The ancestors of most modern humans mated with Neanderthals and made off with important swaths of DNA that helped them adapt to new environments, scientists reported Wednesday.
Some of the genes gained from these trysts linger in people of European and East Asian descent, though many others were wiped out by natural selection, according to reports published simultaneously by the journals Nature and Science.
The stretches of Neanderthal DNA that remain include genes that altered hair and pigment, as well as others that strengthened the immune system, the scientists wrote. Together, they offer intriguing hints about how Neanderthal genes may have helped humans adapt as they spread around the globe.
They also add to evidence that Neanderthals linger in us, about 30,000 years after they mysteriously vanished.
"They are not fully extinct, if you will," said geneticist Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, a coauthor of the Nature study. "They live on in some of us today — a little bit."
Genes controlling keratin, a key component in the development of skin and hair, stand out as the strongest Neanderthal signal in a modern genome, Paabo said. Precisely how these may have helped change modern physical characteristics remains unresolved, he added.
The new studies confirm earlier findings that modern humans did more than bump elbows with Neanderthals when they encountered them after they left Africa.
An estimated 1% to 3% of the human genome comes from Neanderthals, suggesting that members of the two species mated perhaps 300 times about 50,000 years ago, said Joshua M. Akey, a population geneticist from the University of Washington and lead author of the study published in Science. There's no way to tell whether those encounters happened about the same time or were spread out over many generations, he said.
"Individually, we are a little bit Neanderthal," Akey said. "Collectively, there is a substantial part of the Neanderthal genome that's still floating around in the human population that's just shattered into different pieces, and everyone has slightly different parts."
Confirming that there are slivers of Neanderthal DNA in modern humans is one thing; knowing what effect it had on us is another, said UC Berkeley biologist Montgomery Slatkin, who has done similar research on Neanderthal genetics but was not involved in either study. "Now there is convincing evidence that indeed some [genes] were selected in humans."
Overall, at least 20% of the Neanderthal genome made its way into human DNA, and East Asians retained slightly more of it, according to Akey's analysis, which made comparisons among 379 Europeans and 286 East Asians.
The genetic signature of Neanderthals is slightly larger among East Asians. To Akey, that suggests a second wave of matings after they parted from the forebears of Europeans. "It's a two-night-stand theory now," he said.
Akey cautioned that there was a lot of uncertainty surrounding the extent and duration of interbreeding. Other hypotheses, including a smaller group of Asian ancestors, could explain the larger amount of Neanderthal DNA.
In addition to the long strands of DNA that survived, there are vast "deserts" lacking any Neanderthal signal, the studies found. Researchers suspect the areas once contained Neanderthal genes that were erased under evolutionary pressure.
Where did the DNA go? Most of the deserts lie on the X chromosome. They also were more common in genes that play a role in male fertility, the Nature study found. Male sterility, a well-known consequence of mating between species, could have wiped out the missing Neanderthal genes, researchers suggest; the sterile men carried the foreign DNA to their graves.
Sriram Sankararaman, a statistical geneticist at Harvard Medical School and coauthor of the Nature paper, calculated that about one-third of the Neanderthal DNA once in the human genome had been cleared out. That evolutionary purge is "a huge amount in a relatively short period of time," he said.
The Neanderthal genome project has helped scientists understand one of our closest relatives. Short-bodied and brutishly strong, Neanderthals were well-adapted for hardship and colder climates. They made use of fire, crafted simple flaked tools and hunted to supplement forage unavailable in colder months.
For decades, paleontologists and geneticists found little indication of Neanderthal-human interbreeding. But as methods, samples and tools improved, evidence began to accrue in both the fossil record and genetic analyses.
Genes linked to several modern diseases, including Type 2 diabetes, are among the Neanderthal legacy. Though that DNA may not seem helpful in an era of plentiful cheeseburgers and French fries, it could have been valuable at a time when food was often scarce, Paabo said.
Other studies have traced important immune system genes to Neanderthals and another closely related extinct group, the Denisovans.
Although both of the new studies focus on the DNA sequences shared by humans and Neanderthals, some scientists are more interested in exploring the differences that make humans unique.
"That's what really burningly interests me in the coming years," Paabo said.