Neanderthal genes in Africans: a confirmed fact

Last October I posted about a paper that disclosed that Africans had a higher Neanderthal signature in their mtDNA than Asians or Europeans.

African lack of Neanderthal DNA (and mtDNA) is used as proof of the Out of Africa (OOA) event, because it is said that Neanderthals and Homo sapiens admixed outside of Africa after H. sapiens migrated from Africa on their OOA journey.

A recent paper cast a shadow of doubt on this assumption: they have found signals of Neanderthal DNA in Africans!

The paper is: Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals by Lu Chen, Aaron B. Wolf, Wenqing Fu, Liming Li, and Joshua M. Akey. Chen et al., 2020, Cell 180, 1–11 February 20, 2020 https://doi.org/10.1016/j.cell.2020.01.012.

It summarizes their research as follows:

"Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date"

The paper finds that some of the ancestors of modern Europeans back migrated into Africa after they had split from those who would later become East Asians.

They found 13 African-specific high-frequency Neanderthal haplotypes which are unique to Africans, and only found in Africa, and another 31< haplotypes shared with Europeans. Specific African genes means that selection preserved them because they gave those carrying them some immune benefits and also protection against UV radiation in sunlight.

So now we know that ALL humans have Neanderthal genes in their genome, including Africans.

This gene flow, which had not been recognized until now also caused biased estimations of Neanderthal admixture in Asians and Europeans: East Asians seemed to have 20% more Neanderthal DNA than Europeans, which was odd, considering that Neanderthals lived in western Eurasia so admixture there would have been higher than in the Far East.

But now it seems that roughly 0.3 to 0.5 % of African genome was inherited from Neanderthals (vs. 1.8% in Non-Africans).

So factoring in this African Neanderthal content, the East Asians ended up with only 8% more Neanderthal genes than Europeans.

The study found "[in] African populations, we identified approximately 17 Mb of putative Neanderthal sequence per individual"

Compare thiese 17Mb with what they found in Europeans and Asians:

"we found similar levels of Neanderthal ancestry in Europeans (51 Mb/individual), East Asians (55 Mb/individual), and South Asians (55 Mb/individual)"

So Africans have roughly one third of the Neanderthal admixture that non-Africans have! See the image below which shows exactly this (non-Africans in Blue, Africans in brown):

Neanderthal genetic admixture in humans. From Fig. 2 in Chen et al.

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Finally, around 94 percent of Neandertal DNA sequences found in Modern Africans is also shared with Non-Africans.

The paper explains the Neanderthal admixture into Africa as follows: "In summary, these data indicate that both pre-OOA human-to-Neanderthal gene flow and elevated historic backmigration contribute to the signal of Neanderthal ancestry detected in Africans.".

The first wave of humans to leave Africa between 250 and 150 kya, mixed with Neanderthals in Eurasia and passed on to them some archaic human genes. These were lost as this pre-OOA wave became extinct. The Neanderthals then mixed with the OOA wave and part of these admixed modern Humans returned to Africa bringing the genes with them.

Perhaps further studies -Science news reports an unpublished study that ratifies Chen et al. findings: "as-yet-unpublished work by Sarah Tishkoff, an evolutionary geneticist at the University of Pennsylvania. She told Science she has also found higher-than-expected levels of apparent Neanderthal DNA in Africans."

I have written many posts about "into Africa events", but this one is the first paper to conclusively prove the presence of Neanderthal genes in modern Africans.

This will open the gates to more scrutiny on the origin of the higher "African" diversity when compared to the rest of humankind. This diversity is surely due to admixture with archaic populations and not only to bottlenecks caused by an OOA migration.

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