People of European and African ancestry have got more Neanderthal DNA in their genomes than previously thought. This is the finding of a study that identifies, for the first time, the Neanderthal genes present in modern day people of African ancestry, and indicates that this “ghost” DNA spread through Africa via migrations of modern humans back from Europe.
“What’s surprising about our results is the magnitude of the Neanderthal signal that we see in all of the African populations we’ve looked at. There’s more Neanderthal ancestry in Africa than we thought,” says Joshua Akey at Princeton University, who led the study.
Neanderthals arose about 430,000 years ago, living in Europe and central Asia until their demise some 40,000 years ago. Thanks to genetic studies, we know that modern humans interbred with Neanderthals after they left Africa, leaving traces in each other’s DNA.
Previous research showed that approximately 1.5 per cent of the DNA of people of European ancestry originated from these sexual encounters, and that people of east Asian ancestry had about 20 per cent more Neanderthal DNA than this, possibly due to more interbreeding.
The genomes of people of African ancestry, however, showed little or no evidence of this genetic transfer – which makes sense, because Neanderthals never inhabited Africa. But these Neanderthal genes were identified in people of European ancestry by comparing their genomes to people of African ancestry, on the assumption they were a Neanderthal-free baseline.
To find out if this assumption was correct, Akey and his colleagues devised a new method for detecting archaic ancestry in DNA. Using data from the 1000 Genomes Project to look at the genomes of people of African ancestry in Africa today and elsewhere in the world, it revealed unexpectedly high Neanderthal signatures of 0.3 per cent in people of African ancestry, compared with less than 0.02 per cent shown in previous studies. Some of these genes play a role in the immune system and sensitivity to ultraviolet light.
The researchers think that Neanderthal DNA reached African populations through modern humans in Europe migrating back. “European ancestors introduced a substantial part of Neanderthal sequence to Africa and that spread around the continent,” says Akey.
The new study also shows that the Neanderthal component of the genomes of modern-day people of European ancestry was underestimated in previous studies, because it was masked by the previously unrecognised Neanderthal signatures in the genomes used as reference samples in genetic analyses.
“Everyone living today bears that legacy of admixture with the Neanderthals,” says Akey. “We show compelling evidence that migrations, both out of Africa and into Africa have played a prominent role in shaping patterns of human genetic variation.”