Ancient DNA upends the horse family tree

Horses radically changed human history, revolutionizing how people traveled, farmed, and even made war. Yet every time we think we’ve answered the question of where these animals came from, another study brings us back to square one. Such is the case with an extensive new study of ancient horse DNA, which largely disproves the current theory: that modern horses arose more than 5000 years ago in Kazakhstan. Instead, the new work suggests that modern-day domestic horses come from an as-yet-undiscovered stock. The research also shows that the world’s only remaining wild horses, called Przewalski’s horses, are not truly wild.

“This paper radically changes our thinking about the origin of modern horses,” says Molly McCue, a veterinarian and equine geneticist at the University of Minnesota College of Veterinary Medicine in St. Paul, who was not involved with the work. “It’s an exciting and surprising finding.”

Until now, many researchers had thought that the Botai culture, an ancient group of hunters and herders that relied on horses for food and possibly transport in what today is northern Kazakhstan, first harnessed horses 5500 years ago. Researchers have discovered horse meat fat and milk fat in Botai pottery, suggesting these people ate horses and kept mares in captivity for milking. Markings on horse teeth indicate that the Botai tethered the horses with bits and either rode or herded them, suggesting some degree of domestication. The site is also home to lots of horse bones, and modern genetic evidence has pointed to the region as the source of domestic horses.

With this history in mind, paleogeneticist Ludovic Orlando at CNRS, the French national research agency in Toulouse, and the University of Copenhagen decided to analyze the ancient DNA of these horses. “I expected to catch evolution red-handed, when domestication first started,” Orlando recalls.

He teamed up with longtime Botai zooarchaeologist Alan Outram from the University of Exeter in the United Kingdom, and together they discovered an ancient corral at the site, another sign of domestication. They collected and later sequenced DNA from 20 Botai horse remains; they did the same for a similar number of horses living in various regions over the past 5000 years. They then compared these sequences to scores of already existing sequences, including Przewalski’s horses, and built a family tree showing which breeds were most closely related. The tree “was really quite a shock,” Orlando says.

For one, Przewalski’s horses were in the same part of the tree as the Botai horses. From their relationship, it was clear that these “wild” horses were escaped Botai horses, the team reports today in Science . “We have now found that there are no truly wild horses left” anywhere in the world, Outram says.

Another surprise was that all the other horses were on a separate branch of the tree, suggesting they were not Botai descendents as many have long thought. “We are now back to the intriguing question—who were the ancestors of our modern horses, and who were the peoples that were responsible for their early husbandry?” says Emmeline Hill, an equine scientist at University College Dublin who was not involved with the study. This new work, which hints that other horses may be represented in these ancient genomes, shows “that [horse] domestication could have been a process with many phases, experiments, failures, and successes,” says Ernest Bailey, a geneticist at the University of Kentucky’s Gluck Equine Research Center in Lexington.

Orlando and his colleagues lay out two possible scenarios to explain their family tree. In one, as Botai horsemen expanded to other parts of Europe and Asia, they bred their herds with so many wild species that almost none of the original Botai DNA remained. As a result, those horses don’t seem related to the Botai, even though they actually are.

In the second scenario, the Botai horses didn’t survive, and were replaced by horses domesticated elsewhere, creating at least two centers of horse domestication (as there may have been for dogs, cats, and other animals). Outram suspects that in addition to the Botai horses east of the Ural Mountains, there may have been domesticated horses to the west that won out thanks to migrations, he explains.

One major barrier remains to knowing which scenario is right: a dearth of DNA samples from between 4000 and 5000 years ago. So Orlando and his colleagues are collecting more. But another kind of DNA might help them in their work—ancient human DNA that details migration and population patterns from that time. Indeed, they already have some evidence from unpublished studies. But Outram is keeping quiet about that work. “My mouth is zipped for now.”