"It's not every day you get a sixfold improvement in ancient genome sequencing," says Harvard geneticist George Church, who wasn't involved in the new study.
DNA typically begins to degrade just after an organism dies, rapidly breaking into smaller and smaller chunks that become increasingly difficult for scientists to piece back together into a complete genome. In this case the new genome comes from a leg bone dug up from the permafrost in the Yukon Territory of Canada. And so the scientists had ice on their side: The cold temperatures had slowed the degradation process, though the DNA was still broken into many small pieces.
To put the pieces back together, researchers used a modern horse genome, sequenced in 2009, as a reference for what the ancient genome should look like. "It's very much like a puzzle where everything is mixed together, and you try to put it back from where it came from," says the study's lead author Ludovic Orlando, who studies ancient DNA at the University of Copenhagen. But 700,000-year-old horse DNA doesn't match up perfectly with the modern horse genome. So Orlando's team also compared the sample with DNA from another ancient horse from 43,000 years ago, as well as with DNA from a donkey, several modern horse breeds, and a Przewalski's horse, a wild cousin to the domesticated horse that is still living in Asia.
By studying the similarities and differences between genomes, the team concluded that modern equines?horses, donkeys, and zebras?share a common ancestor that lived approximately 4 million years ago. That's twice as old as conventional wisdom suggested. The data also revealed regions of the modern horse genome that appear to have been heavily shaped by the domestication process, and proved that Przewalsky's horses are a distinct group. Previously some scientists thought Przewalsky's horses might be a subset of domestic horses that reverted back to wildness, but the new data show these animals come from a different branch that was never domesticated.
Przewalsky's horse. Credit: Claudia Feh
"Until this study many experts would have thought that it was impossible to recover a genome from a sample of this age because of the rapid degradation of DNA," molecular biologists Craig Millar and David Lambert wrote in a commentary in Nature. The new analysis suggests that, given the right conditions, scientists may be able to unlock valuable information from fossils that previously would have been considered much too old to sequence.
"In an environment similar to the one we have studied, we could predict that very short molecules of DNA, which have information to work with, could very well survive over millions of years," Orlando says.
Millar and Lambert write that the study "encourages us to wonder if it might be possible to recover DNA from a wide range of Middle Pleistocene samples. Of particular interest would be material from ancestral human species such as Homo heidelbergensis and Homo erectus." Complete or partial genomes from ancient hominins would help clear up humanity's messy family tree. Orlando says he'd also like to check out the genomes of mastodons, cave lions, and other specimens preserved in permafrost.
Although Church cautions that the new method may not be applicable to all species, he says that some future technique "may enable us to get much older information than today's record of 700,000 years."
And completing genomes of ancient animals might offer more than just information. Church has been pioneering methods to resurrect extinct species using modern genomics (read more about this in the July/August issue of PopMech, on newsstands now). By copying and pasting genes of extinct species into the genomes of their living relatives, Church has said that biologists could revive species that are up to 200,000 years old. That time-frame estimate has to be revised in light of the new findings, Church says. "We could potentially resurrect this 700,000-year-old horse."
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