The ultimate horse

In June 1973, chestnut colt Secretariat ran the Belmont Stakes so fast that no horse has matched him since. In less than two and a half minutes, Secretariat flew along the track, finally pulling away to win by 31 lengths, nearly three quarters of a football field. The other horses were so far behind they weren’t even in the television frame. Fifty years later, billions of dollars have been poured into breeding and training, yet Secretariat’s record still stands.

This is the paradox of the thoroughbred: breeders have spent centuries trying to create a faster horse, but in doing so, they may have bred away the very genetic diversity that would allow the horse to keep improving, or even to remain robust.

The paradox is not confined to the racetrack. The horse began as a terrier-sized, multi-toed forest dweller and, over 55 million years of evolution and a few thousand years of human intervention, became everything from the compact Icelandic pony to the streamlined racehorse. For most of that history, natural selection shaped horses slowly; only recently has human ambition taken over, breeding animals for speed, endurance, and docility. The result is extraordinary diversity in form and performance, but also a dramatic narrowing of genetic diversity.

The first horses

The story begins 55 million years ago, deep in the warm, humid forests that covered what is now North America. You’d be hard pressed to recognize the earliest equid: known as Hyracotherium, it stood only 14 inches tall, closer to a terrier than a modern horse. With four toes on the front feet and three on the back, it was ideally suited to moving gingerly over soft, marshy ground and nibbling fruits and leaves.

When global temperatures rose between 18 and 15 million years ago, the equid family diversified into more than twenty genera, the subdivision above species living in woodlands and savannas. Most of these lineages have long since died out; today, only the genus Equus survives, which includes horses, zebras, asses, and donkeys.

As grasslands spread over millions of years, equids developed into the horses we see today. Few evolutionary stories are as well documented. In the nineteenth century, when paleontologist OC Marsh unearthed a rich collection of fossil horses in the American West, their significance was immediately recognized. Here, laid out almost step by step, was evolution in action: horses transitioning from small, many-toed forest-dwellers into large, single-toed animals that grazed on grass rather than eating fruit and leaves.

That single toe, of which the hoof is the toenail, is the evolutionary innovation key to horses’ success. Life on the plains favored animals able to run efficiently over long distances. Rigid, lightweight hooves help with this: they minimize sideways wobble while storing and releasing energy like a spring, much like the shoes a human sprinter might wear, or even the prosthetic running blades sometimes used by amputees.

Over millions of years, the number of toes fell gradually from several to just one. Between 43 and 33 million years ago, Mesohippus still sported three toes of roughly equal size, with each touching the ground. By the time of Hipparion, about 23 million years ago, the middle toe carried most of the animal’s weight: the outer two toes had shrunk into vestiges, and the middle toe had become dominant. Finally, Pliohippus took a pivotal step toward the modern form, with a single weight-bearing toe ending in a solid hoof. This evolutionary streamlining produced the feet of today’s horses: a single, sturdy keratin hoof perfectly suited for galloping over open ground.

The route to the modern horse passed through several detours. Hyracotherium, the progenitor of the horse family, appears in the fossil record in North America from around 55 million years ago, disappearing again 8 million years later. Around 12 million years ago, Hipparion, which, though three-toed, otherwise resembled modern horses, colonized Eurasia. Hippidion, which had short limbs and distinctively shaped facial bones, roamed the plains and mountains of South America from around 3 million years ago. Then, around 2 million years ago, the most recent common ancestor of present-day asses and zebras crossed the Bering land bridge formerly joining Alaska and northeastern Siberia.

Within the next half a million years, their descendants rapidly expanded across Eurasia and entered Africa at least two separate times. The descendants of the first migration diversified into various zebras, while the second led to modern donkeys and African wild asses.

