This guest post is by Gundula Povysil and Sepp Hochreiter on their preprint Sharing of Very Short IBD Segments between Humans, Neandertals, and Denisovans, bioRxived here.

We completed our preprint Sharing of Very Short IBD Segments between Humans, Neandertals, and Denisovans in bioRxiv by presenting results not only for chromosome 1 but now for all autosomes and chromosome X.

In this manuscript we analyze the sharing of very short identity by descent (IBD) segments between humans, Neandertals, and Denisovans to gain new insights into their demographic history. In the updated version we included a separate chromosome X analysis (both IBD segment sharing and length of segments). We identified IBD segments in the 1000 Genomes Project sequencing data using our recently published method HapFABIA, many of which are shared with Neandertals or Denisovans.

Here we highlight the most interesting findings of our analysis:

Introgression from Denisovans into ancestors of Asians:

The Denisova genome most prominently matches IBD segments that are shared by Asians and on average these segments are longer than segments shared between other continental populations and the Denisova genome. Therefore, we could confirm an introgression from Denisovans into ancestors of Asians after their migration out of Africa.

Introgression from Neandertals into ancestors of Europeans and Asians:

While Neandertal-matching IBD segments are most often shared by Asians, Europeans share a considerably higher percentage of IBD segments with Neandertals compared to other populations, too. Neandertal-matching IBD segments that are shared by Asians or Europeans are longer than those observed in Africans. These IBD segments hint at a gene flow from Neandertals into ancestors of Asians and Europeans after they left Africa.

Ancient Neandertal and Denisova IBD segments survived only in Africans

Interestingly, many Neandertal- and/or Denisova-matching IBD segments are predominantly observed in Africans – some of them even exclusively. IBD segments shared between Africans and Neandertals or Denisovans are strikingly short, therefore we assume that they are very old. Consequently, we conclude that DNA regions from ancestors of humans, Neandertals, and Denisovans have survived in Africans.

Neandertal but no Denisova introgression on the X chromosome

Neandertal-matching IBD segments on chromosome X confirm gene flow from Neandertals into ancestors of Asians and Europeans outside Africa. Interestingly, there is hardly any signal of Denisova introgression on the X chromosome.

We highly appreciate any comments, discussions, or thoughts on our results.