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Scientists unveil beginnings of Neanderthals' DNA code

Originally posted on sciy.org by Ron Anastasia on Sat 18 Nov 2006 11:13 AM PST  




Scientists unveil beginnings of Neanderthals' DNA code

Scientists yesterday unveiled a partial draft of the genetic code of Neanderthals, a close relative of humans whose genome, when completed, could provide profound insights into what makes us human.

The achievement demonstrates the feasibility of determining the entire genetic makeup of Neanderthals, as well as other extinct species, using DNA from fossils, the researchers said. The draft includes less than 1 percent of the DNA from a 38,000-year-old Neanderthal fossil, but the researchers said they expect to have a complete draft in two years.

An analysis of the partial DNA code shows that Neanderthals separated from the human line about half a million years ago, according to the team of German and American scientists. The team said it found no evidence to support a controversial theory that Neanderthals and ancient humans mated.

But the greatest significance of the announcement, other researchers said, is that it shows that the science of ancient genomics -- once solely the stuff of fiction like "Jurassic Park" -- has arrived. A genetic understanding of the Neanderthals, who made sophisticated tools and buried their dead, could reveal details like the color of their hair and perhaps whether they could speak. And it would allow researchers to identify the final, crucial genetic changes, long after the split with chimpanzees, that set humans apart and allowed their ancestors to prosper while Neanderthals died out.

"It is an amazing thing to be able to reconstruct the genome of an ancient organism," said David Reich , a genetics specialist at Harvard Medical School who was not involved in the research. "What they have done is an incredibly important technical achievement."

The research, published jointly by the journals Nature and Science, is also a testament to teamwork and sheer persistence. The scientists painstakingly examined some 70 Neanderthal bones in various collections before finding one -- recovered by paleontologists in a Croatian cave -- without too much contamination and with enough viable DNA.

German scientist Svante Paabo , who led the research, has worked with ancient DNA for more than two decades, refining techniques for unraveling its secrets. After death, bodies are overrun with microbes that have their own DNA. Then, over thousands of years, the original DNA chemically degrades and breaks into pieces. Finally, when a fossil is recovered, it is contaminated again with modern DNA.

Fishing out enough of the original Neanderthal DNA seemed impossible. But with the help of new technology, Paabo, a scientist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, has overcome the problem.

The fossil DNA was sent to 454 Life Sciences , a Branford, Conn., company that has developed a machine able to rapidly "read" a huge amount of DNA. DNA consists of long chains of four different chemical units -- the "letters" that make up the genetic code -- and the company's machine can decipher 20 million of the "letters" in a few hours.

This finally made the idea practical, because about 95 percent of the DNA is contamination from other organisms, according to Michael Egholm , vice president of molecular biology at 454.

To identify the Neanderthal DNA, the scientists compared the sequence of the DNA pieces they read -- each between about 50 and 150 letters long -- with massive computer libraries of DNA from various species. This allowed them to discard DNA from bacteria and zero in on the segments that most resembled human DNA.

They took a number of technical steps to ensure that they were reading Neanderthal DNA and not human DNA, the scientists said. For example, they were able to see telltale degradation on the DNA molecules, signs of their age.

All told, the team was able to put together about 1 million letters of Neanderthal DNA, according to the paper in Nature. The human genome was used as a guide to place the small pieces. The entire Neanderthal genome is thought to be about 3 billion letters long, the same as for humans.

Parallel work, using DNA from the same Neanderthal bone, was done at the US Department of Energy Joint Genome Institute and the Lawrence Berkeley National Laboratory , both in California. Led by scientist Edward M. Rubin , the team used a slightly different technique and generated about 65,000 letters of Neanderthal DNA.

The two teams came up with different dates for when Neanderthals split from the human line: about 500,000 years ago, and about 700,000. But the estimates are within each other's margin of error, according to the papers.

When more of the genetic code is known, they said, the estimate will become more accurate. The estimates are consistent with the fossil record, according to Ian Tattersall , a Neanderthal specialist at the American Museum of Natural History in New York City.

When a complete genome is available, scientists plan to examine particular genes thought to be important in human evolution. For example, researchers have identified a gene called FOXP2 that they believe plays a vital role in language.

At some point, humans developed a variant of the gene that apparently boosted their language ability. It is thought that this happened after the split with Neanderthals, but the only way to be sure will be to look.

More generally, Harvard's Reich and other scientists said, researchers will look for areas in the genome where there have been extensive changes since the break with Neanderthals. This will show, systematically, the most recent changes that led to modern humans. Nobody knows what these will turn out to be.

The project's success so far also suggests that other genomes of recently extinct species might be reconstructed as well. Scientists have started work on the cave bear and woolly mammoth. And it may be possible to determine many others, revealing much more about the prehistoric world -- and how the animals in it evolved -- than scientists a generation ago could have even dreamed.

"These papers are a manifesto for the future," said Tattersall. "Their main importance is to point toward what is going to come."

Gareth Cook can be reached at cook@globe.com.


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