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Scientists Untangle Woolly Mammoth Genome

19 November 2008 (All day)
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(Illustration) Steven W. Marcus/Exhibit LLC; (inset) S. C. Schuster

Ancient hairball. The hair from a permafrost-preserved mammoth (inset) contains ancient DNA that reveals clues about its evolution.

Researchers who bought mammoth hair on eBay have decoded 70% of the creature's genome, marking the first time the nearly complete genome of an extinct animal has been sequenced. With so much DNA, the team was able to trace the mammoth's evolution and spot genetic mutations that may have helped it adapt to frigid conditions.

Scientists have hoped that ancient DNA would help them study long-vanished species of animals and even humans, such as Neandertals, whose nuclear DNA is also being sequenced. But until recently, they lacked the tools to decipher the fragmentary ancient DNA that was available. That changed with the development of rapid, large-scale sequencing technology like the so-called 454 method (Science, 5 August 2005, p. 862), which actually works best with small fragments of DNA.

In 2005, Pennsylvania State University, State College, genomicist Stephan Schuster and colleagues used the new tools to sequence 13 million base pairs of maternally inherited mitochondrial DNA of a woolly mammoth, which includes DNA that codes for 13 of the mammoth's roughly 20,000 genes and some nuclear DNA. They found that mammoths were closely related to African elephants and that the two lineages split about 6 million years ago (Science, 23 December 2005, p. 1889). More recent work has suggested that there were two species of woolly mammoths living in Siberia, but paleontologists were skeptical of those results because they didn't see enough variation in the bones to warrant separate species.

So Schuster went after the nuclear genome. He didn't have access to the DNA from mammoth bones used in earlier studies, so he bought mammoth hair on eBay from a Russian dealer. First, Schuster followed an elaborate protocol to confirm with Russian scientists that the hair had been obtained with proper permits. The hair is an excellent source of ancient DNA because it is less likely to contain bacteria or fungi than DNA extracted from porous bone, says Schuster. To be sure, he bleached the samples to remove contamination, extracted the DNA, and used the 454 method to sequence a staggering 3.3 billion base pairs of mammoth DNA. "Our data set is 100 times more extensive than any other published data set for an extinct species, demonstrating that ancient DNA studies can be brought up to the same level as modern genome projects," says Schuster.

Once the researchers sequenced the nuclear DNA, they confirmed the earlier reports dating the split from the ancestor of elephants and suggesting that there were two species of woolly mammoths in Siberia. "The mtDNA was a very good proxy for the entire genome," says Schuster. By sequencing most of the nuclear genome, the team was able to date the split of the two species of woolly mammoths to more than 1.5 million years ago and to confirm that mammoths have far less genetic diversity than primates, for example, which may have made them more susceptible to extinction. The researchers also identified new genetic mutations found so far only in mammoths in regions of the genome that are highly conserved in other mammals, including elephants.

Schuster and his colleagues believe these mutations helped mammoths cope with the harsh arctic environment, perhaps by encoding proteins important for metabolism, digesting different foods, or fighting disease. The team is also searching for viral sequences that might have slipped into the genome. Such genetic mutations might offer clues about what adaptations or diseases hastened the extinction of mammoths when the climate warmed in Siberia about 12,000 years ago.

Those mutations are already the target of new research. They "provide us with data we can mine," says evolutionary geneticist Hendrik Poinar of McMaster University in Hamilton, Canada. "We can get to the really sexy stuff of what made a mammoth a mammoth."

The work goes beyond helping researchers understand mammoths. "The authors have accomplished an amazing technical feat by sequencing such a large fraction of an extinct genome," says geneticist David Reich of Harvard Medical School in Boston. "I'm sure there will be more ancient DNA genomics to come."

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