Neanderthal African origins: Study identifies the ancestry in Africa

American researchers from Princeton University have found that Africans have significantly more Neanderthal genes than previously thought. New computational methods helped to discover them. The results of the study are published in the journal Cell.

After the Neanderthal genome was read in 2009, it was revealed that modern inhabitants of Asia, Europe and America inherited approximately 2 per cent of their DNA from Neanderthals. And in Africans, Neanderthal genes were not found. From this, it was concluded that episodes of interbreeding between humans and Neanderthals took place after humans left Africa.

In subsequent research, using increasingly sophisticated methods, scientists continued to catalogue the genes of Neanderthals in non-African populations in an effort to better understand human history, as well as the impact of Neanderthal DNA on modern humans and their diseases.

At the same time, the catalogue of Neanderthal genes in African populations was never compiled due to technical limitations and the assumption that Neanderthals and native African populations were geographically isolated from each other.

Scientists from Princeton University, led by Joshua Akey, have developed a new method for digital processing of genetic information that allows you to search the genome for evidence of Neanderthal ancestors.

The authors named their method IBDmix – from the name of the genetic principle “identity by descent” (IBD), according to which the identity of DNA fragments in two individuals is considered a sign of a common ancestor, and the length of the IBD segment depends on how long ago these people had a common ancestor. For example, siblings have long IBD segments, while fourth cousins are shorter because their common ancestor is several generations away.

Thus, scientists were able not only to identify the DNA of Neanderthals in the genome of modern humans but also to distinguish sequences belonging to common ancestors, which they had 500 thousand years ago, from those sequences that arose as a result of later episodic crossing, which took place about 50 thousand years ago.

Previous methods used the principle of “reference populations” to distinguish common ancestry from recent crosses. It turned out that the reference populations of Africans selected as standards did not have Neanderthal DNA. The researchers called the new method “referential” because it uses internal characteristics of the DNA sequence itself, such as the frequency of mutations or the length of IBD segments, to distinguish common ancestry from recent crosses.

The authors used the IBDmix method to process data from African and non-African populations and found that all modern humans, including Africans, have Neanderthal genes. Moreover, Europeans and Asians have both early and late versions, while Africans have only early ones. That is, Africans, having Neanderthals in their distant ancestors, later did not interbreed with them.

“This is the first time we have found an actual signal in Africans of their Neanderthal descent,” Lu Chen, a researcher at the Institute for Integrative Genomics at Princeton University and co-author of the study, said in a press release that “this level is quite high.”

How Neanderthals appeared in Africa, scientists do not yet know. Perhaps this was due to the return migration of ancient Europeans back to Africa. The discovery confirmed that hybridization between humans and closely related species had occurred periodically in evolutionary history.

The authors note that if the scientific community recognizes that the method based on the reference panels carries a systemic error, it may be necessary to revise most of the previously published results of studying the genomes of different populations of modern people.