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Ancient DNA shows interbreeding between Homo sapiens and Neanderthal

By David Brown
Washington Post Staff Writer
Friday, May 7, 2010; A03

With the help of a pinch of fossil bone dust, scientists have discovered that modern human beings interbred with Neanderthals tens of thousands of years ago, and that 1 to 4 percent of the genes carried by non-African people are traceable to the much-caricatured, beetle-browed cavemen.

The Neanderthal project, which took four years and involved 57 scientists, is the latest and most astonishing example of the recovery of scientifically useful information from ancient DNA.

The new data answer a few of the many questions about modern human beings' relationship with their last big hominin competitors, who died out about 30,000 years ago. The data also hint at what Homo sapiens had -- but Homo neanderthalensis didn't -- that may have made the difference between survival and extinction.

"What this means is that Neanderthals are not totally extinct. In some of us, they live on," said Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Germany, who led the genome reconstruction described in Friday's issue of the journal Science.

The findings show that modern humans and Neanderthals interbred, probably in the Middle East, between about 100,000 and 80,000 years ago, soon after modern humans migrated out of Africa and before they diversified, through chance and natural selection, into the ethnic groups that exist today. That's why northern Europeans, the Chinese and Papua New Guineans carry traces of Neanderthal ancestry, but Africans do not.

The Neanderthal versions of genes differ from the human versions by one or more DNA letters, known as nucleotides, in the string of thousands of letters that make up a gene. The Neanderthal versions are salted through the 20,000-gene human genome in no particular order. Whether they endow their holders with certain traits or hazards isn't known.

On the other hand, there are dozens of genes (and even some long stretches of DNA encompassing numerous genes) that are distinctly different between modern humans and Neanderthals. Whether those differences had real-world consequences when they crept in through mutation eons ago -- and whether they are keys to human success -- are among the tantalizing questions arising from the new research.

"This is a very powerful method for shining light on a really crucial time in human evolutionary history," said Richard E. Green of the University of California at Santa Cruz, who did much of the work as a postdoctoral student in Paabo's laboratory. He and other scientists are eager to study those genes and regions "to understand exactly what changed, and why."

Until recently, the recovery of genetic material from flora and fauna subjected to the elements for 400 centuries was the subject of science fiction. But new methods of toning up degraded DNA, along with fast and accurate nucleotide sequencing, and software that lets researchers assemble the equivalent of a million-piece jigsaw puzzle, have made it possible.

The Neanderthal genes were recovered from three bones excavated in a cave in Croatia about 20 years ago. One is 38,000 years old, another 44,000 years old and one is undated. They appear to be shin bones, and all are from females. They also seem to have been intentionally broken, possibly to get at the marrow to eat.

The researchers removed half a gram of bone powder with a dental drill. More than 95 percent of the DNA in the sample belonged to bacteria and fungi, not to the Neanderthals. The scientists used a variety of techniques to eliminate the microbial DNA, recover the non-microbial DNA through polymerase chain reaction amplification, and assure themselves they had Neanderthal material and not modern human contaminants.

Proto-humans and chimpanzees diverged from each other about 6.5 million years ago. Modern humans and Neanderthals diverged about 300,000 years ago. On a genetic level, Neanderthals and modern humans are almost as closely related as today's ethnic groups are to each other.

But the differences may be important.

The researchers identified 73 genes for which all modern people have the same molecular version but for which Neanderthals have the more ancient, chimpanzee version. Five of the genes have two molecular differences between the human and Neanderthal-and-chimpanzee versions, suggesting there might be something especially distinct about the human version.

One of those genes encodes a protein that helps the sperm cell's flagellum beat. Another is for a protein that seems to be involved in the healing of wounds. A third is for a protein abundant in skin, sweat glands and hair roots. Successful reproduction, survival after injury and the ability to interact optimally with the environment: All are crucial to survival and obvious "targets" for natural selection.

Several other genes in which the human and Neanderthal versions differ are involved in important aspects of physiology and brain function. In damaged form, many of those genes are in turn implicated in human disease.

They include THADA (diabetes); DYRK1A (Down syndrome), NRG3 (schizophrenia) and CADPS2 (autism). One called RUNX2 is involved in deformities of the skull and collarbone -- parts of the skeleton in which modern people and Neanderthals differed visibly.

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