An abandoned Caribbean colony unearthed centuries after it had been forgotten and a case of mistaken identity in the archaeological record have conspired to rewrite the history of a barrier island off the Virginia and Maryland coasts.

These seemingly unrelated threads were woven together when Nicolas Delsol, a postdoctoral researcher at the Florida Museum of Natural History, set out to analyze ancient DNA recovered from cow bones found in archaeological sites. Delsol wanted to understand how cattle were domesticated in the Americas, and the genetic information preserved in centuries-old teeth held the answer. But they also held a surprise.

“It was a serendipitous finding,” he said. “I was sequencing mitochondrial DNA from fossil cow teeth for my Ph.D. and realized something was very different with one of the specimens when I analyzed the sequences.”

That’s because the specimen in question, a fragment of an adult molar, wasn’t a cow tooth at all but instead once belonged to a horse.

This tooth is all that remains from one of the first horses introduced to the Americas, and its DNA is helping rewrite the history of one of the best-known horse breeds in the United States: The Chincoteague pony.
*(Jeff Gage)*

The tooth was excavated from one of Spain’s first colonized settlements. Located on the island of Hispaniola, the town of Puerto Real was established in 1507 and served for decades as the last port of call for ships sailing from the Caribbean. But rampant piracy and the rise of illegal trade in the 16th century forced the Spanish to consolidate their power elsewhere on the island, and in 1578, residents were ordered to evacuate Puerto Real. The abandoned town was destroyed the following year by Spanish officials.

The Chincoteague pony, also known as the Assateague horse, is a breed of horse that developed and lives in a feral condition on Assateague Island in the states of Virginia and Maryland in the United States.

Horse fossils and associated artifacts are incredibly rare at Puerto Real and similar sites from the time period, but cow remains are a common find. According to Delsol, this skewed ratio is primarily due to the way Spanish colonialists valued their livestock.

“Horses were reserved for individuals of high status, and owning one was a sign of prestige,” he said. “There are full-page descriptions of horses in the documents that chronicle the arrival of [Hernán] Cortés in Mexico, demonstrating how important they were to the Spanish.”

The specimen’s biggest surprise wasn’t revealed until Delsol compared its DNA with that of modern horses from around the world. Given that the Spanish brought their horses from the Iberian Peninsula in southern Europe, he expected horses still living in that region would be the closest living relatives of the 500-year-old Puerto Real specimen.

Instead, Delsol found its next of kin over 1,000 miles north of Hispaniola, on the island of Assateague off the coast of Maryland and Virginia. Feral horses have roamed freely across the long stretch of barrier island for hundreds of years, but exactly how they got there has remained a mystery.

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