On the Hoof: Ancient DNA Reveals Story of the Horse

PetMD Editorial
Published: July 02, 2013
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PARIS - Scientists last Wednesday said they had unravelled the DNA of a horse that lived some 700,000 years ago, a record-breaking feat in the young field of palaeo-genomics.

The ancient find indicates that all horses today, as well as donkeys and zebras, shared a common ancestor that lived some four million years ago, twice as early as thought.

The breakthrough also raises hopes that many fossils deemed useless for DNA sampling may in fact be crammed with genetic treasure, researchers said.

Reporting in the journal Nature, the team said the tale began 10 years ago, with the discovery of a piece of fossilised horse bone in the permafrost at a location called Thistle Creek, in Canada's Yukon territory.

"It's a piece of metapodial bone" from the leg, said Ludovic Orlando, a French researcher at the Centre for Geogenetics at Denmark's Museum of Natural History.

"It's a fragment about 15 centimetres (six inches) long by eight centimetres (3.2 inches) wide."

Radiodating of the ground in which the bone was found indicates that the organic material there -- decomposed leaves and so on -- was deposited about 735,000 years ago.

The sample had been astonishingly preserved in the deep chill -- but time was bound to have damaged its cells and thus limit chances of teasing useful DNA out of it.

"It was a unique chance to push our technology to the limit," Orlando told AFP.

"To be frank, I myself didn't think it would be possible when we first tackled the idea."

These early doubts began to lift in the lab, when the researchers managed to pinpoint remnants of collagen -- the main protein found in bones, as well as biological markers for blood vessels.

What about cellular DNA?

At that point, disappointment came. Technology available at the start of the analysis three years ago fell far short of being able to take these tiny scraps of DNA and turn them into intelligible code.

"We were only able to get a piece of DNA sequence about once in every 200 attempts," said Orlando.

What changed things was a generational change in sequencing technology.

Exploiting an innovation in medical research, the scientists found a way of unravelling DNA molecules without having to "amplify" them in a sequencing machine.

This approach meant the precious sample was not wasted through endless failures, and risk of further degradation through handling and air exposure was minimised.

The outcome was a three-to-fourfold improvement in the success rate, which rose to a factor of 10 when the temperature and method of extraction were further tweaked.

"We went from one in 200 to about one in 20," said Orlando.

"What emerged from this were tiny scraps of sequences, which we then had to reassemble into a full genetic code," he said.

"It's like mending a vase which has broken into a thousand pieces -- only this one has billions of pieces!"

The result is the oldest genome that has been fully sequenced -- from an animal that lived between 560,000 and 780,000 years ago.

The previous record was held by the sequencing of an enigmatic human known as the Denisova hominin, who lived 70,000 to 80,000 years ago.

The horse sequence was compared against the genome of a horse that lived in the Late Pleistocene, 43,000 years ago, as well as those of five modern horse breeds, a Przewalski's horse (a wild equine species that diverged from the domestic horse), and a donkey.

"Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated four to 4.5 million years before present, twice the conventionally accepted time," the study says.

It also suggested that efforts to preserve the Przewalski's horse, by crossing it with domestic breeds, are genetically valid. There seems to be have been little genetic intrusion into the wild variant.

Beyond this immediate discovery, the scientists are confident their work will one day shed light on prehistoric animals or even our own forebears, through fossils whose DNA is conventionally considered too degraded for sequencing.

"In very cold conditions, roughly 10 percent of small-sized molecules have a good chance of surviving beyond a million years," said Orlando.

"We have opened a door that we thought had been closed forever. It all depends on technological progress, but we have loads of arguments for believing that the future will lead us to treasure, not a dead end."

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