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About halfway along the United States East Coast, where Delaware meets Maryland and Virginia, there’s a tiny island called Assateague. The most notable permanent residents on Assateague are the wild horses. 

“Assateague’s wild horses are well-known, even to people who’ve never been to the island,” according to National Park Service officials.  

Despite their popularity, it’s always been a question of where they came from? Nicolas Delsol, Florida Museum of Natural History researcher, said early Spanish explorers are the likely source of the horse population. 

Delsol was originally investigating a very different question to the one he ended up answering. “I was sequencing chromosome from fossil cow teeth,” he explained. “I realized something was very different with one of the specimens when I analyzed the sequences.” 

The tooth was originally the molar of an adult horse that lived more than 400 years ago in Puerto Real. An early 16th-century town in what is now Haiti, Puerto Real served as last port for ships sailing from the Caribbean. 

Illegal trade forced the Spanish to consolidate elsewhere on the island, and residents were ordered to evacuate in 1578. “The abandoned town was destroyed the following year by Spanish officials,” writer Katie Spalding informed. 

It took four centuries for the site to be rediscovered. But since then, there have been many archeological finds from what was once Puerto Real.  

“Most, though, had nothing to do with horses,” Delsol said. “Of 127,000 specimens identified from Puerto Real thus far, only eight were attributed to horses.”  

Delsol’s find is the oldest chromosome ever obtained from a domesticated horse in the Americas. But when Delsol compared the specimen to the chromosome of modern horses the real surprise came. 

The specimen that presents the closest affinities with the Puerto Real horse belongs to the Chincoteague pony breed. They are the wild horses of Assateague. 

“That’s rather exciting, because it ties nicely with the main original myth of the equine population,” Spalding said.  

“The origin of the Chincoteague ponies is popularized by the mid-20th century children’s novel Misty of Chincoteague,” Spalding noted. “According to this story, Chincoteague ponies are descendants of horses escaping from a Spanish galleon shipwreck during the colonial era. 

“The galleon was sailing from the Caribbean, but a storm caused shipwreck close to Assateague’s neighbor Chincoteague Island.” 

Not everyone has accepted this idea. “The dramatic tale of struggle and survival is popular, but there are no records yet that confirm it,” Spalding noted 

“Common opinion is that they’re descendants of horses brought to Assateague in the 17th century. Mainland owners wanted to avoid fencing laws and taxation of livestock.” National Park Service officials said.  

“Still early colonial literature is often patchy. Just because they don’t mention the horses doesn’t mean they weren’t there,” argued Delsol.  

The new study lends strong evidence to the Spanish story, according to gene sequencing.  

“The Puerto Real horse belongs to the equine maternal branch found in Central Asia and Southern Europe,” Delsol explained. “Most importantly, this type of horse has been found in Spain since the Bronze Age. So, the Puerto Real horse can be seen as a ‘missing link’ between Spanish horses and their Assateague cousins.”  

While researchers acknowledge their conclusion rests on a single gene, they argue that the results are significant for many reasons.  

“The study highlights how ancient chromosomes can help us understand cultural and historical processes,” Delsol said. “That is not only in the remote past but also in understudied episodes of more recent history.”  

“Analysis of the introduction of European domesticates like horses in the Americas is a fascinating yet understudied topic,” Delsol said. “Results support Iberian origins of these animals and indicate Spanish exploration of the mid-Atlantic coast early during the colonial period.”