Ancient Yukon horse yields oldest genome ever

A 700,000-year-old horse bone found in the permafrost of a Yukon gold mine has yielded a complete genetic profile, breaking scientific records and revealing many new insights about the evolution of horses.

700,000-year-old DNA reveals history of horse evolution

Most of the horse fossils found by Duane Froese and his team, like this skull, have been from the Late Pleistocene, when Arctic horses were pony-sized. (D.G. Froese/University of Alberta)

A 700,000-year-old horse bone found in the permafrost of a Yukon gold mine has yielded a complete genetic profile, breaking scientific records and revealing many new insights about the evolution of horses.

The analysis of the ancient genome suggests that it is likely possible to piece together the genomes of organisms that lived as far back as a million years ago, said Ludovic Orlando, the lead author of the paper describing the discovery, at a press briefing organized by the journal Nature in which the paper was published Wednesday.

That "obviously opens great perspective as to the level of details we could reconstruct [about] our own origins and actually, the evolutionary history of almost every single species living on the planet," Orlando added.

Previously, the oldest genome ever reconstructed — one belonging to an ancient human relative — was just 70,000 years old.

Found in a gold mine

Duane Froese, an earth sciences professor at the University of Alberta, found the metapodial bone from the horse's leg, equivalent to bones found in the palm of a human hand, about a decade ago in the Thistle Creek gold mine, about 100 kilometres south of Dawson City.

The 700,000-year-old bone from a horse's lower leg was'exceptionally well preserved. (Ludovic Orlando/Natural History Museum of Denmark)

At the time, he and his colleagues were hunting for fossils in the permafrost and trying to understand the age of the sediments that hosted the fossils and preserved ancient plant material.

It's not uncommon to find bones in the region from pony-sized horses from within the last 100,000 years during a period called the Late Pleistocene, Froese said in a phone interview Wednesday.

But this particular metapodial bone was distinctive because it was so much larger.

"This was really domestic horse sized," said Froese, who has just returned from another fossil-hunting trip in the Yukon. "I had a pretty good idea that it was old. But unlike most of the other fossils like that I've found in the past, this one was exceptionally preserved. It had come right out of the permafrost. So we knew it was quite significant."

Based on the surrounding volcanic ashes, the bone was likely 500,000 to 700,000 years old — from a time called the Middle Pleistocene when horses and mammoths roamed the cold, dry grasslands of the Yukon and much of the rest of Canada was covered by ice sheets. The fossil's age was later confirmed using other techniques.

The trouble with old DNA

"We thought this fossil was simply too old to yield DNA," Froese recalled.

The ancient horse's DNA was compared to that of modern domestic horses and donkeys as well as to that of the Przewalski's horse, above, the only living wild horse species. (Claudia Feh/Association pour le cheval de Przewalski)

That's because DNA degrades over time, shredding into smaller and smaller bits that make it increasingly difficult to piece everything back together again.

However, different kinds of proteins remained preserved in the bone, making other scientists optimistic about the possibility of it yielding useable DNA.

In the end, using new technology, researchers were able to do what many would have thought to be impossible.

"All of the tiny bits we were are able to piece back together and reconstruct informatically the entire genome," Orlando said. It wasn't easy — Orlando said only one out of 200 DNA molecules sequenced by his team belonged to the horse. The other 199 belonged to bacteria that colonized the bone after the horse died.

But once the task was complete, and the ancient horse's genome was compared with that of the only living wild horse species, the Przewalski's horse; modern horses; and donkeys, the team learned a lot about horse evolution.

They found that the common ancestor of the species they analyzed arose around four million years ago — twice as early as previously thought. It appears the Przewalski's horse diverged from the modern domestic horse about 50,000 years ago and hasn't mixed with the domestic horse since. Over time, some parts of the genome that showed the biggest changes were the genes that control the ability to smell and the animal's immune system.

Horse populations fluctuated with climate

The DNA analysis also showed that horse populations fluctuated with the climate over the ages.

"Basically, when it's fairly cold, it's good to be a horse. When it's warm, it's pretty bad," said Eske Willerslev, another co-author of the report, at the press briefing.

Froese said that was likely because during warmer times, the boreal forest would have invaded the horses' grassland habitat. The researchers hope to be able to refine the horse genome in the future to get information so they are able to look at any single gene they want, Willerslev said. They also hope to be able to do a similar analysis of other fossil bones.

While permafrost can do an exceptional job at preserving DNA, Orlando said even in more temperate environments, small pieces of DNA can survive as long as 400,000 years.

Meanwhile, Froese is still hunting for fossils in the Canadian Arctic, taking advantage of access to buried permafrost provided by mining operations and trying to collect as much as he can before the permafrost warms and melts.

"There's this incredible natural history in permafrost in the Yukon and … this horse fossil really is a testament to this incredible natural history," he said. "None of this would be possible without permafrost."