The origins and historical makeup of modern horses

02.05.2019: The domestication of the horse came rather late in the course of human history, some 5,500 years ago. This is long after dogs, cattle and pigs. However, once humans started riding and milking horses, and once they controlled their reproduction, the whole face of history would no longer be the same. In particular, the horse transformed the way we made war, the way we traveled the world and the way we transported goods until the rise of motor engines in the first half of the 20th century.

In a new article released today in the scientific journal Cell, an international team of 121 scientists led by Prof Ludovic Orlando and under collaboration with Barbara Wallner from the Institute of Animal Breeding and Genetics at Vetmeduni Vienna reconstruct the complex history of domestic horses. The authors not only track transformations in the horse genome from the very early domestication stages at the global geographic scale but also follow the legacy of important equestrian civilizations until the revolution of modern agronomy. This work grouped together a truly multidisciplinary research team, merging together the expertise of archaeologists, geneticists, and evolutionary biologists across 85 institutions around the world. Leveraging methods at the forefront of ancient DNA research, the study gathered genome-scale data of 278 horse specimens spanning the last 42,000 thousand years. 

Antoine Fages, leading author of the study, undertook most of the molecular work. He says: “With the new dataset generated, horses become the animal species with the largest number of ancient genomes characterized after humans. This extensive dataset provides unprecedented information on how the animal looked like in the past but also on how herders exchanged, mixed and selected their horses in the course of human history.”

The scientists discovered that a previously unknown lineage of horses was present in Iberia until at least 4,000 years ago. This lineage no longer exists and contributed only marginally to the genome of modern horses around the world. The same is true for another lineage of horses that roamed the vast territory of Siberia in the Upper Paleolithic and until the third millennium BCE, from the northern end of Yakutia to the Altai mountains range. The work, thus, demonstrates that even though only two main lineages of horses exist today – the domestic horse and the Przewalski’s horse, the available diversity of lineages was considerably larger by the time humans first domesticated the animal.

Pablo Librado, who coordinated the bio-informatic analyses, states: “Iberia has a long-standing tradition of horse breeding and a cave art record featuring many horses. It was, thus, proposed as one possible domestication centre for horses. Our new genome information reveals for the first time that a yet undescribed horse lineage was roaming in the peninsula some four to five thousand years ago. They however disappeared and are not the ancestors of the modern horses in Iberia and more generally around the world.”

Previous work from the Orlando team released last year in the scientific journal Science, demonstrated that Przewalski’s horses represent the descent of a lineage that was first domesticated in Central Asia during the Copper Age, some 5,500 years ago (see 1). Modern domestic horses, however, were found to descend from another genetic lineage that spread across Eurasia during the early Bronze Age, by the end of the third millennium BCE. The new genetic data generated now help track how this new lineage has developed since then and diversified into the hundreds of modern breeds that we know today.

Orlando says: “Humans and horses have interacted a lot over the course of history. It is not just the fate of major historical battles that was settled on horseback, but horses were also paramount to the economic life of big cities such as New York, London and Paris in the 19th century, as they transported extraordinary amounts of people and good every day. Our main goal is to understand how humans and their activities transformed the horse throughout history to fit their purpose, which and how many horse types were developed by different cultures, and how these circled back to and influenced human history.”

The work presented reveals that the 7th-9th century AD was marked by a major transition in Europe. So much that the only horse breeds genetically close to the horses populating the main continent during the Iron Age and Gallo-Roman times can only be found now in some British Isles and in Iceland. These were probably brought to these islands by the Norse people. In mainland Europe, however, another horse group tracing its origins in the Persian Sassanids became so popular that it provided the source of most modern breeds found across the planet. This influence was not limited to Europe but also extended to Central Asia.

In order to identify the factors that underlie the increasing success of this type of horse, the researchers scanned the genomes of Byzantine horses, which descended from this new type. They found signatures of positive selection in no fewer than 11 genes involved in the development of the body plan, included in two clusters of HOX genes. This suggests that the morpho-anatomical traits first acquired in Persian Sassanid horses became increasingly appreciated and spread out following the Persian wars and the Muslim expansion. 

In addition to detecting changes in the horse morpho-anatomy, the researchers could leverage their extensive genome time-series to track the frequency of specific gene variants underpinning key equine traits, such as coat coloration, speed and gait. The authors reveal that a number of gene variants associated with racing performance increased in frequency during the last 1,500 years. The first occurrence of the DMRT3 ambling gene variant was found in a specimen that lived in the late Middle Ages, and increased in frequency in the past centuries. This suggests that locomotor changes in speed and gait types were selected mostly during the last millennium.

But the most striking signal identified by the researchers did not take place during deep historical times. It brought them right into the modern era instead. Orlando adds: “Our most striking finding was that the overall horse genetic diversity was relatively steady for most of the last four millennia. However, it dropped significantly during the last few centuries, at a time coincident with the development of close studs and modern breeding techniques”.

This is perhaps the most important lesson of this work: the modern world we live in can hardly give an idea of the diversity of domestic resources that were available in the past, be it even a few centuries ago. This surges for more multidisciplinary research including history, archaeology and ancient DNA, and aimed at understanding the true evolutionary origins of modern domesticates, animals and plants alike.


The article "Tracking five millennia of horse management with extensive ancient genome time-series" by Ludovic Orlando et al. was published in Cell. 2

Press release in partnership with Université Paul Sabatier (Toulouse) & University of Copenhagen (Denmark) / University of Veterinary Medicine Vienna (Vetmeduni Vienna)




Further information


Scientific Contact

Barbara Wallner

Institute of Animal Breeding and Genetics

University of Veterinary Medicine Vienna (Vetmeduni Vienna)

T +43 1 25077-5625

Email to Barbara Wallner


Released by

Nina Grötschl

Science Communication / Corporate Communications

University of Veterinary Medicine Vienna (Vetmeduni Vienna)

T +43 1 25077-1187

Mail to Nina Grötschl


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Lipizzaner © Spanish Riding School/Lipizzaner Stud Farm Piber
Lipizzaner © Spanish Riding School/Lipizzaner Stud Farm Piber


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