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."
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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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