Densities of Population Proportions and Archaic Genomes

We plot densities of population proportions for IBD segments that match a particular archaic genome (30% or more SNVs match) and for those that do not match that genome. Figure 7 shows the density of Asian proportions of Denisova-matching IBD segments (pink) vs. density of Asian proportions of non-Denisova-matching IBD segments (cyan). Figure 8 shows analogous densities for Europeans. Denisova-matching IBD segments are observed more often in Asians and Europeans than non-matching IBD segments. This can be seen by the higher densities of matching IBD segments (pink) compared to densities of non-matching IBD segments (cyan) if the population proportions are not very close to zero -- or, conversely, it can be seen at the lower peak at zero (less IBD segments that match the Denisova genome without Asians or European sharing). Many Denisova-matching IBD segments are shared exclusively among Asians which is indicated by the high density at a population proportion of 1 (pink density in Fig. 7). Population proportion of 1 means that IBD segments are only shared among Asians. Figs. 10 and 11 show analogous densities as in Figs. 7 and 8, but for the Neandertal genome. The differences we already observed for Denisova are even more prominent for Neandertal: Neandertal-matching IBD segments are observed even more often in Asians and Europeans than non-matching IBD segments. The higher densities (pink) are now more clearly observable if the population proportion is not close to zero -- or conversely, it can be seen at the lower peak at zero (less IBD segments that match the Neandertal genome without Asians or European sharing). For Asians, the peak at 1 in Fig. 10 is very prominent, representing IBD segments that are shared exclusively among Asians. IBD segment sharing exclusively within one population is very common, as the blue peaks at 1 in Fig. 7 and Fig. 10 show. Figs. 9 and 12 show the same densities for Africans. Both the density of African proportions of Denisova-matching and the same density for Neandertal-matching IBD segments have two peaks: one at a low and one at a high proportion of Africans. For Neandertal-matching IBD segments, the density at low proportions of Africans is even larger than for high proportions. Thus, IBD segments that match archaic genomes are either shared by a very low or a very high proportion of Africans. The low proportion of African density peak hints at admixture of ancestors of modern humans and Denisovans / Neandertals outside of Africa. The density peak at high proportions of Africans may be be archaic DNA segments shared by hominid groups.

IBD segments that match the ``Archaic genome'' are the IBD segments that match both the Denisova and Neandertal genome. Population proportion densities for the ``Archaic genome'' are presented in Figs. 13, 14, and 15 for Asians, Europeans, and Africans, respectively. For the ``Archaic genome'' we see the same figure as for the Neandertal and Denisova genome: the African density is bimodal that means either it is dominated by Africans or it contains no or only few Africans.

We found that Japanese share parts of the Denisovan genome. An example of an IBD segment that is shared by Japanese and that matches the Denisovan genome can be found in Fig. 28. Further examples can be seen in Figures 34 and 35.

Figure 7: Panel A (click image to enlarge): Density of Asian proportions of Denisova-matching IBD segments (pink) vs. density of Asian proportions of non-Denisova-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Panel B (click image to enlarge): The same density as in Panel A but zoomed in.

Figure 8: Panel A (click image to enlarge): Density of European proportions of Denisova-matching IBD segments (pink) vs. density of European proportions of non-Denisova-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Panel B (click image to enlarge): The same density as in Panel A but zoomed in.

Figure 9: Panel A (click image to enlarge): Density of African proportions of Denisova-matching IBD segments (pink) vs. density of African proportions of non-Denisova-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Peaks for non-Denisova-matching IBD segments are found at 0.5, 0.66, 0.33, 0.75, and 0.8, which corresponds to 1/2, 2/3, 1/3, 3/4, 4/5 (number of Africans / all individuals that have the IBD segment). The density of African proportions of Denisova-matching IBD segments has two peaks: one at a low and one at a high proportion of Africans. Panel B (click image to enlarge): The same density as in Panel A but zoomed in.

Figure 10: Panel A (click image to enlarge): Density of Asian proportions of Neandertal-matching IBD segments (pink) vs. density of Asian proportions of non-Neandertal-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Many Neandertal-enriched IBD segments are shared mainly or exclusively by Asians as the proportion close to 1 shows. Panel B (click image to enlarge): The same density as in Panel A but zoomed in.

Figure 11: Panel A (click image to enlarge): Density of European proportions of Neandertal-matching IBD segments (pink) vs. density of European proportions of non-Neandertal-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Many Neandertal-enriched IBD segments are shared mainly or exclusively by Asians as the proportion close to 1 shows. Neandertal-enriched IBD segments are shared by Europeans but fewer segments are shared exclusively among Europeans than for Asians (see Fig. 10). Panel B (click image to enlarge): the same density zoomed in.

Figure 12: Panel A (click image to enlarge): Density of African proportions of Neandertal-matching IBD segments (pink) vs. density of African proportions of non-Neandertal-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Peaks for non-Neandertal-matching IBD segments are found at 0.5, 0.66, 0.33, 0.75, and 0.8, which corresponds to 1/2, 2/3, 1/3, 3/4, 4/5 (number of Africans / all individuals that have the IBD segment). The density of African proportions of Neandertal-matching IBD segments has two peaks: one at a low and one at a high proportion of Africans. The density of low proportions of Africans is even larger than for high proportions. Panel B (click image to enlarge): the same density zoomed in.

Figure 13: Panel A (click image to enlarge): Density of Asian proportions of Archaic-genome-matching IBD segments (pink) vs. density of Asian proportions of non-Archaic-genome-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Panel B (click image to enlarge): the same density zoomed in.

Figure 14: Panel A (click image to enlarge): Density of European proportions of Archaic-genome-matching IBD segments (pink) vs. density of European proportions of non-Archaic-genome-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Many Archaic-genome-enriched IBD segments are shared mainly or exclusively by Asians as the proportion close to 1 shows. Panel B (click image to enlarge): the same density zoomed in.

Figure 15: Panel A (click image to enlarge): Density of African proportions of Archaic-genome-matching IBD segments (pink) vs. density of African proportions of non-Archaic-genome-matching IBD segments (cyan). IBD segments were extracted from phased genotyping data of chromosome 1 of the 1000 Genomes Project. Dotted lines indicate the respective means. Peaks for non-Archaic-genome-matching IBD segments are found at 0.5, 0.66, 0.33, 0.75, and 0.8, which corresponds to 1/2, 2/3, 1/3, 3/4, 4/5 (number of Africans / all individuals that have the IBD segment). The density of African proportions of Archaic-genome-matching IBD segments has two peaks: one at a low and one at a high proportion of Africans. Panel B (click image to enlarge): the same density zoomed in.