At some point in the past two millennia — peanuts on an evolutionary time scale — humans transformed their horses into equine speed demons. Selective breeding had a price, though, beyond $30,000 vials of pedigreed racehorse sperm. Unhelpful mutations plagued the animals. The current population of domesticated horses is about 55 million, but at some point in their history, their genetic diversity crashed. The Y chromosomes of all the world's stallions are now quite similar, suggesting that only a relatively few males were the ancestors of today's horses.

Humans have not always bred so selectively, according to a study published in the journal Science on Thursday. Horse domestication began about 5,500 years ago. Ancient equestrians “were not interested in superfast animals. They were more interested in diversity and potential,” said Ludovic Orlando, a professor of molecular archaeology at the University of Copenhagen's Natural History Museum of Denmark and an author of the new study.

Orlando and his colleagues sequenced the genomes of 14 ancient horses: one 4,100-year-old mare and 13 stallions, which dated back 2,700 to 2,300 years. The stallions, ridden by the nomadic Scythians, had genes linked to an array of coat colors and traits associated with endurance or sprinting, as well as many diverse Y chromosomes.

Orlando and his colleagues chose to sequence Scythian stallions for several reasons: The animals lived about halfway through the 5,500-year timeline of horse domestication. The horses also offered a ready supply of genetic material. To honor their royalty, Scythians sacrificed animals from many different tribes and buried the remains in underground chambers in what is now Kazakhstan.

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Kazakhstan's permafrost kept ancient DNA fresh. “It’s like we had a natural freezer waiting for us for 2,300 years,” Orlando said. In places, the scientists dug up not just tooth and bone material but hairs. Some horse skulls still wore the decorations their owners had created millennia ago.

Scythians had a reputation as bloodthirsty warriors — literally. The Greek historian Herodotus wrote that the “Scythian soldier drinks the blood of the first man he overthrows in battle” out of a cup made from a human skull. But skull mugs or no, they were excellent horsemen. “They mastered the horse like no others before them,” Orlando said.

(The Scythians probably also drank horse milk. DNA analysis of the frozen stallions suggested that the Scythians bred some horses for enlarged mammary glands.)

Some, but not all, of their horses carried genetic variants seen in today's sprinting horses. A single gene mutation can dictate a horse's gait — how motor neurons connect to muscle tissues allows an animal to amble. Ambling gaits have a four-step pattern, bringing the legs of the same side together for a smoother ride. The scientists could test whether Scythians cared about breeding for a more comfortable ride: The nomads did not.

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Among the sacrificed were horses with bay, spotted, chestnut, black and cream-colored coats. The variety of coat colors — still found in Kazakhstan today — supported what is known as the neural crest hypothesis, Orlando said.

As a rule, domesticated mammals develop coats of varied colors and floppy ears; this is sometimes called the “domestication syndrome.” In Russia, for instance, a decades-long experiment to tame the fox has produced animals with droopy ears and shorter, curlier tails. Biologists proposed that a pool of cells called the neural crest, which pops up in animal embryos and turns into tissues like skin and ear cartilage, might explain why different species grow similar traits.

DNA from the Scythian horses was some of the “first empirical evidence that supports the neural crest hypothesis,” Orlando sad.

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What's more, for the first 3,000 years of domestication, horse breeders were able to keep unhelpful mutations at bay. Modern horses have several “nasty mutations,” Orlando said, that make some animals prone to seizures or wounds that won't heal, for instance.

But something happened to horses on the way from the Kazakh steppe to Churchill Downs: Somehow, breeders swept away horse genetic diversity. Orlando is trying to figure out why. He offered three likely scenarios for when hyperselective breeding eliminated diversity from the gene pool in the quest for specialized traits. Perhaps it was the fault of the Roman Empire and its horses. Or perhaps horse breeders in the Middle Ages were highly selective. Or maybe the rise of the modern racehorse in 18th-century Britain did the horse genome in.

Orlando is more interested in history than in rewinding the harmful effects of domestication, which he said would be a fruitless effort. “We cannot give lessons to modern breeders,” Orlando said. “It’s not like they have a different population to choose from.”

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And yet the history of horses is no idle thing. It is our history, Orlando argues. “I believe horses are the most important domesticated animal in history,” he said. “Without horses, the history of warfare would be different, and therefore the history of humanity.”

He cited cavalry, chariots and accomplished equestrians like Alexander the Great who became ancient leaders. Chickens kept us fed, and dogs kept us company. Horses, though, allowed humans to travel faster and farther, not only spreading our descendants to other lands, but our ideas and cultures, too.