Modern-day Africans also have Neanderthal DNA

After sequencing the Neanderthal genome, scientists discovered that all current non-African individuals have neanderthal ancestry in their DNA. Now, a team of researchers from Princeton University (U.S.) have presented evidence of Neanderthal ancestry also in African populations. The intricacies of human history are still being unraveled today.

Humans who emigrated from Africa about 60,000 to 80,000 years ago crossed paths with Neanderthals. This set the stage for some groups to return to Africa carrying Neanderthal genes that spread across the continent, according to experts in the study by Cell magazine.

Sets of Neanderthal genetic variants inherited by modern-day Africans include genes related to strengthening the immune system and modifying sensitivity to ultraviolet radiation. These genes seem to spread rapidly once introduced into African humans.

"Our study is significant because it provides important new insights into human history and patterns of Neanderthal ancestry in globally diverse populations," states lead author Joshua Akey of Princeton University. "Our results refine the catalogues of genomic regions where the Neanderthal sequence was harmful and advantageous and show that the remains of Neanderthal genomes survive in every modern human population studied to date".

How was it discovered?

New findings suggest that these estimates may have been skewed due to methodological limitations. Thanks to a new statistical approach to detecting old genetic material still present in modern DNA, it has led to the discovery of a genetic heritage that had passed unnoticed until now. The new technique also revealed a journey out of Africa approximately 100,000 to 150,000 years ago that led to the introduction of human genes into Neanderthals through crossbreeding.

The researchers applied the new approach to 2,504 modern individuals of 1000 Genomes Project, which represents geographically diverse populations, and used the Altai Neanderthal reference to identify the Neanderthal sequence in these individuals. They distinguished, on average, 17 megabases (Mb) of Neanderthal sequence per individual in the analyzed African samples (corresponding to approximately 0.3% of the genome), compared to less than one megabase according to the results of previous studies. More than 94% of the Neanderthal sequence identified in African samples was shared with non-Africans.

In conclusion, Africans today have more Neanderthal ancestry than previously thought.

Limitations of the study

The authors point to several limitations in their approach. Due to the fact that IBDmix (the new approach used) requires an archaic reference genome, it is not suitable for discovering shared sequences between modern humans and unknown or uncorrupted lineages. In upcoming studies, experts plan to apply their approach to additional African populations and to study the implications of these archaic sequences on modern human health and disease.

Reference: Cell, Chen et al.: "Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals" https://www.cell.com/cell/fulltext/S0092-8674(20)30059-3 , DOI: 10.1016/j.cell.2020.01.012