300,000-year-old equine genomes reveal deep roots of modern horses

The fossilised remains of horses found
next to hunting spears at Schöningen
. (c) Nicholas Conard

  For the first time, scientists have reconstructed the genomes of an extinct horse species, Equus mosbachensis, that lived around 300,000 years ago in what is now Lower Saxony, Germany. The achievement, announced by researchers from the Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen and the Schöningen Research Centre, represents a breakthrough in the study of horse evolution.

Thanks to exceptionally favourable preservation conditions at the archaeological site of Schöningen, the team was able to extract the oldest DNA ever recovered from an open-air site, pushing back the known survival limit of ancient DNA beyond 240,000 years. Their findings, published in Nature Ecology & Evolution, reveal that the Schöningen horses belong to a genetic lineage that ultimately gave rise to all modern horses.

Modern domestic horses, along with donkeys and zebras, all belong to the genus Equus, the sole surviving branch of a family that once included over 35 genera and hundreds of now-extinct species. Fossils trace the equine family tree back around 55 million years, making it one of the most thoroughly studied lineages in evolutionary history.

“This family is one of the most thoroughly researched animal groups in evolutionary history. Their fossils can be traced back over a period of around 55 million years,” explains Prof. Dr. Cosimo Posth from the Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 

He continues, “For a long time, genetic research focused primarily on changes caused by the domestication of horses in the recent past. But to understand the evolution of the horse, yoflssilu also have to examine their earlier history. Archeological finds, for example, show that horses already played a central role for early human species, particularly as a source of food.”

Arianna Weingarten, doctoral researcher and the study’s first author explains, “Schöningen is famous for its wooden spears which date back around 300,000 years ago and are the oldest known complete hunting weapons in the world.”

“The fossil remains of at least 20 hunted horses were found right next to the spears. Impressive evidence of the close relationship between humans and horses long before they were domesticated,” she added. Our study’s aim was to clarify the position and origin of Equus mosbachensis in the equine family tree and to better understand the genetic relationship to today’s horses.”

Recovering DNA from material this old, and from an open-air site rather than a cave or permafrost, is a major technical leap. Normally, exposure to oxygen, microbes, and temperature fluctuations destroys genetic material over time. But at Schöningen, the horse bones had lain preserved in waterlogged, low-oxygen sediments, creating natural conditions that shielded the DNA for hundreds of millennia.

Using carefully selected samples from the dense inner portions of petrous bones (a part of the skull known for its DNA protection) and new bioinformatic methods, the team reconstructed two largely complete mitochondrial genomes.

“Until now, it was found that DNA could only be preserved for a maximum of around 240,000 years outside caves or permafrost. The Schöningen horses now push back this limit significantly,” says co-author Häusler. She continues, “Normally, DNA decays quickly in open air contexts because temperature changes and microbes destroy the genetic material. But in Schöningen, the bones were preserved in permanently moist, low-oxygen sediments. This unique environment likely acted as natural protection.”

The genetic analysis revealed that the Schöningen horses fall within a lineage ancestral to all modern horses, including today’s domestic breeds. This finding bridges a long-standing gap between early fossil horses and the animals that eventually spread across Eurasia and North America.

Over the course of horse evolution, Equus ancestors repeatedly crossed the Bering Land Bridge between Asia and North America. Two major migration waves are known: the first, around 2.6 million years ago, led to the ancestors of today’s zebras and donkeys; the second, about 900,000 years ago, brought the so-called “caballine” horses — the group from which modern horses ultimately descend.

Many branches of this family tree, including Equus mosbachensis, later went extinct. But the Schöningen DNA shows that their genetic legacy continued.

“With our study, we were able to fill a temporal and geographic gap in the study of horse evolution,” says Posth.  “Our results also show that surprisingly even in seemingly unfavourable environments, such as open-air excavation sites, extremely ancient DNA can still survive and be recovered. This opens up the possibility of extending our method to other species, thereby uncovering the genetic diversity of the distant past.” 

Such studies also remind us how long the human–horse connection has existed. While domestication didn’t occur until around 5,500 years ago, the Schöningen find shows that humans were already interacting closely with horse populations hundreds of thousands of years earlier. 

For more details, see:

Arianna Weingarten, Meret Häusler, Jordi Serangeli, Ivo Verheijen, Ella Reiter, Rita Radzevičiūtė, Alexander Stoessel, Johannes Krause, Maria A. Spyrou, Nicholas J. Conard, Kay Nieselt & Cosimo Posth.

Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen. 

Nat Ecol Evol (2025). 

https://doi.org/10.1038/s41559-025-02859-5