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Pinky DNA Points To Clues About Ancient Humans

Aug 30, 2012
Originally published on August 30, 2012 6:09 pm

Scientists in Germany have been able to get enough DNA from a fossilized pinky to produce a high-quality DNA sequence of the pinky's owner.

"It's a really amazing-quality genome," says David Reich of Harvard Medical School in Boston. "It's as good as modern human genome sequences, from a lot of ways of measuring it."

The pinky belonged to a girl who lived tens of thousands of years ago. Scientists aren't sure about the exact age. She is a member of an extinct group of humans called Denisovans. The name comes from Denisova cave in Siberia, where the pinky was found.

Two years ago, scientists at the Max Planck Institute for Evolutionary Anthropology in Leipzig reported that they had been able to get just enough DNA from the fossil to make a rough sequence of her DNA. But Matthias Meyer developed a far more efficient way of recovering ancient DNA, so he went back to the tiny amount of DNA left over from the first effort, and reanalyzed it.

"And from this little leftover, we were able to determine the sequence of the Denisova genome 30-fold over," says Meyer.

What that means is they were able to look at every single location along all of this girl's chromosomes 30 times to be absolutely certain that they had the right DNA letter in the right spot. The new results appear in the online edition of the journal Science.

The high-quality sequence gives scientists valuable new data for studying ancient humans. Researchers have begun, for example, to explore which modern human populations may have inherited genes from Denisovans.

"We still cannot detect a trace of any Denisovan genetic material at all in mainland Eurasia" — places such as China and Japan, says Harvard's Reich. "It's only in Southeast Asia and Australia that we detect it."

Understanding the flow of genes will tell scientists about where and when ancient humans moved around the planet.

Reich says for the moment, nearly all scientists know about the Denisovans comes from a girl's pinky. "One of the amazing things about the Denisovans is we still don't know what kinds of artifacts they left behind, what kinds of archaeology. We really only know them from their DNA," he says. "So it's really a genome in search of an archaeology."

Svante Pääbo, senior author on the new research paper, says it will now be possible to comb through the Denisovan genome to see how it differs from that of modern humans.

"This is perhaps, in the long term, to me, the most fascinating thing about this — what it will tell us in the future about what makes [modern humans] special in the world relative to Denisovans and Neanderthals," says Pääbo.

Now that they've completed a high-quality genome sequence of their Denisovan, the German scientists have begun work on improving the sequence of another extinct group of humans: the Neanderthals. They expect that work to be published in a year or so.

Copyright 2013 NPR. To see more, visit http://www.npr.org/.

Transcript

MELISSA BLOCK, HOST:

This is ALL THINGS CONSIDERED from NPR News. I'm Melissa Block. You may not be able to get blood from a stone but scientists in Germany have shown that you can get DNA. They started with a fossilized pinky found in a cave, and extracted enough DNA to read out the entire genetic sequence of the pinky's owner. NPR's Joe Palca explains.

JOE PALCA, BYLINE: The pinky belonged to a girl who lived tens of thousands of years ago - around the time of the Neanderthals. She's a member of an extinct group of humans called Denisovans. The name comes from Denisova Cave in Siberia where the pinky was found. Now, getting DNA from a stone may seem absurd, but it's not. DNA is a hardy little molecule. It may break into pieces - but it doesn't degrade entirely, even after thousands of years.

Matthias Meyer and his colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, developed a new technique for retrieving and reassembling ancient DNA. Using a tiny bit of material from an earlier attempt, they were able to sequence the pinky owner's genome.

MATTHIAS MEYER: And from this little leftover, we were able to determine the sequence of the Denisova genome 30-fold over.

PALCA: What that means is they were able to look at every single location along the girl's chromosomes 30 times to be absolutely certain they had the right DNA letter in the right spot.

DAVID REICH: It's really an amazing quality genome. It's as good as modern human genome sequences from a lot of ways of measuring it.

PALCA: David Reich is a co-author on the paper describing the new work that will appear in the journal Science. Reich is at Harvard Medical School in Boston. Because it's such a good sequence, you can make detailed comparisons between someone who's alive today and someone who's been dead for tens of thousands of years. Reich has been doing that with genomes collected from people all over the world.

REICH: We still cannot detect a trace of any Denisovan genetic material at all in mainland Eurasia.

PALCA: Places like China, for instance.

REICH: It's only in Southeast Asia and Australia that we detect it.

PALCA: How did a group of people that apparently lived in Siberia and Eurasia end up co-mingling with people in Australia? Good question. Scientists hope the new sequence will help them figure that out. They'd also like to know a lot more about Denisovans.

REICH: One of the amazing things about Denisovans is we still don't know what kinds of artifacts they left behind, what kinds of archeology. We really only know them from their DNA.

PALCA: Now that they've completed a high quality genome sequence of their Denisovan, the German scientists are turning their attention to another extinct group of humans: the Neanderthals. That sequence should be published in a year or so. Joe Palca, NPR News, Washington. Transcript provided by NPR, Copyright NPR.