Although the Americas were home to the earliest proto-horses, horses (including Hippidion and others) later became extinct in the Western Hemisphere around 10,000 years ago, alongside other megafauna like giant sloths, human-sized beavers, and armadillos as big as cars. All horses in the Americas today, including the free-roaming mustangs of the American West, come from European horses introduced after the Spanish conquest – descendants of the branches of the horse family that crossed into Eurasia and avoided extinction.

The first horse tamers

Exactly when, where, and how horses were domesticated remained a mystery until recently, because fossils of wild and early domestic horses look very similar. For decades, archaeologists pointed to the Botai people of northern Kazakhstan, who lived around 5,500 years ago, as the original domesticators. Excavations revealed corrals, possible evidence of harnesses, and even pottery with residues of horse milk, a clear sign that the Botai people were not merely hunting and eating wild horses but had integrated them into many aspects of their lives.

While the Botai horses seemed like the obvious ancestors of modern horses, DNA told a different story: when scientists sequenced the genomes of twenty horses from the Botai site, they were not genetically similar to modern domestic breeds. Instead, Botai horses grouped closely with the Przewalski’s horse (pronounced shuh-VAHL-ski), a species discovered roaming the Mongolian steppe in the late 1870s and long considered the only truly wild horse.

This means that, contrary to the long-held belief that Przewalski’s horses were the last surviving truly wild horses, they are instead the feral relatives of the earliest known domestic horses found at Botai. While the Botai likely did domesticate horses first, their culture died out and their horses returned to the wild.

From steppe to stable

The horses we know and love came from a different source. They emerged more than a thousand years later, about 4,200 years ago, in the Pontic-Caspian steppes of what is now southern Russia, the same region that gave rise to famous horse-riding warriors like the Cossacks, the Golden Horde, and the Huns.

Scientists have worked this out through genetic analysis of ancient horse remains, combined with carbon dating to establish their precise age. A foal inherits half of its DNA from each of its parents. This is passed on with almost incredible accuracy, with around 2.7 billion base pairs (the data units of DNA) being copied correctly, but even so a few dozen errors creep in each time. A scientist can take the DNA of an ancient ancestor from a fossil, compare it with the DNA of a modern descendant, and then estimate how many generations have passed by counting the number of mutations that have accumulated.

In 2021, scientists did just this, sequencing genomes from 273 sets of bones ranging from 50,000 to 200 years old. By looking at the mutation rate and carbon dating the bones to confirm their exact age, they could calculate how quickly generations passed. About 4,200 years ago, the generational clock began to tick twice as fast, halving relative to wild horses, suggesting deliberate breeding.

Although bones can’t tell us how ancient horses behaved, their genomes give us clues. The researchers found that certain genetic variants became unusually common in these steppe horses. Such a pattern signals strong selective pressure: something in the environment consistently favored animals carrying particular versions of genes. 

One region under heavy selection lies near a gene called ZFPM1, thought to play a role in the development of brain cells involved in mood, fear, and aggression. This suggests that early breeders might have been either deliberately or indirectly choosing animals that were more docile, allowing training, handling, and eventually riding. A second region under strong selection sits just upstream of GSDMC, a gene linked in humans to spinal problems such as chronic back pain and narrowing of the spinal canal. The signal of selection at this locus in horses suggests that breeders may have favored genetic variants associated with stronger, more resilient backs. As horseback riding spread, horses that could bear weight without developing spinal pathologies would have been more desirable.

These steppe horses, known to geneticists as DOM2 (that is, domesticated lineage two), spread like wildfire. By 2200 to 2000 BC, the DOM2 genetic profile spread beyond its region of origin to Anatolia, the lower Danube region, and Bohemia.

Archaeological evidence suggests that as DOM2 expanded, the populations of other wild horses gradually dwindled. By around 1500–1000 BC, almost all had been either absorbed or replaced. The tarpan horse, which roamed Eastern Europe, became extinct in 1909. By 1969, Przewalski’s horse was declared extinct in the wild. All living Przewalski’s horses stem from just 15 individuals captured around the year 1900. Only in 1992 did the descendants, numbering about 2,000, begin to be reintroduced on the Eurasian steppes. 

