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Neanderthal Genome Unraveled

Scientists announce the first complete draft of our closest relative’s genome.
February 12, 2009

Man’s closest ancestors, the Neanderthals, disappeared about 30,000 years ago, leaving little more than their bones behind. But those bones may help decipher what makes us human, and they are beginning to divulge their ancient secrets. Now researchers have revealed a first draft of the complete Neanderthal genome, a sequence of three billion or so base pairs.

Missing links: Shown here is a three-dimensional reconstruction of a Neanderthal skull based on a CT scan of a skull found in 1909 in La Ferrassie, Dordogne. Using DNA isolated from Neanderthal bones such as this one, scientists have generated a draft of the Neanderthal genome.

At a joint press conference held during the annual meeting of the American Association for the Advancement of Science, Svante Pääbo, head of the project and director of genetics at the Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany, said that this first overview covers about 63 percent of the Neanderthal genome. Most of it derived from just a half gram of bone removed from 38,000-year-old fossils excavated from Vindija Cave in Croatia. “The attraction of the Neanderthal genome,” Pääbo says, “is that it’s our closest relative in all categories, and we diverged only about 300,000 years ago.”

“Studying them will tell us what makes modern humans really modern, and really human; why we are alone; why we have these amazing capabilities,” says Jean-Jacques Hublin, who is the director of human evolution at Max Planck and was involved in the research.

Despite its draft quality, the genome is already beginning to reveal a few of our ancestors’ traits. As researchers expected, Neanderthals lacked the lactase gene, present mostly in European humans, which allows adults to digest milk. But the researchers confirmed that the ancient hominid did share with us the only gene known to be implicated in speech and language, FoxP2, which earlier studies had only suggested was the case. “There’s no reason to assume they couldn’t articulate as we do,” Pääbo says.

However, the new data do little to further the idea that humans and Neanderthals interbred–something that has been the subject of much debate, but for which most experts agree there is little evidence. “We have looked at the contribution from Neanderthals into the present-day [human] gene pool–that is very little, if anything,” Pääbo says. “But the cool thing is that interbreeding is a two-way street, and for the first time we can look at it the other way, from human ancestors into Neanderthals. So we’re currently analyzing if we see evidence in the Neanderthal genome of a contribution from human ancestors.”

A little over two years ago, Pääbo and his colleagues, including a team headed by Michael Egholm at 454 Life Sciences, published the first proof that they could extract genetic material from Neanderthal bones. This is an incredibly complex, obstacle-riddled task when dealing with such ancient DNA. The longer bones lie in the ground, the more their DNA degrades, leaving researchers with only short fragments with which to work. Microbes also invade a skeleton and saturate it with their own DNA; in even the most well-preserved bones, only 4 percent of the DNA belongs to its original owner. Because the genome in question is from man’s closest relative, things get even more complicated. Human contamination is inevitable, and researchers must find a way to differentiate between human and Neanderthal DNA, even while the two species share almost all the same genes.

The proof-of-principle papers published in 2006 were a huge advance, made possible through high-throughput sequencing technology developed by 454 Life Sciences. Their sequencing machine can analyze millions of strands of DNA all at once, in a process that uncouples the double-stranded DNA, chops it up into fragments, attaches those fragments to minute beads, and creates millions of clones of the original fragments. These beads are then packed into individual wells on a slide, and analyzed in a machine that determines the fragments’ sequences by recording the identity of every base as it binds with its complementary nucleotide.

The new results, Egholm says, relied both on the 454 machine and on one made by Solexa, which can analyze hundreds of millions of wells at once. Speed was key: since only 4 percent of what was sequenced actually belonged to a Neanderthal, the researchers had to sequence over 100 million base pairs of unrelated DNA just to get 3 million base pairs of Neanderthal DNA. “With lower throughput sequencers, it would have been really difficult to generate enough data to sequence the entire genome,” says Rachel Mackelprang, a postdoc in genetic analysis at the Department of Energy Joint Genome Institute.

Using previously sequenced genomes from other species was also crucial, says John Hawks, a biological anthropologist at the University of Wisconsin. “Bootstrapping computer information about genomes really made all of this possible,” he says. “To be able to take snippets of DNA of 50 base pairs or less and have the computer say that it’s the same as a bacterial sequence has enabled the reconstruction of genuine Neanderthal sequence.”

But more than anything, the largest challenge has been finding ways to detect and eliminate sequences from human DNA from the Neanderthal samples. The 2006 research was scrutinized heavily by Pääbo and Egholm’s peers. Despite the researchers’ caution, human DNA had infiltrated the samples and been included in the original sequence. This time around, to correct for contamination, they used a number of technological innovations, including the placement of genetic tags on all bone-derived DNA, which allowed them to detect and discard all untagged DNA as contaminants.

“Having a genome allows us to look for things that we can’t see in fossils,” Hawks says. “It’s so much more than the bones that we have. It’s exciting for me because here’s this ancient group of people, and you’ve opened a new door into what their lives are like.” More than anything, he says, he just wants to get his hands on the data. “If you think about everything that’s been written on Neanderthals for the past 150 years … we have the potential to change everything.”

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