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Genome of ancient Denisovans may help clarify human evolution

New technology enabled scientists to obtain a high-precision genetic sequencing of the extinct Denisovan people, a relative of humans.

August 30, 2012|By Rosie Mestel, Los Angeles Times
  • Excavation work of a cave in Siberia where fossils of the extinct Denisovan people were found.
Excavation work of a cave in Siberia where fossils of the extinct Denisovan… (Max Planck Institute for…)

Our ancestors didn't walk alone: Neanderthals and other ancient peoples shared Earth with them tens of thousands of years ago.

Now, using new technology, scientists have sequenced with high precision the genome of one of those close but little-known relatives: an extinct people known as the Denisovans, who lived in and around modern-day Siberia.

The Denisovan genome, reported online Thursday in the journal Science, was derived from tiny quantities of shredded DNA extracted from a finger bone found in a Russian cave in 2008, as well as a tooth found later.

What is striking, scientists said, is that it is every bit as detailed as a sequence generated with a fresh blood or saliva sample from someone alive today.

Analysis of the genome and comparisons with ours and the Neanderthals' will offer insights into the history of Homo sapiens — who we mated with, where and when — as well as the unique genetic changes that make modern humans who they are, scientists said.

Study leader Svante Paabo, a pioneer in decoding ancient genomes, said it would take biologists decades to understand the meaning of all these tiny differences.

"Many of them may have no function — but among them will undoubtedly hide some crucial changes that are essential for what made modern human history possible," said Paabo, director of the department of evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Already, he and his coauthors have highlighted several intriguing genetic differences between modern humans and our primitive relatives that could be significant, including genes involved in wiring the brain and ones that are known to be linked to autism.

Their analysis also suggests that the Denisovans had dark skin, brown hair and brown eyes, but scientists can't yet say much more than that about their appearance.

The advance hinged on new techniques designed to investigate scant and highly degraded genetic material found in fossils. Their application to these and other specimens promises to draw back the curtain on our species' complicated and much-debated history, said John Hawks, a paleoanthropologist at the University of Wisconsin in Madison, who wasn't involved in the study.

Very likely, modern humans have other undiscovered ancient relatives whose fossilized bones are waiting to give up their secrets.

"It's got to be just the beginning," Hawks said.

The part of the world where the Denisovan fossils were discovered could contain a particularly rich trove of archaic humans, said Michelle Glantz, a biological anthropologist at Colorado State University in Fort Collins, who was not involved in the study.

Among the other intriguing finds from Central Asia is a fossil from Uzbekistan with a Neanderthal-like inner ear and a cranium resembling a modern human's. But it will take a lot more than DNA data to piece together the picture there, she said.

The evolutionary path of humans is in many respects still mysterious, and the exact timing of events is uncertain. But the story goes something like this: Ancestors of humans emerged in Africa and migrated out to the rest of the world in several successive waves.

The first globe-trotter was Homo erectus, whose trek began 1 million to 2 million years ago. Then came the ancestor of the Neanderthals and Denisovans, who left Africa as far back as 800,000 years ago and replaced or interbred with descendants of Homo erectus.

The third wave of people, Homo sapiens, left Africa perhaps 100,000 years ago and sometimes mated with the Neanderthals and Denisovans they encountered. The result is you and me and everyone else on the planet.

The new genome gives scientists a sense of just how much of our genomes we owe to our extinct relatives. About 3% to 5% of the DNA in people native to Papua New Guinea, Australia, the Philippines and other islands nearby came from Denisovans, the study found, confirming reports based on a draft version of the Denisovan genome. The authors of the study didn't find any significant contribution of Denisovans to the DNA of people from mainland Eurasia, however.

The new gene-sequencing techniques also allowed scientists to more precisely calculate how much of modern humans' DNA came not from Denisovans but Neanderthals. They found, to their puzzlement, that Native Americans and people in East Asia have more Neanderthal DNA than do people whose ancestors are from Europe, where most Neanderthals lived.

That is "really, really interesting," said study coauthor David Reich, a geneticist at Harvard Medical School in Boston.

The study authors don't know how this happened, but they have theories. Perhaps Neanderthals bred with modern humans during more than one time and place, which would overturn theories that DNA mixing occurred only in the period when modern humans first came out of Africa and met the Neanderthals, presumably in the Middle East.

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