The many so-called wild horse populations found around the world, including mustangs, Sable Island ponies, and Australian brumbies, all descend from modern domestic horses that became feral again within the past few centuries.

Horses for courses

Over time, humans developed distinct horse breeds with a wide range of phenotypes, from the tiny Argentinian Falabella, barely reaching a meter tall at the shoulder, to the towering French Percheron, capable of hauling tons; from horses with the standard gaits (walk, trot, canter, and gallop) to horses able to perform alternative gaits, like ambling, with no bounce, making them more comfortable to ride. The Icelandic horse's tölt is so smooth that a rider can carry a full glass of beer without spilling a drop.

This diversity is the product of millennia of human intervention, selection, and preference, which left distinct traces in the horse’s genome. Compared with many other species, horses have a lot of diversity in the mitochondrial genome, inherited from the mother, but extremely limited variation within the Y chromosome, passed down from father to son. This contrast suggests a pattern in domestication: many local mares (female horses) were bred with a fairly narrow pool of stallions (males), concentrating paternal lineages while preserving variety in the maternal line.

Ancient DNA has given us a window beyond fossils, allowing us to track how phenotypes changed in ways that don’t show up in the fossil record. After humans, horses are one of the species ancient genomics has studied the most. In fact, the very first successful recovery and analysis of ancient DNA was from 150-year-old tissue from the extinct quagga, a close relative of the zebra, in 1984 – a year before the same was achieved with ancient human DNA. One of the oldest genomes ever successfully recovered and decoded comes from a horse bone preserved in the Yukon permafrost for over half a million years.

Coat color offers another window into early horse breeding. In living horses, the genes behind colors and patterns, like leopard spotting, tobiano patches (like the coloring of a cow), and cream dilutions (that lighten the color of a horse’s coat), are well understood. Genetic variants for dun (gray-gold, or tan), black, and leopard spotting appear in wild horses from the Upper Paleolithic, long before domestication began.

In the early Bronze Age, leopard-spotted horses were abundant at Kirklareli-Kanlıgeçit in present-day Turkey. But leopard spotting comes at a cost: horses with two copies of the gene coding for it have night blindness (the inability to see in low light). Its prevalence in certain ancient populations suggests breeders made deliberate choices, where aesthetic or symbolic value outweighed the trait’s practical drawbacks, to favor certain traits unlikely to persist in the wild. Tastes shifted with time: leopard-spotted horses lost their appeal after the early Bronze Age but gained favor in some regions during the Iron Age. And while spotted coats were popular in antiquity, solid chestnut horses prevailed in medieval Western Europe.

In the Middle Ages, horses were inseparable from power and status. Chivalry itself shares an etymological root with the Old French chevalier, literally ‘horseman’. Breeding and maintaining horses became a major industry of nobility and royalty. But they didn’t think in terms of fixed breeds the way we do today. Medieval writers grouped horses by function: the destrier trained for combat, the courser valued for speed, and the palfrey prized for a comfortable ride. Archaeological evidence backs this up. A large study of horse remains from thirteenth- and fourteenth-century London shows a range of sizes and builds, not the uniformity that we would expect from tightly restricted breeding.

Contrary to the modern idea of the medieval warhorse as a massive, towering beast, measurements from excavated horse bones across England show that most stood around 13 to 14.2 hands high, roughly the size of a sturdy modern pony. Even horses associated with elite or military contexts rarely approached the heights of today’s heavy draught breeds. What medieval riders valued instead were animals that were compact (meaning cheap to feed), strong, and agile enough to handle long distances, uneven terrain, and the demands of warfare.

The need for speed

By the seventeenth century, horses had been serving human purposes for thousands of years, plowing fields, carrying soldiers, and pulling carts. But in early-modern England, one goal came to dominate: speed. In the 1660s, King Charles II, a fervent horse racing fan, set up a horse breeding and racing center at Newmarket, near London. While horse racing had been popular in previous centuries, Charles II and other racing enthusiasts were the first to methodically breed horses at scale to improve their race performance.

