No bones about it, Ice Age fur is found rich in DNA
Scientists seeking to decode ancient DNA from woolly mammoths and other Ice Age beasts have found an abundant new source of unsullied genetic material: ordinary hair.
Using samples of fur from mammoths that roamed Siberia 17,000 to 50,000 years ago, the researchers were able, they say, to reconstruct the complete mitochondrial genomes of 10 animals, even though some of the hair had been stored at room temperature for 200 years.
By multiplying the potential sources of ancient DNA, the discovery could accelerate efforts to clone woolly mammoths and other extinct beasts, though scientists said it would take millions of dollars and decades of work to overcome the daunting technical hurdles that remain.
The findings, released today by the journal Science, suggest that heaps of ancient DNA are readily available in natural history museums and other collections, not just in fossil bones buried beneath layers of permafrost, said Tom Gilbert, a biologist at the University of Copenhagen in Denmark, who led the study.
“Think about all the extinct furred animals that are displayed in museums around the world,” Gilbert said. “There is a lot of work waiting for us.”
The workload could get even bigger if scientists rethink the value of ancient fur and begin collecting it in earnest. Caves in the southwestern United States contain lots of hair from such bygone species as dire wolves, short-faced bears, ground sloths and mastodons, said Ross MacPhee, a curator in the division of vertebrate zoology at the American Museum of Natural History in New York.
“My guess is that hair recovery will now be de rigueur in certain kinds of archaeology,” said MacPhee, who wasn’t involved in the study. “It’s kind of amazing stuff.”
This isn’t the first time scientists have tried to coax DNA out of ancient hair. Efforts in the 1990s produced erratic results, and hair shafts were thought to be especially vulnerable to contamination, which is a problem with bone samples as well.
“It just didn’t cut the mustard,” MacPhee said. “People had more consistent success with bone.”
But a decade later, Gilbert decided to try again.
In earlier studies, he found that the hair shaft was actually quite resistant to bacteria and other potential contaminants, offering protection to any DNA that might be inside. He suspects that keratin in hair shafts protects the interior from water and bacteria, two of the primary culprits in DNA degradation.
“I like to think of keratin as a kind of plastic that the DNA is embedded in, completely protecting it,” Gilbert said.
Adding to the allure was scientific speculation that mitochondrial DNA -- the genes that control the energy sources of cells -- would be abundant in hair because it takes so much effort to form the shaft.
Gilbert and his colleagues used a relatively new technique called sequencing-by-synthesis, which randomly picks hundreds of thousands of DNA fragments out of a sample and sequences them all. About 10% of the fragments contained mitochondrial DNA, which was more than enough to piece together each mammoth’s entire mitochondrial genome with high accuracy, Gilbert said.
Mitochondrial DNA is passed virtually unaltered from mother to child, and that makes it useful to researchers interested in studying mammoth migrations and herd relationships.
“We thought if we sequenced 20 samples, maybe one or two would actually work,” said Webb Miller, a professor at Pennsylvania State University’s Center for Comparative Genomics and Bioinformatics and a senior author of the study. “We were pretty flabbergasted that it would work every time.”
Each genome cost $5,000 to $15,000 to assemble, said Stephan Schuster, a Penn State geneticist and senior author of the study. The research was partially funded by Roche Applied Science, the company that makes the DNA sequencing machine used by the researchers.
The new study demonstrates that hair can be a viable source of ancient DNA and appears to be less contaminated than bone, said Hendrik Poinar, an evolutionary geneticist at McMaster University in Canada, who has used the same sequencing technique on mammoth bones. But he disagreed with the conclusion that hair is necessarily a better source than bone.
“There are pros and cons of each,” said Poinar, who wasn’t part of the research team.
Svante Paabo, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who is trying to decode the Neanderthal genome, called the study “very promising” but questioned the researchers’ assertion that Ice Age hair is more plentiful than bone. For some species, including Neanderthals, “only bone and teeth are preserved,” he said.
The sequencing-by-synthesis method also decodes snippets of nuclear DNA, the genetic code that contains instructions for how any organism is made. But since nuclear DNA is hundreds of thousands of times longer than mitochondrial DNA, it would take much longer -- and cost millions of dollars -- to generate an entire mammoth genome. With current technology, it would also produce snippets that are too short to combine in a reliable way.
But all those things will change as DNA sequencing gets faster and cheaper, just like computers.
Deciphering the complete mammoth genome is “doable, and it’s on the horizon” in the next 50 to 100 years, Poinar said.