Examples of IBD Segments that Match Archaic Genomes

Figure 28 shows a typical example of an IBD segment that matches the Denisova genome and is shared exclusively among Asians. Figure 29 shows an IBD segment that matches the Denisova genome and is shared by Africans and admixed Americans, and Fig. 30 shows an IBD segment that matches the Denisova genome and is shared across all populations. Furthermore, Fig. 30 reveals three phasing errors in the individuals where a yellow line starts from the left hand side: HG01271, NA12890, and NA19137. Figure 31 shows an example of an IBD segment that matches the Neandertal genome and is shared by Europeans and admixed American. Figure 32 shows an example of an IBD segment that matches the Neandertal genome and is shared by Europeans and Asians. Figure 33 shows an IBD segment that matches the Neandertal genome and is found exclusively in Africans. Another phasing error is visible in this figure in individual NA19317. Interestingly, IBD segments containing parts of the Denisova genome or the Neandertal genome are often shared by Africans.

Figure 34 shows an example of an IBD segment that matches the Denisova genome and is shared by Japanese. Further it can be seen that only a part of the IBD segment matches the Denisova genome. Figure 35 shows a second example of an IBD segment that matches the Denisova genome and is shared by Japanese. Again only a part of the IBD segment matches the Denisova genome.

Figure 28: Example of an IBD segment matching the Denisova genome shared exclusively among Asians (click image to enlarge). The data analyzed by HapFABIA were phased genotypes from chromosome 1 of the 1000 Genomes Project. The rows give all chromosomes that contain the IBD segment and columns consecutive SNVs. If both chromosomes of an individual contain the IBD segment then two adjacent identical row labels are present. Major alleles are shown in yellow, minor alleles of tagSNVs in violet, and minor alleles of other SNVs in cyan. The row labeled ``model L'' indicates tagSNVs identified by HapFABIA in violet. The rows ``Ancestor'', ``Neandertal'', and ``Denisova'' show bases of the respective genomes in violet if they match the minor allele of the tagSNVs (in yellow otherwise). Neandertal tagSNV bases that are not called are shown in orange.

Figure 29: Example of an IBD segment matching the Denisova genome shared by Africans and admixed Americans (click image to enlarge). See Fig. 28 for a description.

Figure 30: Example of an IBD segment matching the Denisova genome shared by Africans, Europeans, and admixed Americans (click image to enlarge). Phasing errors can be seen at individuals that share only some part of the IBD segments (partly empty rows): HG01271, NA12890, and NA19137. See Fig. 28 for a description.

Figure 31: Example of an IBD segment matching the Neandertal genome shared by Europeans and admixture Americans (click image to enlarge). See Fig. 28 for a description.

Figure 32: Example of an IBD segment matching the Neandertal genome shared by Europeans and Asians (click image to enlarge). See Fig. 28 for a description.

Figure 33: Example of an IBD segment matching the Neandertal genome shared exclusively among Africans (click image to enlarge). A phasing error is visible at individual NA19317. See Fig. 28 for a description.

Figure 34: Example 1 of an IBD segment that matches the Denisovan genome and is shared by Japanese (click image to enlarge). Only a part of the IBD segment matches the Denisovan genome. See Fig. 28 for a description.

Figure 35: Example 2 of an IBD segment that matches the Denisovan genome and is shared by Japanese (click image to enlarge). Only a part of the IBD segment matches the Denisovan genome. See Fig. 28 for a description.