IBD Segment Lengths of Human Populations

Figure 18 shows the density of the lengths of IBD segments that are private to Asians vs. the density of the lengths of IBD segments that are private to Europeans. Since IBD segments are private to each population, the densities are based on disjoint IBD segment sets. Asians show a global peak at 25,800 bp (39 kya in the past from present), while Europeans show a global peak at 24,200 bp (41 kya). Europeans have also smaller peaks at 17,000 bp (59 kya) and 29,000 bp (34.5 kya).

Figure 18: Density of lengths of IBD segments that are private to Asians vs. the analogous density for Europeans (click image to enlarge). Interesting peaks are marked by dashed lines. Asians have a global peak at 25,800 bp (red), while Europeans have the global peaks at 24,200 bp (blue). Europeans have smaller peaks at 17,000 bp and 29,000 bp (blue).

Figure 19A shows the density of lengths of IBD segments that are private to Asians vs. lengths of IBD segments that are only shared between Asians and Africans. Figure 19B shows the same plot for Europeans instead of Asians. A small difference is visible in the global peaks of lengths distributions of IBD segments that are private to a population and those shared with Africans (blue dashed lines): 25,800 bp (39 kya) vs. 22,200 (45 kya) for Asians and 24,200 bp (41 kya) vs. 22,000 (45.5 kya) for Europeans. Interestingly, even though the IBD segments used in both plots are disjoint, African-sharing IBD segment lengths distributions agree in their major peak at about 22,000 bp (45.5 kya) and in a peak at 5,000 bp (200 kya). The global Asian peak is at 25,800 bp (red dashed line in Fig. 19A), while the global peak for Europeans is at 24,200 bp (red dashed line in Fig. 19B). Europeans in Fig. 19B have additional peaks at 16,500 bp and 28,900 bp. The peak at 5,000 bp is in a range where African-sharing IBD segment lengths are enriched. This range is from 3,000 bp (333 kya) to 10,000 bp (100 kya). We follow up on the 5,000 bp peak by investigating the lengths of IBD segments that are shared by Asians, Europeans, and Africans.

Figure 19: Panel A (click image to enlarge): Density of lengths of IBD segments that are private to Asians vs. density of IBD segment lengths shared only by Asians and Africans. Panel B (click image to enlarge): Density of lengths of IBD segments that are private to Europeans vs. density of IBD segment lengths shared only by Europeans and Africans. Both for African-Asian and for African-European IBD segments, peaks coincide at 5,000 bp and at about 22,000 bp (blue dashed lines). The global Asian peak is at 25,800 bp (red dashed line in panel A), while the global peak for Europeans is at 24,200 bp (red dashed line in panel B). Europeans (in panel B) have additional peaks at 16,500 bp and 28,900 bp.

Figure 20A shows the density of lengths of IBD segments that are private to Asians vs. lengths of IBD segments that are shared between Asians, Europeans, and Africans. Figure 20B shows the same plot for Europeans instead of Asians. Of course, the peaks for Asians and Europeans are the same as in the previous plot. The peak at 5,000 bp (200 kya) is also visible for lengths of IBD segments that are shared by all populations and which marks the higher density range 3,000-10,000 bp (333-100 kya). IBD segments that are shared by all populations seem to be very old. Fu et al. (20) found that the SNVs shared between European Americans and African Americans date back 104,400 and 115,800 years, respectively. We would date our rare tagSNVs even further back. However, the estimated age of the IBD segments should be considered with care. The computation of the time since the last common ancestor depends on many assumptions like the length of a generation, the recombination rate (ratio between centiMorgans and megabases), and the distribution of IBD lengths.

Figure 20: Panel A (click image to enlarge): Density of lengths of IBD segments that are private to Asians vs. density of IBD segment lengths shared by Asians, Europeans, and Africans. Panel B (click image to enlarge): Density of lengths of IBD segments that are private to Europeans vs. density of IBD segment lengths shared by Asians, Europeans, and Africans. The peak at 5,000 bp is again visible marking the range 3,000-10,000 bp, where the density of lengths of shared IBD segments is larger (blue).

Next we investigated the effect on the lengths distribution if IBD segments are removed that are shared by Africans. Figure 21A shows the density of lengths of IBD segments that are private to Asians vs. the density of IBD segment lengths shared by Asians and Europeans, but not by Africans. In Fig. 21B, the same plot as in Fig. 21A is shown, but now compared to IBD segments that are private to Europeans. In Fig. 20A and B, the density for IBD segments that are shared with Africans, has high values in the range 3,000-10,000 bp (blue). In Fig. 21A and B, this peak vanishes, because IBD segments that are shared with Africans are removed. A density peak at 50,000 bp (20 kya) becomes very prominent for the lengths of IBD segments that are shared between Europeans and Asians, but not with Africans. The density of lengths of IBD segments shared between Europeans and Asians (blue) is higher between 35,000 bp (28.5 kya) and 55,000 bp (18 kya) than all lengths densities of IBD segment that are shared by Africans .

Figure 21: Panel A (click image to enlarge): Density of lengths of IBD segments that are private to Asians vs. density of IBD segment lengths shared by Asians and Europeans but not by Africans that means, African-sharing IBD segments are removed as opposed to Fig. 20A. Panel B (click image to enlarge): The same plot as in panel A but, but IBD segments that are shared by Europeans and Asians are compared to IBD segments that are private to Europeans. African-sharing IBD segments are removed as opposed to Fig. 20B. Both panels show that removing IBD segments shared with Africans in turn remove the peak at 5,000 bp and the high density range 3,000-10,000 bp which were visible in Fig. 20. In panel B a peak at 50,000 bp (blue) becomes very prominent for lengths of IBD segments shared between Europeans and Asians (no Africans).