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Ancient Bear DNA Mapped -- A 1st for Extinct Species

Stefan Lovgren
for National Geographic News
June 6, 2005
 
Scientists have sequenced the DNA of two cave bears that roamed the Austrian Alps some 40,000 years ago. It marks the first time researchers have been able to completely sequence the DNA of a species that has long been extinct.

The research opens the door to sequencing the DNA genome of other extinct species, including the Neandertals (often spelled "Neanderthals").

"We have shown that it is possible to sequence the genome of a long-extinct organism, something previously considered to be in the realm of science fiction," said James Noonan, a geneticist and postdoctoral fellow in the genomics division at the Lawrence Berkeley National Laboratory in California.

Noonan is the lead author of the study, which appeared in the June 2 online edition of the journal Science.

DNA Nucleus

Until now scientists have been unable to extract pure DNA from the cell nuclei of ancient animals. Not only does DNA start to degrade at death, but the microbes that eat away at dead animals contaminate genomic DNA, which is found in cell nucei. Other contaminants may include human DNA left through contact, such as when a scientist handles the bones.

Rather than use genomic DNA, most studies of ancient DNA have used mitochondrial DNA. A sort of cellular power plant, mitochondria have their own type of DNA and are believed to have evolved separately from genomic DNA. (See our quick overview of genetics.)

Only genomic DNA, however, can help scientists understand the functional differences between extinct and living species.

Because unbroken strands of ancient DNA are so hard to come by, previous ancient-DNA studies have used a biochemical amplification method to create a string of DNA. In effect, they take an unbroken fragment of DNA and copy it over and over to create a complete strand. But this only works for mitochondrial DNA, not genomic DNA.

Needle in a Haystack

This time the scientists took a different approach. First they extracted genomic DNA from two 40,000-year-old cave bear bones from Austria.

Extinct for more than 10,000 years, cave bears (Ursus spelaeus) were related to the ancestors of modern brown bears and polar bears. Cave paintings show that ancient humans encountered cave bears.

The researchers sequenced all of the genomic DNA they could get out of the cave bear bones. Without amplifying any of it, they then identified each sequence by comparing it to the complete dog-genome sequence that is publicly available. Dogs and bears, which diverged some 50 million years ago, are 92 percent similar on the sequence level.

"[It was] sort of like looking for a needle in a haystack," said Eddy Rubin, the director of the U.S. Department of Energy's Joint Genome Institute in Walnut Creek, California, where the work was done. "Fortunately the computer was a great magnet for finding the needles we were interested in."

About 6 percent of the sample that was sequenced yielded undamaged cave bear DNA, while the rest was a hodgepodge of microbial contaminants. Within those fractions of cave bear DNA were bits of genes.

Comparing the ancient bear sequences with those of modern bears, the scientists showed that cave bears were more closely related to brown bears than to black bears.

"It shows that we got enough ancient genomic DNA to learn something biologically relevant about the cave bear," Noonan said.

Human Evolution

The cave bear DNA sequencing opens the door to the testing of other extinct species, including our nearest prehistoric relatives, the Neandertals. The scientists say they plan to sequence the Neandertal genome over the next several years.

Another possibility is to apply these techniques to the remains of Homo floresiensis, found recently in Indonesia. Researchers nicknamed this human ancestor "the hobbit" because of its tiny stature. (See pictures of the hobbit.)

H. floresiensis is believed to have diverged from modern humans two million years ago. Neandertals may have diverged from humans 500,000 years ago.

The successful DNA sequencing of the two human-ancestor species could help scientists describe the evolutionary events that led to modern humans.

What about sequencing the DNA from dinosaur fossils?

"Unfortunately, we don't think [that] will ever be possible," Noonan said. "DNA does not survive beyond a hundred thousand years under the environmental conditions in which we found our cave bear remains. And of course, dinosaur fossils are at least 65 million years old."

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