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Straight from the horse's toe: the world's oldest genome

Scientists have reconstructed the genome of a horse that lived some 700,000 years ago, mapping out the evolutionary history of the modern horse.

By Contributor / June 26, 2013

A Przewalski's horse is shown in Khomyntal, western Mongolia, in one of three reintroduction sites. From a tiny fossil bone found in the Yukon, scientists have deciphered the genetic code of an ancient horse about 700,000 years old. The researchers also found new evidence that the endangered Przewalski's horse, found in Mongolia and China, is the last surviving wild horse.

Claudia Feh/Przewalski's Horse Association via Nature/AP

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Researchers have sequenced the genome of a horse that lived some 700,000 years ago – the oldest genome ever sequenced – making it possible to reconstruct an evolutionary narrative of the modern horse, whose journey through history has been intimately bound to our own.

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According to a study published in the current issue of the scientific journal Nature, the genome of an ancient horse that lived in what is now Canada’s Yukon is about 10 times older than the previous oldest genome – that of a human who lived about 70,000 years ago. That means the hindsight of paleogenomics has been dialed backward some 630,000 years from where it was, offering up the extraordinary possibility that scientists may be able to reproduce our prehistoric record in greater detail than ever before, tracing not just the evolution of horses but – tantalizingly – of humans.

"We have beaten the time barrier,” said evolutionary biologist Ludovic Orlando of the University of Copenhagen, a lead author of the study, in a statement. “All of a sudden, you have access to many more extinct species than you could have ever dreamed of sequencing before.”

Discovered in 2003, the ancient horse bones were bound in the world’s oldest known permafrost at Canada’s remote Thistle Creek site. A multinational team of scientists, headed by Dr. Orlando and Eske Willerslev, also of the University of Copenhagen, then extracted DNA from one of the animal’s toes after determining that the bone was a promising candidate to still have viable DNA: Had the DNA not been kept cold and dry, it would not have survived those more than half-million years.

Sequencing DNA as fantastically old as that of the ice-encased horse is tough work, and the successful mapping of its genome is a testament to just how far sequencing technology has come since the first genome, of a virus that infects bacteria, was sequenced in 1976. 

The scientists mulled over fragmented and deteriorating DNA, building from disjointed strings of just 25 individual letters a complex genome that is billions of bases long. And since the DNA had accumulated bacteria tenants during its long, icy repose, scientists also had to ferret out which sequences belonged to the horse and which to the bacteria.

That complex sequencing needed fact checking. To confirm the horse’s age, scientists compared it with younger horses’ genomes, sequencing a DNA sample from the frozen bones of a horse some 43,000 years old, as well as samples from a donkey, five modern domestic horses, and a wild horse native to Mongolia. They say they are now confident that the horse is a staggering 700,000 years old. 

Scientists had once believed that horses had followed a simple, linear evolutionary road – the sort that can be easily printed onto a T-shirt – growing from a tiny version to the modern domesticated horse, frolicking cowboy astride it. But recent developments have complicated that linearity, suggesting that the horse’s evolution looked less like a T-shirt design and more like an unruly river, swelling to enormous volumes and pitching over waterfalls, and splitting off into tributaries, some with dead ends.

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