Overview of the Results

We extracted very short identity by descent (IBD) segments (see definition in next subsection) from the 1000 Genomes Project genotyping data (2). On chromosome 1, we identified 160,588 different very short IBD segments that are characterized by rare variants. These segments contained 751,592 rare variants, which amounts to 39% of the rare variants and 23.5% of all SNVs. The length of IBD segments ranged from 34 base pairs to 21 Mbp, with a median of 23 kbp and a mean of 24 kbp. The vast majority (152,120) of the detected IBD segments are shared by Africans. We estimate that these short IBD segments are on average from about 40 thousands years ago (kya) and up to 200 kya. The following results report IBD sharing within human populations, IBD sharing between humans and Denisovans and between human and Neandertals. The analyses relate the length of an IBD segment to the recent common ancestor of all the individuals that possess the IBD segment. The IBD lengths reveal facts about separations of populations, introgression from archaic genomes, and conserved parts of the human genome stemming from archaic hominids.

Overview of results concerning IBD sharing within human populations:

• The lengths of IBD segments shared between Non-Africans and Africans are enriched at 5,000 bp ($\sim$ 200 kya) and 22,000 bp ($\sim$ 45.5 kya).
• The lengths of IBD segments shared between Non-African populations and not observed in Africans is enriched at 35,000 bp (28.5 kya) and 55,000 bp (18 kya).
• IBD segments that are found in only one population are contrasted to IBD segments that are only found in this population but also in Africans. Asians: 25,800 bp (39 kya) vs. 22,200 (45 kya); Europeans: 24,200 bp (41 kya) vs. 22,000 (45.5 kya). IBD segments shared with Africans are shorter and older.
• For IBD segments that are shared between Europeans and Asians (out-of-Africa), but not with Africans, a peak in length is at 50,000 bp (20 kya). (Are these segments rare or lost in Africans? Did they enter the genome before ancestors of Asians and Europeans separated but after they left Africa?)

Overview of results concerning IBD sharing between humans and Denisovans (20 kya time off-set due to archaic DNA, see Section 4.1.3):

• Denisova matching IBD segments have a peak for African-observed at 8,500 bp (137 kya) and for African-private at 9,700 (123 kya). (``African-observed'': IBD segment is found in at least one African; ``African-private'': IBD segment is only found in Africans)
• Denisova matching IBD segments have a peak for Asian-observed in the range 18,000-28,000 bp (75-56 kya) and for Asian-private at 27,000 (57 kya).
• Denisova matching IBD segments have peaks for European-observed at 18,000 (75 kya), 25,500 (59 kya), and 40,000 (45 kya) and for European-private at 14,800 (87 kya).
• Denisova matching IBD segments have peaks for IBD segments that are not observed in Africans at 20,000 (70 kya) and 28,000 bp (56 kya).

Overview of results concerning IBD sharing between humans and Neandertals (20 kya time off-set due to archaic DNA, see Section 4.1.3):

• Neandertal matching IBD segments have a peak for African-observed at 17,000 bp (79 kya) and for African-private at 15,500 bp (84.5 kya).
• Neandertal matching IBD segments have a peak for Asian-observed at 25,800 bp (59 kya) and for Asian-private at 23,800 bp (62 kya).
• Neandertal matching IBD segments have a peak for European-observed at 24,000 bp (62 kya) and for European-private at 22,800 bp (64 kya).
• Neandertal matching IBD segments have a a peak around 42,000 bp (44 kya) if they are private to Europeans or to Asians.

Overview of results concerning IBD sharing between humans, Neandertals, and Denisovans (20 kya time off-set due to archaic DNA, see Section 4.1.3):

• For IBD segments that are shared between humans, Neandertals and Denisovans, a global density peak of the IBD lengths is at 11,200 bp (103 kya), but a smaller peak at 42,000 bp (44 kya). The global peak gives also the African peak.
• For IBD segments that are shared between Europeans, Neandertals and Denisovans the length peak is at 22,000 bp (65.5 kya).
• For IBD segments that are shared between Asians, Neandertals and Denisovans the length peak is at 24,400 bp (61 kya).
• For IBD segments that are shared between Europeans, Asians, Neandertals and Denisovans, a smaller length density peak is visible 42,000 bp (44 kya) which was also observed in Neandertal-matching IBD segments.

These results hint at:

• (1) an admixture of humans and archaic genomes outside of Africa and
• (2) an admixture of humans and archaic genomes within Africa or survival of ancient DNA segments in humans.