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

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.

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.

The data from the ancient horse, coupled with the data collected from the younger horse and modern samples, now suggest that Equus lineage, which includes all living horses, zebras, and donkeys, evolved from a common ancestor that galloped across the intermittently frozen grasslands some 4 million years ago – about twice as long ago as was previously believed.

“This means that our horse evolutionary record stretches back 700,000 years,” Beth Shapiro, one of the senior authors on the paper and an associate professor at the University of California, Santa Cruz, told the Monitor.

The amalgamated data also helps to tell a narrative of natural selection that created the domestic horse, Dr. Shapiro said. Scientists looked at genetic variants known as single nucleotide polymorphisms in the horse’s DNA to investigate which variants had been selected throughout the horse’s evolutionary trajectory, identifying some 29 regions in the domestic horse’s genome where variants were favored over time. The Mongolian horse, called Przewalski's horse, is now believed to be the last surviving wild horse, after being isolated from the domestic horse's lineage some 50,000 years ago.

And the new data have contributed to scientists’ understanding of the population booms and busts that have dotted and complicated the horse’s evolutionary trajectory, said Shapiro. “We can now ask how large-scale geological changes affected the diversity of horses,” she said.

Scientists now believe that horses have undergone some three cycles of population peaks and valleys over about 2 million years, with the most recent high point during a glacier-covered period some 25,000 years ago, at the end of the last ice age. Cold periods provided sufficient grasslands for horses, while warm spells created forests that sent the horse population plunging, the scientists said.

But perhaps the most stunning part of the discovery is the very discovery itself: the fact that scientists were able to reach so far backward in the animal kingdom’s evolutionary path and then piece together a rough tale of where the domestic horse came from, and how it did so.

The challenge for scientists now lies in recovering DNA from bones found in warmer and wetter zones, where the DNA is often so mangled that it is beyond the investigative limits of current sequencing technology, Shapiro said. To extract that DNA, if any is left at all, scientists will need currently unavailable technology to put together complete genomes from the tiniest fragments of decomposed DNA.

“It’s not that all of a sudden we’re going to be able to get DNA out of any bone,” said Shapiro. “To do so, we will have to be able to capture the smallest fragments of DNA, and in most cases there won’t be any DNA left in a bone that’s 700,000 years old.”

The field of paleogenetics has been in rapid acceleration in recent years, especially in studies of human bones. The previous oldest genome was sequenced from DNA extracted from the pinky of a 70,000-year-old girl found in Siberia’s Denisova Cave.