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12/23/2010 04:25 PM

The Denisovan Code

Researchers Decipher DNA of Mysterious Human Ancestor

By Johann Grolle

The human family just got a new relative. Genetic researchers in Leipzig have deciphered the DNA of a hominid species that coexisted with Homo sapiens and Neanderthals around 40,000 years ago. A tiny piece of bone was enough for them to sequence the genome.

The miniscule amount of powder could have sat on a knife point, and yet, according to Johannes Krause, it contains something sensational. The Leipzig-based genetic researcher extracted the fine powder from a minute piece of fossilized bone -- and discovered a whole chapter of mankind's history inside it.

Krause and his colleagues at the Max Planck Institute for Evolutionary Anthropology in the eastern German city of Leipzig were able to sequence almost the complete genome of a hitherto unknown type of hominid from molecules that they extracted from bone meal. In addition to the DNA sequence of modern Homo sapiens and Neanderthals, they also unlocked a genome from a third type of hominid, according to a paper published Thursday in the journal Nature. The researchers have dubbed the new hominids "Denisovans," after the Denisova Cave in the Altai Mountains of Siberia where the bone was found.

Krause announced to the world's media earlier this year that he had discovered the remains of a new type of human. The only surviving fossil was a tiny piece of finger bone from a girl who had died around 50,000 years ago that had been found in the Denisova Cave.

The Leipzig scientists -- who focus on the era when modern humans shared the Earth with their Neanderthal cousins -- had registered their interest in the find immediately. But when Krause drilled into the tiny finger bone for the first time in his clean-room laboratory in Leipzig, he had no inkling of the sensational discovery that awaited him.

At first it seemed to be a routine examination. Krause only wanted to ascertain whether this little bone came from a modern human or a Neanderthal. However, the DNA sequence he found did not match anything he had ever seen before. Krause had stumbled upon a completely new being, a third type of human, who had competed with modern humans and Neanderthals for dominance in Eurasia.

Complete Genetic Code Deciphered

Since the discovery was announced in March, the researchers have been focused on the task of decoding the entire 3 billion DNA building blocks in the complete genetic makeup of the newcomer from the Altai Mountains. It is only now becoming clear what kind of "wonder bone," as Klause puts it, that they are working on.

Seventy per cent of the DNA code snippets that they found in the bone powder came from the Denisova girl. Never before had scientists found such a high level of purity in Stone Age DNA. Normally with such ancient discoveries, 99 per cent of all DNA consist of contaminants of a bacterial origin. Thanks to the unparalleled purity of the sample, a tiny amount of bone dust was enough for the scientists to assemble an almost-complete DNA sequence of the prehistoric girl. This now enables them to draw remarkable conclusions about the fate of the mysterious Denisovans.

Some 300,000 years ago, they split off from the branch which eventually developed into the Neanderthals. Whereas the Neanderthals spread westwards into ice-age Europe, the Denisovans moved east.

So far, the discovery in Siberia is the only example of this new type of hominid. But researchers believe that the Denisova may have hunted across large swaths of Asia. It is an assumption borne out of the perhaps most stunning part of their analysis.

Few Traces of Intermingling

The scientists posed the question as to how different types of hominids might have interacted with each other. Did they hunt each other? Did they avoid each other? Might they have stolen each other's women? To find the answers to these questions, the Max Planck scientists compared DNA from the Denisova cave with that of modern man. They found no traces of Denisova characteristics in people from Africa, Europe or China. Indeed, clear indications of intermingling were only found among the inhabitants of Papua New Guinea.

The two types of hominids, researchers believe, must have encountered each other somewhere in Southeast Asia. They hypothesize that different Denisova tribes had settled there long before modern man made his way to East Asia some 30,000 years ago. The two groups must have interbred, perhaps not as a matter of course, but periodically. Later, the modern humans and their genetic dowry moved further south, whence today's Melanesians developed.

The Leipzig researchers now want to search Russian and Chinese collections for more fossils that could belong to the Denisova. The hope is to understand what they may have looked like. While the DNA provides hints on several characteristics of the Denisova, appearance is not one of them.

Massive Molar

But the researchers did present an additional find. In the same Siberian cave, a molar was found. The tooth's owner, according to DNA analysis, was closely related to the Denisova girl.

This molar is distinctly different to those of all other known types of humans. Its massive size alone leads the scientists to suppose that it once belonged to a man. "Theoretically, it could also have come from a woman" said Svante Pääbo, the head of the Leipzig-based team of genetic researchers. "But in that case I would prefer not to meet the corresponding male."

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