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University of Alberta researcher Duane Froese with the skull of the extinct Late Pleistocene horse, Equus lambei in the Klondike area, Yukon.Grant Zazula/The Globe and Mail

When Duane Froese, a University of Alberta geoscientist, pulled the remains of a large horse from the Yukon permafrost in the summer of 2003, he knew it was an interesting find. What he could not have known, or even hoped for, was just how illuminating a window he had opened up into the past. A decade later, DNA fragments painstakingly extracted from that skeleton have yielded an archaic horse genome that could be more than 700,000 years old – 10 times older than any previously sequenced genome of any other creature.

The feat is a tour de force for a technique rapidly gaining importance in evolutionary biology. It also sheds new light on an ancient animal whose descendants would eventually be domesticated by humans and go on to play a key role in the history of civilization.

"Ancient DNA has promised the opportunity to see evolution in real time from the fossil record," Dr. Froese said. "This horse takes us a long way there."

Dr. Froese and his colleagues describe the fossil genome and its relationship to existing horses in a paper published online this week by the journal Nature. The results can be used as a genetic telescope to peer back across the millennia, allowing scientists to identify key changes in horse DNA over that time, which could eventually be linked to physiology and behaviour.

What did the fossil horse look like?

Large but otherwise very similar to a modern horse. Probably the closest modern comparison would be a Norwegian fjord horse, Dr. Froese said, "but I'd be keen to play time traveller just to make sure."

How do scientists know how old it is?

The fossil horse was recovered in a placer gold mining area known as Thistle Creek, Yukon. It was found in ancient permafrost beneath a layer of volcanic ash called "tephra" that has been dated at around 740,000 years old.

What was the environment like back then?

Although most of Canada was buried under a kilometres-thick layer of ice, it was too dry in that part of Yukon for glaciers to form. Horses at that time were able to wander over an open grassland that stretched westward from Dawson City across the Bering land bridge and as far as modern-day Britain.

What does the fossil genome reveal about horses?

It shows that the last common ancestor of all modern horses, zebras and donkeys lived about four to 4.5 million years ago, roughly twice as far back as some researchers have previously argued. It also shows that horse diversity plummeted at certain times in the distant past that appear to correlate with episodes of warming in the Arctic. And that's probably just the beginning. "The ability to watch genomes evolve is completely new, and we don't yet know what we're going to be able to learn," said Beth Shapiro, an evolutionary molecular biologist at the University of California, Santa Cruz, who worked on the specimen. She added that one exciting possibility would be comparing modern with ancient horse genomes across time "and use that to explicitly and precisely identify the genes that were involved in domestication."

How might researchers use the information?

The study also reveals that Przewalski's horses, a population of Asian wild horses that were once down to just a few dozen animals, have not mixed with domestic horses as much as some experts feared. That's good news, says Richard Reading, a conservation biologist with the Denver Zoo. "It suggests that as long as we work quickly with these populations of animals that decline to very lower numbers … we're able to retain a significant amount of the genetic variation that was originally in the species."

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