News of the WeekANCIENT DNA

New Methods Yield Mammoth Samples

Science  23 Dec 2005:
Vol. 310, Issue 5756, pp. 1889
DOI: 10.1126/science.310.5756.1889a

Ancient DNA has always held the promise of a visit to a long-vanished world of extinct animals, plants, and even humans. But although researchers have sequenced short bits of ancient DNA from organisms including potatoes, cave bears, and even Neandertals, most samples have been too damaged or contaminated for meaningful results.

Now in a paper published online by Science this week*, an international team reports using new technology to sequence a staggering 13 million basepairs of both nuclear and mitochondrial DNA from a 27,000-year-old Siberian mammoth. Also this week, a Nature paper reports using a souped-up version of more conventional methods to sequence a mammoth's entire mitochondrial genome.

Mammoth achievement.

Researchers managed to sequence a large chunk of DNA from a Siberian mammoth.

CREDIT: GIANNI DAGLI ORTI/CORBIS

Besides helping reveal the origins of mammoths, the new nuclear data serve as a dramatic demonstration of the power of the new technique to reliably sequence large amounts of ancient DNA, other researchers say. “The 'next generation' sequencer that was used [in the Science paper] will revolutionize the field of ancient DNA,” predicts evolutionary biologist Blair Hedges of Pennsylvania State University in University Park. Ancient DNA pioneer Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who co-led the independent mitochondrial study, calls the nuclear DNA work “really great—the way forward in ancient DNA is to go for the nuclear genome with technologies like this.”

To get mammoth samples for the new method, molecular evolutionary geneticist Hendrik Poinar of McMaster University in Hamilton, Canada, took bone cores from woolly mammoths found in permafrost and stored in a frigid Siberian ice cave. When Poinar returned the samples to his lab, he was surprised by the amount of DNA that emerged, particularly from one mammoth jawbone. This specimen had been recovered from the shore of Lake Taimyr, where very cold winters and short, cool, and dry summers turned out to be ideal conditions for preserving DNA.

Poinar sent the DNA-rich sample to genomicist Stephan C. Schuster at Pennsylvania State University, University Park, who is working with a new genome sequencer developed by a team at Stanford University and 454 Life Sciences Corp. of Branford, Connecticut (Nature, 15 September, p. 376). This rapid, large-scale sequencing technology sidesteps the need to insert DNA into bacteria before amplifying and sequencing it. Instead, scientists break DNA into small fragments, each attached to a tiny bead and encapsulated by a lipid bubble where the DNA is multiplied into many copies for sequencing. Because each fragment is isolated before copying, the method avoids bias from copying large amounts of contaminant DNA from bacteria or humans.

The researchers were stunned by how well the method worked on ancient DNA, which is notoriously difficult to extract and sequence: “I would have been happy if we got 10,000 bases of mammoth DNA,” said Poinar. Instead, they got 28 million basepairs, 13 million from the mammoth itself. Their preliminary analysis shows that the mammoth was a female who shared 98.55% of her DNA with modern African elephants. But mammoths were apparently closest kin to Asian elephants, as shown by Pääbo's mitochondrial study, which retrieved about 17,000 basepairs.

Poinar's team also found sequences from bacteria, fungi, viruses, soil micro-organisms, and plants, which the researchers say will help reconstruct the mammoth's ancient world. The technique was so productive that the authors predict it will be used soon to sequence entire genomes of extinct animals.

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