It would be difficult to overstate how instrumental the horse has been in shaping the world around us today. That’s easy to forget now that most of us get around by other means, but horses were central to human mobility for millennia, and much of our history of warfare and economy depended on that mobility.

But when did horse and human history become intertwined? For a long time, archaeological and genetic evidence has pointed to the steppes of central Asia as the likely site of horse domestication. Remains from the Botai culture in present-day Kazakhstan point to evidence of horse milking and possible riding more than 5,000 years ago.

But a paper in this week’s Science analyzed ancient horse genomes from the region and presents a startling finding: modern horses appear not to be descended from the Botai horses. This means that we still don’t know very much about the history of our crucial relationship got started.

An unexpected family tree

Today, there are horses that roam wild in central Asia: Przewalski’s horse is an endangered population that was pulled back from the brink of extinction by a captive breeding program and reintroduced to its natural habitat. But they aren’t the ancestors of modern domesticated horses; research from 2011 suggested that modern horses share an ancestor with Przewalski’s horse but aren’t its direct descendants.

Charleen Gaunitz, a researcher at the Natural History Museum of Denmark, led a team of 47 researchers trying to uncover the genetic relationships between modern domesticated horses, ancient domesticated horses, and Przewalski’s horse. To do this, Gaunitz and her team sequenced the genomes of 42 ancient horses across Eurasia. Then they compared the data to published genomes from 18 ancient horses and 28 modern horses.

The results were surprising. They found that modern horses formed their own genetic cluster, separate from the ancient domesticated horses at Botai. And those Botai horses appear to be the ancestors of another ancient breed of domesticated horse, called the Borly4—which in turn appear to be the ancestor of Przewalski’s horse.

Przewalski’s horse, write the researchers, “are considered the last true remaining wild horses, that have never been domesticated. Our results reveal that they represent instead the feral descendants of horses first herded at Botai.” This would make Przewalski’s horse similar to the free-roaming, feral American mustang.

This is an “exciting new finding,” said Oliver Ryder, who researches Przewalski’s horse genomes and wasn’t involved in this paper. But Vera Warmuth, a geneticist who researches horse domestication and also wasn’t involved in this study, says that this conclusion isn’t as strong as it might be. “Only one of the seven [Przewalski’s] horses they analyzed shows evidence of direct Borly ancestry,” she pointed out to Ars. And the family tree the researchers present is also compatible with a different ancestry scenario, she suggested: one where Przewalski’s horses’ ancestors were wild horses that were part of the same population that people domesticated to create Botai horses.

The supplementary data the authors published “point to a more complex situation with a large, diverse wild population [and] lots of gene flow between managed herds and their wild ancestors,” she noted, adding that it would be worth seeing whether alternative ancestry scenarios would also be a good fit for the genomic data.

So horse domestication happened elsewhere?

Maybe. Modern horses did indeed cluster as a separate group, but they are still a tiny bit related to the Botai horses. This points to two possible scenarios. In the first, horses were domesticated at Botai, but were interbred so much with other wild horses that “the Botai ancestry was almost completely replaced,” write Gaunitz and her colleagues. In the second scenario, horses were domesticated elsewhere and, at some point, came into contact with Botai horses and incorporated “minute amounts of Botai ancestry.”

The finding that the Botai horses contributed so little to the modern sequenced horse genomes is “very interesting and exciting,” said Warmuth. “If the Botai horses contributed only a little genetic material to our domestic horses, what lineage(s) did?”

Ryder pointed to the need for future research to draw on both genetics and archaeology to shape our understanding of modern domestic horses, their relatives, and their ancestors—a relationship that is still proving tricky to pin down.

Science, 2018. DOI: 10.1126/science.aao3297 (About DOIs).