Nearly all modern horses derive from two ancient lineages brought to Europe about 700 years ago.

Gerard Lacz/Minden Pictures

Most modern horses came from just two ancient lineages

Horse breeding records are some of the most impressive efforts to chronicle animal lineages in human history, with some stretching back thousands of years. Yet decoding the genetic origins of today’s horses has proved remarkably difficult. Now, a new study finds that nearly all modern horse breeds can be traced to two distinct, ancient Middle Eastern lines that were brought to Europe about 700 years ago. Understanding how these horses were traded, gifted, or stolen could shed light on human history as Eastern and Western civilization commingled and collided.

People first domesticated horses some 6000 years ago in the Eurasian Steppe, near modern-day Ukraine and western Kazakhstan. As we put these animals to work over the next several thousand years, we selectively bred them to have desirable traits like speed, stamina, strength, intelligence, and trainability. People have tracked horse pedigrees for almost as long as we have kept them, but it wasn’t until the 1700s that detailed “studbooks” emerged in Europe to keep tabs on which horses fathered which foals and what characteristics the foals inherited.

The new study’s lead author, Barbara Wallner, an evolutionary biologist at the University of Veterinary Medicine in Vienna, paired these old, yet meticulously kept data with modern DNA sequencing techniques to investigate the origins of today’s horse breeds.

Wallner and colleagues first located dozens of variations in a segment of DNA along the Y chromosomes of 52 living male horses representing 21 modern breeds. As tiny mutations pop up in a stallion’s Y chromosome, they are inherited by all of its future male progeny, allowing geneticists to trace which males came from which paternal line.

That may seem simple, says Ernest Bailey, a geneticist at the University of Kentucky’s Gluck Equine Research Center in Lexington, who wasn’t involved with the study, but it’s actually quite a challenge: Locating functional genes within the Y chromosome is notoriously tricky because of its long, repetitive sequences of nonfunctional DNA. Horses in particular have extremely low genetic diversity along the Y chromosome, making it even more difficult to locate meaningful variations between individuals.

“[The Y chromosome’s] tangle is a genome sequencer’s worst nightmare,” Bailey says. “They have done an excellent and thoughtful job in marshaling materials and using current genomic technology to address the question.”

Following their horses’ pedigrees back hundreds of years, Wallner and her team identified exactly when those mutations showed up, allowing them to calculate how frequently such mutations occur. “In the years before paternity testing was available, we didn’t expect that the pedigree data would be so accurate, so we were pleasantly surprised,” Wallner says.

Based on the mutation rate and assuming an average of 7 years between each generation, Wallner estimates the most recent common ancestor to 18 of the 21 modern breeds lived about 700 years ago. Three Northern European breeds—the Shetland pony, the Norwegian Fjord horse, and the Icelandic horse—appear more distantly related to the others.

Next, the scientists expanded their analysis to include 363 males representing 57 modern breeds (about one-fifth of all recognized modern breeds), giving them a comprehensive chart of which stallion lines founded these breeds. They found two major lineages responsible for almost all modern horses: Arabian horses from the Arabian Peninsula and the now-extinct Turkoman horses from the Eurasian Steppe, the researchers report today in Current Biology. Most horse researchers have suspected that these two lines played a major role in modern horse genetics, but few would have expected their influence to be this vast, Wallner says.

Some of these horses would have arrived in Europe with merchants, others would have been gifts between rulers, and still others might have been captured during warfare, says Wallner, who has two Icelandic horses at her own home in Vienna. Untangling these waves of imported horses could actually help shine a light on human history over the same time period, she notes.

Over hundreds of years, European horse breeders found that stallions from these Arabian and Turkoman lines produced more desirable offspring, repeatedly reinforcing those two lineages in their breeding programs until they were practically ubiquitous. Today, they form the patrilineal backbone of nearly every modern horse breed, including Thoroughbreds, the American Quarter horse, the South German draught horse, and the Appaloosa.

Whereas the Arabian and Turkoman lines have long been known to have contributed to the iconic English Thoroughbred racehorse, other breeds like the Lipizzan and Franches-Montagnes weren’t known to have these influences, Bailey says. “What they found was remarkable.”

But he cautions that not everybody will be convinced by the team’s calculation. “Frankly, the speculation about mutation rates and generation times is controversial but even so, plus or minus a thousand years, it’s [still] interesting.”