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. 2016 Dec 1;8(12):3406-3416.
doi: 10.1093/gbe/evw234.

IBD Sharing between Africans, Neandertals, and Denisovans

Gundula Povysil  1 , Sepp Hochreiter  1
Affiliations

IBD Sharing between Africans, Neandertals, and Denisovans

Gundula Povysil et al. Genome Biol Evol. .

Abstract

Interbreeding between ancestors of humans and other hominins outside of Africa has been studied intensively, while their common history within Africa still lacks proper attention. However, shedding light on human evolution in this time period about which little is known, is essential for understanding subsequent events outside of Africa. We investigate the genetic relationships of humans, Neandertals, and Denisovans by identifying very short DNA segments in the 1000 Genomes Phase 3 data that these hominins share identical by descent (IBD). By focusing on low frequency and rare variants, we identify very short IBD segments with high confidence. These segments reveal events from a very distant past because shorter IBD segments are presumably older than longer ones. We extracted two types of very old IBD segments that are not only shared among humans, but also with Neandertals and/or Denisovans. The first type contains longer segments that are found primarily in Asians and Europeans where more segments are found in South Asians than in East Asians for both Neandertal and Denisovan. These longer segments indicate complex admixture events outside of Africa. The second type consists of shorter segments that are shared mainly by Africans and therefore may indicate events involving ancestors of humans and other ancient hominins within Africa. Our results from the autosomes are further supported by an analysis of chromosome X, on which segments that are shared by Africans and match the Neandertal and/or Denisovan genome were even more prominent. Our results indicate that interbreeding with other hominins was a common feature of human evolution starting already long before ancestors of modern humans left Africa.

Keywords: identity by descent; interbreeding; Denisova; human evolution; gene flow; Neandertal.

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Figures

F<sc>ig</sc>. 1.—
Fig. 1.—
Example of a Denisovan-matching IBD segment shared among Africans. The rows represent all individuals that have the IBD segment, and columns represent consecutive variants. Major alleles are shown in yellow, minor alleles of variants that tag the IBD segment (tagSNVs) in violet, and minor alleles of other variants 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). For the “Ancestor genome”, we used the reconstructed common ancestor sequence that was provided as part of the 1000 Genomes Project data.
F<sc>ig</sc>. 2.—
Fig. 2.—
Example of a Neandertal-matching IBD segment shared among Africans. This segment is tagged by more than 100 minor alleles. See figure 1 for a detailed description.
F<sc>ig</sc>. 3.—
Fig. 3.—
Predominant population for an IBD segment and genome. For each IBD segment, the population in which it is predominantly found is determined. “All” stands for all IBD segments found, while “Neandertal” and “Denisovan” denote all IBD segments matching the Neandertal and Denisovan sequence, respectively. The color indicates the population to which more than 50% of the individuals with the corresponding IBD segment are assigned to. Gray slices indicate IBD segments for which neither of the populations has a share of more than 50%. The pie charts show prominent IBD sharing between Africans and ancient genomes, visualized by the green slices of the pies.
F<sc>ig</sc>. 4.—
Fig. 4.—
Population specific IBD segment lengths for Neandertal- and Denisovan-matching segments. Densities of lengths of IBD segments on the autosomes that match the Neandertal (left) or Denisovan (right) genome and are private to Africans (red) versus IBD segments matching ancient genomes that are not observed in Africans (blue). The dotted lines emphasize peaks of the densities. Compared with those of non-Africans, African IBD segments that match an ancient genome are enriched in regions of shorter segment lengths.
See this image and copyright information in PMC

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