Breeders discovered that horses from Arabia, Central Asia, and North Africa were often faster: they were lighter, had a greater drive to run, and were better able to dissipate heat, allowing them to sustain high speeds without overheating. From three exceptional horses imported to England, Byerley Turk (imported in the 1680s), Darley Arabian (1704), and Godolphin Arabian (1729), breeders created the ‘thoroughbred’, a new type of horse designed for speed. Today, 95 percent of all living thoroughbreds are thought to descend from just one of these stallions, Darley Arabian, through his phenomenally successful great-great-grandson, Eclipse.

Horse breeding used to be guesswork: breeders paired fast stallions with fast mares and hoped for the best. But in 1791, the General Stud Book started recording every thoroughbred’s ancestry, turning pedigree into data. Breeders could now track bloodlines, deliberately plan matings, and see which combinations actually worked. Thoroughbreds today are defined as horses whose ancestry can be traced entirely to horses listed in the General Stud Book.

Harder, better, faster, stronger

Racing and breeding evolved side by side. Races in the seventeenth and eighteenth centuries involved multiple heats over distances of two to four miles, favoring horses with stamina. Horses didn’t race until they were five or six years old. But by the late eighteenth century, new races like the Derby and the St Leger reset the terms of competition. Horses now raced at three years old, over shorter distances of one to two miles. 

This new format meant an increased premium on speed and precocity, and it has persisted, particularly in the United States and Australia. In Britain and Ireland, the tradition of long-distance races held on in parallel, leading to distinct types: horses that specialize in explosive speed at a young age, classic middle-distance horses, and horses bred for the stamina needed to excel in longer races.

After the creation of the thoroughbred and the Stud Book, Anglo-American breeders hit what appears to be an upper limit for speed surprisingly quickly. From the middle of the nineteenth century, when timing and record keeping became good enough to make reliable comparisons, race times improved steadily for about half a century. But although there was consistent improvement, it was small: times only fell by 1 to 2 percent, or 2 to 4 seconds over a 1.5-mile race. Race times for prominent races have not significantly fallen since around 1910. Secretariat’s 1973 Belmont time eclipsed the previous record by a stunning 2.6 seconds. However, the best time since then (Easy Goer in 1989 at 2 minutes 26 seconds) was a full 2 seconds slower than Secretariat’s.

Outside the elite, there has been continued improvement: one study found that between 1997 and 2012, accounting for differences such as ground softness and the number of runners, the average British thoroughbred increased its speed by 0.011 yards per second per year. So while we have likely reached the ceiling for how fast an exceptional horse can run, the median horse is beginning to close in on that limit, too.

The genes for speed

Until 2007, the Stud Book was the cutting edge of horse breeding technology. That changed when scientists sequenced a horse genome for the first time, that of a thoroughbred mare named Twilight. This allowed researchers to study the genetic basis of variation between individual horses far more systematically.

Another step forward in understanding thoroughbred genetics came with a paper published in 2010 that investigated the gene in horses that codes for myostatin, a protein that regulates muscle development. Mice, cattle, dogs, and even humans with mutations in this gene grow outlandishly large muscles because the gene normally acts as a brake on muscle development; with that brake damaged, muscles continue to grow unchecked.

The gene coding for myostatin in horses has around 1,100 base pairs. Looking at the exact sequence of this gene, called MSTN, in 148 thoroughbreds revealed that horses could have three different versions of the gene, differing by just one of those base pairs (either a letter ‘C’ or a ‘T’), and that each version was associated with success in different race formats. Horses with two copies of the ‘C’ version tend to be the best sprinters, those with two ‘T’s tend to be high-stamina long-distance runners, and those with one of each tend to fall between the two running profiles.

