Giant Genetic Study Detects ‘Ghost’ Species in Today’s Horses

Horses have only been bred for speed in the last few centuries, says the study – and the passion for breeding thoroughbreds is diminishing resistance to disease

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Horses: Today's Arabian-type horse arose from an extinct species that we never knew - and two others that left ghostly signals in their DNA. Credit: Andy Barron,AP
Ruth Schuster
Ruth Schuster
Ruth Schuster
Ruth Schuster

Only two horse species exist today: the one you know and Przewalski’s wild horse. A giant study shows that the horse you know originated mainly from an extinct species that mixed eons ago with two other extinct species that left faint “ghost” signals in the horse’s genome.

This is the conclusion of a huge team in the journal Cell based on horse remains going back more than 42,000 years. Scientists had previously figured out that the main ancestor of today’s horses was a species we did not know; now the massive study has found two more hitherto unknown contributors.

Still, the origin of the horse you bet on at the track remains a mystery even after the effort by 121 scientists at 85 institutions around the world. What science can say, after the biggest genetic study not on humans, is that the horses common today in Eurasia were hugely influenced genetically by Sassanid Persian horses over the last thousand years.

The stumpy ponies once common in Northern Europe and Britain survive only in remote pockets such as Iceland and the Shetland Islands. The spread of the leggy Persian, or Arabian, horse apparently happened with the expansion of Islam.

Man discovered he can go farther and faster when utilizing horse power.Credit: \ ILYA NAYMUSHIN/ REUTERS

One of the “ghost” species found hiding in horse DNA lived in Iberia, in the West, and the other in Siberia, in the East. In other words, these horse species interbred with the unknown ancestor of today’s horses, then died out.

The Iberian and Siberian ghosts are a “sort of horse equivalent of what Neanderthals are to modern humans,” says Ludovic Orlando, a research director with France’s CNRS research institute and the University of Toulouse, and a professor of molecular archaeology at the University of Copenhagen. Meaning: In prehistory there was interbreeding between these extinct species and the ancestors of today’s horses, whoever that was.

Horse feathers

Man takes selfie with his brother's horse who won the Arabian horse festival race in Karhuk, Hassakeh, Syria.Credit: Baderkhan Ahmad,AP

In fact, thanks to several studies in recent years, it turns out that almost everything we had thought about horse history was horse feathers.

For one thing, today’s horses did not all arise from “the last wild horse,” Przewalski’s, a rather short-legged, low-bellied beast also known as the Mongolian wild horse. Genetic analysis concluded that far from being actually wild, Przewalski’s descended from the first horse to be domesticated, apparently by a people known as the Botai who lived in central Asia 5,500 years ago.

Second, the Botai did not domesticate the Przewalski’s, they tamed a species predating the Przewalski’s, and their tame horse went extinct too.

So none of today’s horses descend from either the Przewalski’s or the horse the Botai tamed. We don’t know where today’s horses came from.

Przewalski's horse, which isn't wild after all but a descendant of an extinct horse domesticated by the Botai people 5,500 years agoCredit: AP

Whoever they came from, people have been exploiting horses since discovering the pleasures of riding on one instead of hoofing it. “Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages,” writes the team, and that’s a drop in the ocean of what the equine does for us, even though it was quite the late addition to the human household.

Dogs have apparently been with us for over 14,000 years, cats (albeit never quite domesticated) over 9,500 years. The goat and sheep were domesticated (in Mesopotamia) around 11,000 years ago, but it would take thousands more years before the horse joined the household.

French bulldog (illustration)Credit: Tina Fineberg,AP

Cats may consider themselves lucky never to have been fully domesticated, judging by the results of taming other creatures, from dogs to roses. Canine “purebreds” are largely inbred and can suffer from genetic disorders that make them sick and shorten their lives; in extreme cases, such as the bulldog, they can’t even procreate naturally.

Meanwhile, the sheep wasn’t always a docile moron. And all roses used to have a scent and wheat seeds used to be disseminated by the wind, not farmers.

The goat is a more complicated case; the ancestor bezoar ibex seems to have spawned four base populations, but scientists are still arguing over whether the goat was domesticated more than once: in Iran, Turkey and the Levant, or whether the bezoar was very, very genetically diverse.

But the horse was a whole other kettle of fish, because once people had, belatedly, tamed it, people but could ride it as well as milk it and eat it. It seems that people have suffered from wanderlust even before they evolved – early hominin remains have been found all over Eurasia.

Taming horses meant people (and their diseases) could wander a lot faster. They could even use the beasts to fight one another, whether by looming over the enemy on horseback or having the animals pull war chariots.

Pretty in Persia

Apropos war chariots, the chunky ponies of Northern Europe survive only in isolated far-flung pockets such as Iceland and the Shetlands – and were evidently imported to these islands by Viking invaders.

Horses were only bred for speed in the last 1,000 years or soCredit: Brian Spurlock-USA TODAY Sports/File Photo

In the rest of Europe and Asia, the horses are predominantly Persian-type, having apparently been disseminated during the Islamic conquests over a millennium ago, when the species clearly began to be selected for sheer speed, the study proposes. Today’s “thoroughbreds” – a euphemism for inbred – can race at over 40 miles per hour, a pace probably unsustainable in the past.

But horses can’t outpace everything. They’re in danger, and not only from climate change. Modern breeding has significantly diminished their genetic diversity, and fast, the researchers found. This has happened in just the last few hundred years. It seems that the breeding stock for horses has become severely diminished.

In the Persian horses, the team found evidence of selection in genes associated with body shape. “What we picture as a horse today and what we picture as a horse from a thousand years ago or two thousand years ago was likely actually very different,” Orlando says.“Some of those traits that we’re most familiar with are only a modern invention, and in the last few hundred years we have actually impacted the horse genome a lot more than in the previous 4,000 years of domestication.”

This is not a good thing. All the modern breeds in this vast collaboration checked showed a significant decrease in genetic variation relative to just 200 years ago. There has been an increase in so-called mutational loads, say the scientists: a hallmark of inbreeding.

Their conclusion is that in just a couple of hundred years, breeding for “desirable traits” such as speed in horses actually reduced change. Y-chromosome diversity is extremely limited in modern horses compared with the past, indicating that especially from the Middle Ages on, only specific stallions were allowed to procreate.

Horses: We don't know where they came from.Credit: Rick Bowmer,AP

The legacy of this history remains with us: The majority of modern breeds cluster genetically with the Sassanid Persian horses.

The upshot of this overly-selective breeding is that the common horse could face a similar danger to the cheetah, and to the banana.

True, the horse isn’t a wildcat poached to the point of near-extinction or a self-cloning plant that can’t resist diseases wreaking havoc on banana plantations worldwide. But a similar lack of genetic diversity could spell its doom; for instance, through a disease that none of the surviving variants have the capacity to fight.



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