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Deep in Human DNA, a Gift From the Neanderthals

People of Asian and European descent — almost anyone with origins outside of Africa — have inherited a sliver of DNA from some unusual ancestors: the Neanderthals.

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Carl Zimmer
, New York Times

People of Asian and European descent — almost anyone with origins outside of Africa — have inherited a sliver of DNA from some unusual ancestors: the Neanderthals.

These genes are the result of repeated interbreeding long ago between Neanderthals and modern humans. But why are those genes still there 40,000 years after Neanderthals became extinct?

As it turns out, some of them may protect humans against infections. In a study published Thursday, scientists reported new evidence that modern humans encountered new viruses — including some related to influenza, herpes and HIV — as they expanded out of Africa roughly 70,000 years ago.

Some of those infections may have been picked up directly from Neanderthals. Without immunity to pathogens they had never encountered, modern humans were particularly vulnerable.

“We were actually able to not only say, ‘Yes, modern humans and Neanderthals exchanged viruses,'” said David Enard, an evolutionary biologist at the University of Arizona and co-author of the new paper, published in the journal Cell. “We are able to start saying something about which types of viruses were involved.”

But if Neanderthals made us sick, they also helped keep us well. Some of the genes inherited from them through interbreeding also protected our ancestors from these infections, just as they protected the Neanderthals.

Lluis Quintana-Murci, a geneticist at the Pasteur Institute in Paris who was not involved in the new research, said that until now, scientists had not dreamed of getting such a glimpse at the distant medical history of our species.

“Five years ago, we would never have imagined that,” he said.

Our immune cells kill off viruses with an arsenal of weapons, such as antibodies and signals that cause infected cells to destroy themselves. But Enard began his research by wondering if humans have evolved other ways to avoid getting infected.

Viruses cannot replicate on their own. They appropriate proteins inside our cells to do the heavy lifting, copying viral genes and building new shells to put them in. If those proteins were to change shape, however, it should become harder for viruses to use them to multiply.

“Instead of a strategy where you attack the virus, you run away from it,” said Enard.

To learn whether this is really a defense the body uses, Enard needed to find all the human proteins known to interact with at least one virus. But no such list existed. So he plowed through the scientific literature, looking for every example.

Once he had built a catalog of 1,300 proteins — it took four months — he studied their evolutionary history. By comparing these proteins across different species, he discovered that many have changed over the course of evolution.

In the several million years since our ancestors split from other primates, one-third of the adaptive changes in our proteins have occurred among those that interact with viruses. And this remarkable discovery led Enard and Dr. Dmitri Petrov, an evolutionary biologist at Stanford University, to wonder about Neanderthals.

The common ancestor both of modern humans and Neanderthals lived roughly 600,000 years ago, probably in Africa. Neanderthals left the continent long before modern humans and spread across a huge range, from the coast of Spain to Siberia, before becoming extinct.

From fossils, scientists have been able to reconstruct entire genomes of Neanderthals. And they have found that living people with non-African ancestry carry 1 percent or 2 percent Neanderthal DNA.

That remnant DNA got into our gene pool through repeated interbreeding. But after Neanderthals became extinct, their DNA gradually declined in our genomes.

It is likely that most Neanderthal genes were bad for our health or reduced our fertility, and therefore were lost in modern humans. But certain Neanderthal genes became more common, probably because they provided some kind of evolutionary advantage.

In recent years, researchers have found that some of those genes encode proteins made by immune cells. They speculated that modern humans benefited by borrowing Neanderthal genes to fight infections.

Enard and Petrov had a more specific question: Did modern humans acquire genes that helped cells evade specific viruses by altering the shapes of cellular proteins?

The researchers pored through the genomes of living Asians and Europeans, and discovered a large fraction of those Neanderthal genes make proteins that interact with viruses.

The viruses that infected Neanderthals must have posed a major threat to modern humans as they left Africa. They had no immunity to these infections. But Neanderthals did, and through interbreeding, Neanderthals provided modern humans with genetic defenses.

“It’s like they brought the knife, but they also brought the shield,” Petrov said. Enard and Petrov also found clues about exactly what kinds of viruses these Neanderthal genes protect against.

In living humans, many of the proteins made by those genes interact only with influenza viruses, for example. Others interact only with HIV.

“We are not saying that viruses that infect the human population now come from Neanderthals,” said Enard. It is clear, for example, that HIV jumped into humans just a century ago from chimpanzees.

Instead, it is likely that modern humans got infected with an ancient relative of HIV. Enard could not say how they were exposed to the new pathogen — perhaps directly through sex with Neanderthals, or by eating animals that both modern humans and Neanderthals hunted.

But it is clear that, for billions of people alive today, Neanderthal genes likely play an important role in defending against such viruses.

“We are not anything but the result of our past,” said Quintana-Murci.

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