Support Provided ByLearn More

Domestic horses have existed for millennia. Modern breeding reduced their genetic diversity in just a few hundred years

A sweeping genomic study expands the equine family tree and pinpoints how humans might have reshaped the equine gene pool.

ByKatherine J. WuNOVA NextNOVA Next

Humans have impacted the horse gene pool more in the last 200 years than in the previous 4,000 years combined. Image Credit: ozgurdonmaz, iStock

Some 5,000 years ago, Homo domesticated Equus—and the histories of human and horse intertwined.

In the millennia since, peoples worldwide have leveraged the speed and power of these once-wild creatures to plow fields, stage hostile takeovers, and carry everything from goods to diseases across contentious borders. Even a good number of modern human languages owe their roots to equines: Before the ancestral tongue of Proto-Indo-European splintered into hundreds of linguistic descendants still spoken today, it was ferried throughout the Eurasian continent on horseback.

Support Provided ByLearn More

Horses have dramatically shaped the human civilization—but researchers still know surprisingly little about how we have shaped them. To this day, even the identity of the wild ancestor of the modern domestic horse remains mysterious.

But now, thanks to a new analysis of ancient DNA, an international team of scientists has constructed the largest collection of horse genomes to date, spanning tens of thousands of years of equine history across Europe and Asia. Their study, published today in the journal Cell, suggests that the genetic diversity of domestic horses has deteriorated only in the last few hundred years, underscoring the toll recent animal husbandry practices have taken on modern breeds.

“This study is brilliant,” says Vagheesh Narasimhan, a mathematical genomicist at Harvard University who was not involved in the study. “Just to see data of this scale being produced for a species other than humans is spectacular.”


Today, only two lineages of horses remain: the modern domestic horse and its small, stocky cousin, the endangered Przewalski's horse. Image Credit: LifeJourneys, iStock

To map out a timeline of equines past, a team of researchers led by Ludovic Orlando, a molecular archaeologist and geneticist at the French National Center for Scientific Research, the University of Toulouse, and the University of Copenhagen, turned to the best source of information it had: ancient DNA, extracted from 250 fossils strewn across sites from Spain to Mongolia.

“DNA is nature’s own written history,” says Samantha Brooks, a horse geneticist at the University of Florida who was not involved in the study. “Horses can’t write or speak their side of their story, but we can read a little bit about the events based on their DNA.”

To deduce how humans may have sculpted the biology of their hoofed companions, the researchers compared ancient genomes from across time and space, and explored how they stacked up against modern breeds. This large-scale approach allowed them to both track the rise and fall of certain traits within the equine gene pool and link those shifts to events throughout human history.

Horses were first bridled by humans sometime between the fourth and third millennium BCE. Through their analysis, the researchers found that breeding priorities have undergone several revolutions in the centuries since. For instance, around 1,000 years ago, strong, sturdy builds came into fashion, ushering in the lasting age of the Arabian horses, which still frequent many a stable today. Traits like speed and the ability to amble—a medium-speed gait that’s considered more comfortable for riders—also became common fixtures in the equine lineage.

Despite these reproductive restrictions, the genomic time series showed that domesticated horses remained relatively genetically diverse for the first 4,000 years or so of their close coexistence with humans. It was only around 200 or 300 years ago that these levels took a sharp downturn.

“This is the moment that genetic diversity started to collapse,” says study author Antoine Fages, a paleogenomicist at the University of Toulouse. “It’s quite amazing that it happened so quickly and so recently.”

The turning point coincides neatly with the latter half of the 18th century, when horse racing began in earnest, paring down the list of “desirable” equine traits, Fages says. As agility and power skyrocketed in importance, breeders began to select only a handful of stallions to sire future generations, keeping large parts of the population from throwing their genetic hats into the ring.

The dip isn’t shocking, though, and it parallels what humans have seen in other domesticated species, like dogs and livestock, Brooks says. The timing, she says, also coincides with cultural and technological evolutions in our history. As humans became less dependent on horses for farming and transportation, the relationship between the two species began to change. Eventually, equines settled into a newer, more specialized niche—recreation—giving breeders less incentive to keep their stables stocked with a diverse set of animals.

Even today, the genetic diversity of horses is in decline, says Molly McCue, a horse geneticist at the University of Minnesota who was not involved in the study. This is “critically important” to keep in mind, she says, because populations with less genetic variation are more vulnerable to accumulating mutations, some of which may lead to disease.

Still, this downward trajectory isn’t a foregone conclusion, Fages says. It’s worth remembering the fact that humans were able to manage horses for thousands of years without negatively impacting their genetics.


The best of today's thoroughbreds can race at speeds up to 55 miles per hour, and have a substantially different genetic makeup than the horses that thundered across the steppes and plains of Eurasia thousands of years ago. Image Credit: Softeis~commonswiki, Wikimedia Commons

Regardless of what awaits horses in the future, though, one key gap in their past has yet to be filled. While Przewalski’s horses—the only other lineage of horse still alive today—are known to hail from Botai horses, the ancestors that once gave rise to our modern domesticates remain anonymous.

Even with so many genomes at their disposal, the researchers were surprised to find themselves no closer to an answer. Their search, however, did rule out two previously unknown candidates: two long-gone lineages that once independently roamed Iberia and Siberia. While both were still thriving during some of the early days of domestication, the DNA in their remains bore little resemblance to that of today’s horses, suggesting that neither lineage directly gave rise to modern breeds before they died out. “These are sort of the horse equivalent of what Neanderthals and Denisovans are to humans,” Orlando says.

Several branches, it seems, are still missing from the equine family tree. But in the meantime, these new lineages add some much-needed complexity to the enigmatic tale of the horse—and, in turn, our own storied past.

“Human cultures and civilizations are what they are today in part because some people had horses, and others did not,” Brooks says. “Knowing more about their history tells us a lot about ourselves.”

To learn more about the rich history of horse domestication, watch “First Horse Warriors,” premiering at 9 p.m. EDT/8 p.m. CDT on Wednesday, May 15 on PBS.

Receive emails about upcoming NOVA programs and related content, as well as featured reporting about current events through a science lens.

Funding for NOVA Next is provided by the Eleanor and Howard Morgan Family Foundation.

National corporate funding for NOVA is provided by Draper. Major funding for NOVA is provided by the David H. Koch Fund for Science, the Corporation for Public Broadcasting, and PBS viewers. Additional funding is provided by the NOVA Science Trust.