Ancient DNA suggests new hominid line

Genetic data unveil a shadowy, previously unknown Stone Age ancestor

A new member of the human evolutionary family has been proposed for the first time based on an ancient genetic sequence, not fossil bones. Even more surprising, this novel and still mysterious hominid, if confirmed, would have lived near Stone Age Neandertals and Homo sapiens.

CAVE OF MYSTERIES Mitochondrial DNA analysis of a finger bone found in Denisova Cave in the Altai Mountains of southern Siberia suggests that a group of unknown hominids ventured out of Africa less than a million years ago. J. Krause

BACK STORY: WHO’S WHO IN THE GENUS HOMO H. Floresiensis: Mauricio Anton/Photo Researchers, Inc.; all others: Maurice Wilson/copyright The Natural History Museum, London

“It was a shock to find DNA from a new type of ancestor that has not been on our radar screens,” says geneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. These enigmatic hominids left Africa in a previously unsuspected migration around 1 million years ago, a team led by Pääbo and Max Planck graduate student Johannes Krause reports in a paper published online March 24 in Nature.

The researchers base their claim on DNA from a finger bone belonging to a hominid that lived in the Altai Mountains of central Asia between about 48,000 and 30,000 years ago.

Anthropologists have generally assumed that hominids left Africa in a few discrete waves, starting with Homo erectus about 1.9 million years ago. Neandertal ancestors left between 500,000 and 300,000 years ago, followed by humans around 50,000 years ago.

But the new genetic sequence supports a scenario in which many African hominid lineages trekked to Asia and Europe in the wake of H. erectus, Pääbo suggests.

This curious sequence was extracted from a piece of finger bone unearthed in 2008 at Denisova Cave in southern Siberia’s Altai Mountains. Previous excavations of stone and bone artifacts in the cave indicated that modern humans and Neandertals lived there periodically beginning at least 125,000 years ago. Few fossils have turned up at the site.

While retrieving DNA from presumed Neandertal fossils in November 2009, Krause noticed an unusual mitochondrial sequence. Mitochondrial DNA is located outside the cell nucleus and inherited from the mother.

Krause conducted tests to confirm that the newly recovered mitochondrial DNA came from an ancient hominid rather than from bacteria or researchers who had handled the fossil. Using advanced techniques for fishing DNA fragments out of fossils, the team then assembled a complete mitochondrial genome for the Denisova individual. The same approach has yielded ancient DNA sequences for Neandertals (SN: 3/14/09, p. 5) and a Greenland man who lived 4,000 years ago (SN: 3/13/10, p. 5).

The researchers compared Denisova mitochondrial DNA to complete mitochondrial sequences from 54 people who are living today as well as a human who lived in Siberia about 30,000 years ago, six Neandertals from more than 40,000 years ago, a modern pygmy chimpanzee and a modern common chimp.

Mitochondrial DNA from the Denisova fossil differs from that of humans at almost twice as many chemical positions as Neandertal mitochondrial DNA does, Krause says.

“That number of differences is good evidence for a new hominid because simple variation can’t account for it,” remarks geneticist Morten Rasmussen of the University of Copenhagen.

Assuming that mitochondrial DNA ancestors of humans and chimps diverged 6 million years ago, the researchers calculate that a mitochondrial ancestor common to the Denisova hominid, Neandertals and modern humans lived between 779,300 and 1,313,500 years ago.

A common mitochondrial DNA ancestor of modern humans and Neandertals lived more recently, an estimated 321,200 to 618,000 years ago.

Krause and Pääbo are now directing an effort to extract nuclear DNA from the Denisova fossil. Comparisons of Denisova, Neandertal and modern human nuclear DNA are needed to confirm that the finger bone comes from a new hominid species and to check for signs of interbreeding with Neandertals or humans.

For now, the researchers refer to the Denisova hominid as “X woman,” although its sex remains undetermined until nuclear DNA can be examined.

X woman’s finger bone came from a soil layer that has yielded bracelets and other artifacts usually attributed to humans, Krause notes.

“What we can say for now is that there were at least three different forms of hominids living in the Altai Mountains around 40,000 years ago,” Pääbo says. At that same time, Homo floresiensis, better known as hobbits, occupied the Indonesian island of Flores (SN: 5/10/08, p. 7). Hobbit DNA has yet to be recovered.

In a comment published with the new report, geneticist Terence Brown of the University of Manchester says that further ancient DNA studies will “possibly increase the crowd of ancestors that early modern humans met when they travelled into Eurasia.”

Anthropologist Ian Tattersall of the American Museum of Natural History in New York City agrees. Hominid evolution over the past 6 million to 7 million years includes at least two dozen species, in Tattersall’s view. It was “practically routine” for two or more species to live in the same general area at the same time, he says.

Tattersall regards the new mitochondrial DNA sequence as so distinctive that, unless disproved by further evidence, it must represent a new type of hominid.

In contrast, anthropologist Erik Trinkaus of Washington University in St. Louis views the new genetic data skeptically. “I don’t know what to make of this, at least not until there is more substantial fossil material than a partial finger bone,” he says. “It may be going too far to propose a new hominid.”

Trinkaus, who sees fewer species in the hominid family than Tattersall, cautions that biologists have difficulty identifying different species even among living primates. For example, groups of baboons that usually live apart as apparently separate species sometimes aggregate and interbreed, muddying their classification.

Pääbo acknowledges the complexity of finding new hominids in mitochondrial DNA, which in animals such as mice can pass from one species to another via interbreeding. “But there are massive genetic differences between X woman and both Neandertals and modern humans,” he says.

Bruce Bower

Bruce Bower has written about the behavioral sciences for Science News since 1984. He writes about psychology, anthropology, archaeology and mental health issues.

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