Neanderthal DNA Leaves Winding Trail

Neanderthal DNA has turned up in present-day Africans’ genes. Find out how this stands current theories about early human history on their heads.

When he was in high school, my brother went on a geography field trip to Craigleith Provincial Park near Collingwood, Ontario. One of the activities was to hunt for some of the fossils that have made Craigleith famous.

At one point his friend, who was the class clown, held a rock up to the teacher and exclaimed in a silly British accent, “Sir! I’ve found it! The missing link!” He hadn’t found much of anything and the teacher gave his little act all the attention it deserved.

His joke came from how we imagine the search for human origins. We picture Louis Leakey or Pierre Teilhard de Chardin wearing a pith helmet and wandering off to exotic climes to pore over fossilized bones.


That’s how they made discoveries in the early 20th century and the fossil record is still vital to anthropologists. More and more though, now that we’ve mapped the human genome, scientists look to DNA to work out early human history.

I mentioned in an earlier story that I have 257 genetic variants from Neanderthal DNA. Neanderthal DNA in modern humans isn’t unusual, especially for someone like me whose ancestors came from Europe. In fact, that much Neanderthal DNA is below average for people like me.

Neanderthals are our closest evolutionary cousins. They lived in parts of Europe and Asia from maybe more than 800,000 years ago to about 40,000 years ago. Modern humans and Neanderthals lived side by side for the last few thousand years of that time. Svante Paabo documents this history in his book Neanderthal Man: In Search of Lost Genomes.


The reason someone like me can send away and find out about the Neanderthal sequences in his genes is that Svante Paabo led a team at the Max Planck Society that put out a map of the Neanderthal genome in the Journal Science back in 2010. That was only ten years after geneticists had mapped out the modern human genome.

From there, geneticists have been able to find the Neanderthal gene in humans. Then, they can use that to trace early human history.

Finding enough Neanderthal DNA to map the genome wasn’t easy. Scientists at the Max Planck Society got it from Neanderthal bones found in Germany, Croatia, Russia and Spain.


They only needed about half a gram of DNA to do their work but even this tiny amount was hard to extract because of contamination from microbes over time. It took a lot of work to separate the Neanderthal DNA from the DNA of the germs.

In one case, over 95% of the DNA recovered from a sample came from bacteria and other germs. The researchers also had to be extremely careful to make sure that no human DNA from the researchers got mixed up with the Neanderthal DNA.

From this first Neanderthal DNA sequencing, the researchers discovered that early humans and Neanderthals interbred. That surprised just about everybody. Experts used to think that human populations didn’t mix with Neanderthals and Denisovans.


Since the Max Planck Society’s discovery, scientists also used to think that Neanderthal DNA only existed in European and East Asian populations. That’s because the interbreeding would have taken place after modern humans left Africa 60,000 to 80,000 years ago.

Scientists believed that African populations had never been exposed to Neanderthal DNA in their gene flow. Now a new analysis by researchers at Princeton University shows that Africans living today have more Neanderthal DNA than anyone thought.

It’s still true today that people from outside Africa have about three times as much Neanderthal DNA as present-day Africans do. Even so, Neanderthal DNA makes up about 0.5% of today’s African DNA, which is far more than we were told in the past.


The team, led by Professor Joshua Akey, published their analysis last week in the journal Cell. They looked at the amount of Neanderthal DNA from 2,504 Africans, Europeans and East Asians living today.

Then they compared each volunteer’s DNA with Neanderthal DNA from Siberia and southeastern Europe. Having gone over the results, the Princeton research team thinks that modern humans must have moved back to Africa at some point, carrying Neanderthal genes with them.

Some of the Neanderthal genes the team discovered strengthened the immune system. Others made people less sensitive to UV rays.


These traits would have come in handy for ancient Africans. Natural selection soon spread the Neanderthal DNA all over Africa.

The team from Princeton also discovered something else. They can tell that modern humans wandered out of Africa sometime between 100,000 to 150,000 years ago.

Those humans interbred with Neanderthals. That added human DNA to their Neanderthal DNA. Then, those early modern human genes found their way back into modern African DNA again.


Professor Akey told Science News, “Our work highlights how humans and Neanderthals interacted for hundreds of thousands of years, with populations dispersing out of and back into Africa, Remnants of Neandertal DNA survive in every modern human population studied to date.”

The team found something else. Geneticists used to think that East Asians had about 20% more Neanderthal DNA than Europeans. That was puzzling because most Neanderthal fossils turn up in Europe.

Based on the team’s work, we now know that Europeans have about 1.7% Neanderthal DNA versus East Asians with about 1.8%. That solves the East Asian puzzle. Now we know that the two groups are practically the same.


When the researchers looked at African DNA, they found that Africans share about 7.2% of their Neanderthal DNA with Europeans. They only share 2% with East Asians.

That tells us that the migration back to Africa probably came from Europe and not Asia. When we look at the overall story, we get a picture of human evolution from about 300,000 years ago.

Early humans kept trying to move out of Africa time after time. Sometimes it was a big success, sometimes it had mixed results and sometimes it failed.


The main point is that there wasn’t just one or two big Out of Africa migrations like experts used to tell us. The moves kept happening over and over and sometimes they came back into Africa again. It’s complicated.

The models that Professor Akey and his team used to come up with all this rely heavily on new ways of using statistics. A lot of it is based on techniques for estimating probabilities that still need peer review.

Even so, a lot of scientists support the findings. If they turn out to be true, it means that we need to take another look at the way fossils and artifacts have been dated, and not just in Africa. We also need to find out a lot more about Neanderthal DNA and other genetic data from modern-day Africans.

We always have more to learn if we dare to know.

Learn more

Max Planck Society
A Draft Sequence of the Neandertal Genome
Science News
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
Hunter-Gatherer Culture and Storytellers
Prehistoric Africa Revealed by Ancient Children’s DNA
Is the Birthplace of All Humans in the Kalahari?
Friendly Faces Drove Human Evolution

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