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Neanderthals died out long ago, but their genes live on in us. In fact, scientists studying human chromosomes say they've discovered a surprising amount of Neanderthal DNA in our genes. And these aren't just random fragments. These are genes that shape what we look like today. NPR's Richard Harris reports on a pair of new and surprising studies.

RICHARD HARRIS, BYLINE: Tens of thousands of years ago, Neanderthals lived side by side with humans who had migrated from Africa to Europe. And sometimes they shared more than territory. They also swapped genetic material, to put it delicately.

JOSH AKEY: Whenever you juxtapose Neanderthal and sex, people get interested.

(LAUGHTER)

HARRIS: Josh Akey at the University of Washington has been fielding a lot of reporters' phone calls this week. He says there's no question that Neanderthals occasionally crossbred with their close relatives: early humans in Europe. And while the Neanderthals died out, their genes live on in modern humans. A few years ago, scientists actually decoded the Neanderthal DNA from old bones, so today we can compare Neanderthal genes with our own.

AKEY: We previously knew that about 1 to 3 percent of all non-African genomes were inherited from Neanderthal ancestors, but the key point is that my 1 percent might be different than the 1 percent of Neanderthal sequence that you carry.

HARRIS: So Akey and his colleagues combed through the genes of more than 600 people living today to look for scraps of Neanderthal genes. And they report in Science magazine that about 20 percent of the Neanderthal genes live on in us. In fact, it seems that some of the Neanderthal genes were better-suited for our fully human ancestors than they genes they had. Those genes came to dominate certain traits. One example is genes related to a protein that affects our appearance: keratin.

AKEY: We don't know exactly what the Neanderthal versions of those genes, which trait they were influencing. But they have something to do likely with skin or hair biology.

HARRIS: Africans didn't pick up those traits since Neanderthals appeared in Europe. But maybe this crossbreeding affects how Europeans and Asians look today. As it happens, a research group at Harvard has also been combing through human genes, looking for Neanderthal leftovers. Sriram Sankararaman is lead author of a Nature paper. He says the genes give us some clues about what happened between Neanderthals and human ancestors way back when.

SRIRAM SANKARARAMAN: My guess is there must have been a small population of Neanderthals with which modern humans would have interbred.

HARRIS: And while human ancestors benefitted from some of the Neanderthal genes they picked up, they also rejected a whole bunch of Neanderthal genes. For example, our X chromosome has very little Neanderthal DNA on it. Svante Paabo at the Max Planck Institute in Leipzig says that suggests that Neanderthals and our human ancestors were barely compatible and many of their offspring ended up being sterile hybrids, like mules.

SVANTE PAABO: So this suggests that the male hybrids might not have been fertile whereas females might have been fully fertile. So it might have been passed on particularly through females, the Neanderthal contribution.

HARRIS: The story is still hazy, but very provocative.

PAABO: I think it's fascinating that the Neanderthals live on to day, so to say, in a little bit in us. And not just in the form of anonymous DNA fragments that we pass on to the next generation, but also in the part of our genome that actually influences how we look or how we behave or what diseases we have.

HARRIS: Reading these genes tells us more about our mysterious Neanderthal relatives. But Josh Akey says they also can tell us a lot about ourselves.

AKEY: Maybe we can use our map of Neanderthal sequences to pinpoint in on regions of the genome that confer unique human phenotypes.

HARRIS: That is the traits that set us apart as human beings. Both research groups are eagerly continuing to mine human DNA for more surprising clues. Richard Harris, NPR News.

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