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DNA from bone shows new human forerunner, and raises array of questions

By David Brown
Thursday, March 25, 2010; A01

A team of European researchers has identified a new lineage of proto-human that left Africa about a million years ago, traveling as far as Siberia and then dying out -- a discovery that raises new questions about early human history.

The existence of the new lineage was discovered by analyzing DNA extracted from a single bone fragment, according to a study published Wednesday in the journal Nature. What the beings looked like, how they lived and what happened to them are a mystery. All that's known is that they existed as recently as 40,000 years ago, which is the approximate age of the bone.

"Whoever carried this DNA out of Africa is some new creature that hasn't been on our radar screen so far," said Johannes Krause, a researcher at the Max Planck Institute for Evolutionary Anthropology in Germany, who helped lead the research team.

The new lineage, which has not yet been declared a separate species, occupied Russia's Altai Mountains during a long period when early modern humans and Neanderthals were also there. Whether its members had contact with those other early people -- or might have bred with them -- isn't known.

Nevertheless, the possible cohabitation of the three groups gives rise to at least two narratives of the first chapter of Eurasian history.

That landmass might have been a peaceable kingdom of competing "hominin" species. Or it could have been the site of genocide, with the Neanderthals and the just-discovered group of beings dying out to the last man and woman.

"People are going to be what we call 'gobsmacked' by this news," said Terry Brown, a molecular paleontologist at the University of Manchester, who wrote a commentary accompanying the paper in Nature. "There is going to be open-mouth amazement."

Apart from adding an unknown prehistoric cousin and a new "out-of-Africa" migration to the story of our origins, the finding marks a first in the way anthropological discoveries are made. The new lineage was determined to be distinct from other early humans not by the shape and size of its skeleton, but exclusively by differences in its genetic material.

That material was extracted from a fragment of a child's pinkie in the form of mitochondrial DNA. The bone, found in 2008 in a cave during a routine archaeological excavation, is the only physical remains of the group. As a consequence, the researchers have no idea what its members looked like compared with the more ancient Homo erectus, the beetle-browed Neanderthals or the recently discovered "Hobbit people" of Indonesia.

The discovery raises the possibility that there might have been many waves of migration out of Africa by evolving proto-humans, each group genetically distinguishable from the others. It is likely to spur the search for other prehistoric bone fragments in places cool and dry enough to have surviving remnants of DNA.

"Maybe it is overly simplistic to think of particular migrations out of Africa," said Svante Paabo, the other leader of the German team. "There might have been a more or less continuous flow of migration. The picture that may emerge in the next few years is likely to be much more complicated."

Most DNA in human cells resides in the nucleus, in long strands called chromosomes. The chromosomes encode about 20,000 genes, which one inherits from both mother and father.

A tiny amount of DNA, however, is in satellite structures outside the nucleus called mitochondria. They are inherited exclusively from the mother. Mitochondrial DNA, or mtDNA, which encodes fewer than 40 genes, defines an unbroken line of mother-to-child descent.

The linear order (called the "sequence") of the DNA "letters" in mtDNA is extremely stable over time. Nevertheless, mutations do creep in, and the rate at which they do is known, at least approximately. For that reason, differences in mtDNA function as a "molecular clock." They can be used to estimate how long ago the two populations had an ancestor in common.

Modern humans differ from Neanderthals by an average of 202 "letters" out of about 16,500 in the complete mtDNA strand. The Siberian bone's mtDNA differs by 385 letters. Chimpanzees and modern humans differ by 1,462 mtDNA letters, on average. Analysis of those differences led the researchers to conclude that the new lineage shared a common ancestor with Neanderthals and modern humans about 1 million years ago.

A more ancient proto-human, Homo erectus, left Africa about 1.9 million years ago. Neanderthals' ancestors left 300,000 to 500,000 years ago. Modern humans left 50,000 years ago.

The researchers think the ancestors of the "Denisova hominin" -- named after the cave where the finger bone was found -- almost certainly left Africa in a migration separate from those of the other species. Paabo thinks it probably occurred 800,000 to 900,000 years ago.

The bone fragment has also yielded remnants of nuclear DNA, which may be enough to sketch a few details of its owner, thought to be a 6- or 7-year-old child.

If the nuclear DNA's genetic fingerprint is similar to that of modern humans or Neanderthals, it will imply that some of the child's ancestors were the product of breeding with those species. On the other hand, if it is as different from those species' as the mitochondrial DNA is, the researchers can conclude the child was a "purebred" member of the newly discovered lineage.

So far, there's no firm evidence of breeding between early modern humans and Neanderthals. To discover that the Denisova hominin was a hybrid -- the answer should be known in a few months -- would change the view of man's prehistory considerably.

Neanderthal remains have been found less than 100 miles from Denisova Cave. Artifacts in nearby caves and in Denisova itself suggest the presence of Upper Palaeolithic-age people, which might include modern humans. The time when the three groups occupied the same region spanned at least 10,000 years; whether they were exact contemporaries is unknown.

If they were, Paabo said, that "raises the potential of all sorts of interactions" between them. One is a fight to the death -- although there's no evidence of that so far.

"Something happened that only we survived," Paabo said. He added that he shares the view that "we were somehow responsible" for the disappearance of the other lineages. "But whether it was in a direct way, or some kind of ecological competition, we don't know."

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