Later research found that variations in MSTN correspond with different muscle physiology. Horses with the ‘C’ version have a higher proportion of fast-twitch muscle fibers, which enable the explosive bursts of speed required for short-distance sprint racing, while those with the ‘T’ version have a higher proportion of slow-twitch fibers, which allow sustained effort. 

Analyzing the DNA of modern horses and museum specimens then showed that the foundation stallions in the Stud Book all had two copies of the ‘T’ variant, and that the ‘C’ mutation probably entered through local British mares. This new variant entered thoroughbred genomes during the late eighteenth and nineteenth centuries, as English races like the Derby and St Leger got shorter. But the genetic trend is less pronounced in Britain than the United States, where races are rarely longer than 2,000 meters, and especially than in Australia, which favors 1,000 to 1,400-meter lengths. Commercial tests for this gene are now widely used by breeders and trainers.

The price of success

Horses’ genetic diversity remained large for thousands of years, before collapsing after the introduction of modern breeding. In nature, diversity is maintained by competing selection pressures that balance one trait against another. A wild horse does not just need to be fast. Its bones need to last. It needs to be resistant to disease. Even a domesticated working horse would, before intensive breeding began, face natural constraints on its traits.

In modern thoroughbred breeding, celebrity stallions with the best race records are in high demand. Their owners charge hundreds of thousands of dollars in stud fees, and they can sire perhaps a hundred foals per year. This means that the genes of particular males can quickly sweep to dominance in a population in a way that would be very unusual in nature.

Along with this loss of diversity, modern horses have accumulated harmful mutations as a result of breeding within a small population. In horses as in humans, repeated inbreeding concentrates harmful traits as parents who are related to each other are more likely to share the same mutations, resulting in offspring with two copies of the mutated gene, rather than one mutated copy and one normal copy, which could mask the mutation’s effects.

A genetic analysis of all Australian thoroughbreds, more than 135,000 horses, showed that inbreeding correlates with slower, shorter, and less lucrative careers. Amazingly, ten heavily crossed eighteenth-century ancestors account for over 80 percent of inbreeding in Australian thoroughbreds. Breeders are not blind to these risks. The American Quarter Horse Association, for example, requires breeding stallions to be tested for several genetic diseases.

As genetics has played such a large role in breeding horses, it is small wonder that horse breeders are moving with the frontiers of science. The world’s first cloned horse, called Prometea, was born in 2003. Horse cloning is now big business, despite an American Jockey Club ban, as other equine sports, including show jumping and polo, allow clones.

In 2024, the Argentinian company Kheiron announced the production of the first CRISPR-edited horses: Polo Pureza, an award-winning mare, was the foundation for five gene-edited clones with increased explosive speed. According to reports, the company modified the MSTN gene, so that the animals would develop more muscle fibers and potentially run faster as a result. Even so, the prospects for exceeding current records through gene editing are slim. Today’s racehorses are already tightly optimized for speed, balancing strength against the cost of carrying additional muscle mass. Adding more muscle is relatively low-hanging fruit, and if this were the key to unlocking greater speed, selective breeding would likely already have brought it about.

The thoroughbred paradox

At the Belmont Stakes in 1973, Secretariat ran in a category of his own. His extraordinary performance seems to have been the result of many unlikely factors aligning. After he died, Secretariat’s heart was reportedly measured at almost 10 kilograms – twice as much as normal. This appears to have been a physiological fluke, however, as it isn’t a trait reliably passed down to offspring. Combined with his unusual stamina, exceptionally powerful legs that allowed him to cover 25 feet per stride, favorable race conditions, and a skilled jockey, this produced a race time that has still never been matched half a century later, despite advances in breeding, training, nutrition, and veterinary care.

Secretariat offers a glimpse of the upper limits of biology. But as racehorses have pushed against that limit to become faster and more powerful, their population has become more fragile as the gene pool has narrowed. Our 4,000-year pursuit of the ultimate horse may not have much further to run.