,000-55,000 bp (50-38 kya). This enrichment seem to be caused by events after humans migrated out of Africa. The introgression from the Neandertal into ancestors of modern humans may also have introduced a part of the Denisovan genome that has been contained in the Neandertal genome. We would consider this part of the human genome as Archaic genome. Another explanation would be that introgression from the Neandertal into human has introduced archaic genome parts that were lost in the human population in Africa, but still match the Denisovan genome.

Figure 27: Panel A (click image to enlarge): Densities of lengths of IBD segments that match the Archaic genome and are private to a population. The peaks are at 13,000 bp for humans, 13,600 bp for Europeans, 19,500 bp for Asians, and 21,000 for Africans. A peak appears at 46,000 bp for Europeans. Panel B (click image to enlarge): Densities of lengths of IBD segments that match the Archaic genome and are private to Africans vs. IBD segments that are not observed in Africans. The peak for Africans is at 22,000 bp, while the lengths of IBD segments that are not observed in Africans have a global peak at 14,700 bp. However, Africans have also a peak at 14,300 bp, while IBD segments that are not observed in Africans have a peak at 21,000 bp. These peaks match quite well. Most prominently, non-African IBD segments that match the Archaic genome are enriched in the range 33,000-55,000 bp (blue density).