Africans carry surprising amount of Neanderthal DNA

For 10 years, geneticists have told the story of how Neanderthals—or at least their DNA sequences—live on in today’s Europeans, Asians, and their descendants. Not so in Africans, the story goes, because modern humans and our extinct cousins interbred only outside of Africa. A new study overturns that notion, revealing an unexpectedly large amount of Neanderthal ancestry in modern populations across Africa. It suggests much of that DNA came from Europeans migrating back into Africa over the past 20,000 years.

“That gene flow with Neanderthals exists in all modern humans, inside and outside of Africa, is a novel and elegant finding,” says anthropologist Michael Petraglia of the Max Planck Institute for the Science of Human History. The work, reported in this week’s issue of Cell, could also help clear up a mysterious disparity: why East Asians appear to have more Neanderthal ancestry than Europeans.

As members of Homo sapiens spread from Africa into Eurasia some 70,000 years ago, they met and mingled with Neanderthals. Researchers knew that later back-migrations of Europeans had introduced a bit of Neanderthal DNA into African populations, but previous work suggested it was a just a smidgen. In contrast, modern Europeans and East Asians apparently inherited about 2% of their DNA from Neanderthals.

Previous efforts simply assumed that Africans largely lacked Neanderthal DNA. To get more reliable numbers, Princeton University evolutionary biologist Joshua Akey compared the genome of a Neanderthal from Russia’s Altai region in Siberia, sequenced in 2013, to 2504 modern genomes uploaded to the 1000 Genomes Project, a catalog of genomes from around the world that includes five African subpopulations. The researchers then calculated the probability that each stretch of DNA was inherited from a Neanderthal ancestor.

The researchers found that African individuals on average had significantly more Neanderthal DNA than previously thought—about 17 megabases (Mb) worth, or 0.3% of their genome. They also found signs that a handful of Neanderthal genes may have been selected for after they entered Africans’ genomes, including genes that boost immune function and protect against ultraviolet radiation.

The results jibe with as-yet-unpublished work by Sarah Tishkoff, an evolutionary geneticist at the University of Pennsylvania.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.

The best fit model for where Africans got all this Neanderthal DNA suggests about half of it came when Europeans—who had Neanderthal DNA from previous matings—migrated back to Africa in the past 20,000 years. The model suggests the rest of the DNA shared by Africans and the Altai Neanderthal might not be Neanderthal at all: Instead, it may be DNA from early modern humans that was simply retained in both Africans and Eurasians—and was picked up by Neanderthals, perhaps when moderns made a failed migration from Africa to the Middle East more than 100,000 years ago.

Akey’s study might help explain another “head scratcher,” says computer biologist Kelley Harris of the University of Washington, Seattle. Studies had suggested East Asians have 20% more Neanderthal DNA than Europeans, she notes. “Europe is where Neanderthal remains are found, so why wouldn’t Europeans have more Neanderthal ancestry than any other group?”

By suggesting that Europeans introduced Neanderthal sequences into Africa, the new study points to an explanation: Researchers previously assumed that Neanderthal sequences shared by Europeans and Africans were modern and subtracted them out. After correcting for that bias, the new study found similar amounts of Neanderthal DNA in Europeans and Asians—51 and 55 Mb, respectively. It’s a “convincing and elegant” explanation, Harris says.