Genome of Ancient Denisovans May Help Clarify Human Evolution

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.

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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.

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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.

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In another first, the authors used the DNA sequence to estimate the age of the Denisovan pinkie finger bone.

They started by counting up all the tiny genetic changes that have accrued in the genomes of both modern humans and Denisovans since our lineage diverged from that of chimpanzees 6.5 million years ago. Then they compared the two numbers.

Genetic changes build up regularly through the ages, like the ticking of a clock, so the tally allows scientists to estimate the passage of time. Not surprisingly, the Denisovan sample had amassed fewer changes than its human counterparts. From the difference, the authors estimated that our ancient relative, believed to be a female child, met her end somewhere between 74,000 and 82,000 years ago.

The authors used the same approach to estimate how long ago our lineage branched away from the line that led to the Denisovans and Neanderthals. It happened somewhere between 170,000 and 700,000 years ago, they concluded.

The range is broad because the modern DNA revolution has overturned notions of how fast the internal genetic clock is ticking, said study coauthor Matthias Meyer.

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