BioEd Online

The degraded DNA of ancient cave bears has been sequenced, despite the fact that many considered the genetic information unrecoverable. The achievement leads researchers to think they might be able to perform the same trick with DNA from ancient human relatives, such as the Neanderthals.

In the past, scientists have managed to retrieve genetic material for analysis from animals or humans that died in icy or desert environments, because these allow for good preservation. But the remains of animals and humans are mostly found in caves, and are heavily decomposed. The DNA from such specimens is usually mixed up with DNA from soil microbes and later cave inhabitants, making it difficult to sequence.

The standard practice for sequencing genes involves making numerous copies of the initial sample through a process called a polymerase chain reaction, or PCR. Subjecting ancient DNA to this does not produce good results because PCR picks up and duplicates the sequences of modern animals more efficiently. This means that bits of contaminating DNA often drown out samples from the prehistoric animal.

"The prevailing idea was that this was impossible," says James Noonan of the Lawrence Berkeley National Laboratory in California, who is lead author of the paper that appears in Science this week¹.

Keeping it simple

To overcome this challenge, Noonan and his colleagues decided to skip the replicating step and directly sequence the tiny amount of DNA extracted from two Austrian cave-bear bones that are more than 40,000 years old. To make sure each portion of DNA was really from the bears rather than a contaminating source, they compared each sequence produced with the genome of the dog, a modern relative of the bear.

The technologies needed to examine such tiny amounts of DNA directly, along with the reference genome from the dog, have become available to scientists only recently.

The team determined that nearly 6% of the sequences analysed from one of their animal samples belonged to ancient bear: an unexpectedly large amount. The rest of the DNA probably came from soil microbes or the palaeontologists handling the bones, the team says.

"I think that this really is a convincing proof of the approach," says geneticist Edward Rubin, also of the Lawrence Berkeley lab, who oversaw the investigation. He says the same technique should work on Neanderthal samples of about the same age or younger.

But challenges remain. Most important, it will be much harder to weed out contaminating DNA from the people who excavated the Neanderthal samples, as both sets of DNA will come from humans. "This is a problem," admits Noonan.

There were no such worries for the published study. "We have a strict policy of not employing bears at our sequencing facility," jokes Rubin.