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Pirates, shipwrecks, mutiny, and murder are hallmarks of fictional swashbuckling adventures. But they were also features of an ill-fated French expedition to colonize part of North America. Now, human bones discovered in the wreckage of the expedition’s flagship are adding a new level of mystery to the story thanks to cutting-edge DNA analysis.

In 1682, French explorer René-Robert Cavelier de La Salle explored and claimed the Mississippi region for France, naming it La Louisiane after King Louis XIV. Two years later, La Salle set sail from France with 400 sailors and colonists aboard four ships, intending to colonize the mouth of the Mississippi River.

But the expedition didn’t go according to plan. Privateers plundered one ship en route and the remaining vessels, including the flagship La Belle, mistakenly landed at Matagorda Bay, some 650 kilometers southwest of the Mississippi in what is now Texas. Then one ship ran aground and another returned to France, leaving only La Belle afloat to support the remaining expedition.

After several failed attempts to locate the Mississippi, La Salle started building a settlement inland called Fort St. Louis. In 1686, however, La Belle was sunk by a storm while anchored in the bay, taking the expedition’s remaining provisions with it. Ultimately, La Salle led a party to seek help, but mutineers murdered him before turning on each other. Later, the few colonists in Fort St. Louis who had survived hunger and disease were killed by the local Karankawa people.

Details of the doomed expedition exist in accounts written by the expedition’s chronicler, Henri Joutel, and five other survivors who reached Canada before sailing back to France. But it was only in 1995 that archaeologists found and recovered La Belle and its contents. Much of the ship had decomposed long before, but the bottom third survived buried in mud which, lacking oxygen, prevented aerobic organisms such as shipworms from consuming the wood and other organic matter.

Among the 1.8 million artifacts was a complete human skeleton which was found on top of a coil of anchor rope. Leg, foot, and hand bones from another person were found in a cargo hold. Those bones were from a man who appeared to be taller and tougher—with bigger, denser bones—than the average 17th-century Frenchman.

In the 1990s, researchers attempted to use DNA analysis to glean more information about these two people, but there was insufficient genetic material for the techniques of the day. That left researchers with little choice but to assume that the bones were those of two French colonists who drowned when the ship sank.

Now, however, state-of-the-art techniques have allowed forensic scientists to extract and analyze the bones’ preserved DNA for the first time, offering a new narrative of the wreck.

“The work detailed is extraordinary, as the researchers used multiple methods and multiple tests per sample to estimate biogeographic affinities, genetic sex, eye and hair color,” says Graciela Cabana, an anthropological geneticist at the University of Tennessee, Knoxville, who wasn’t involved in the study.

As expected, the complete skeleton belonged to someone of Western European descent. His genes were common to people from the part of France where the expedition began. However, the partial skeleton did not fit the existing narrative: the extracted DNA had features common among North American Indigenous peoples.

“This was a huge surprise for us,” says Brad Jones, a research team member from the Texas Historical Commission. “There was no indication in historical accounts that an adult male Native American was present aboard the ship at the time of the wreck.”

Historians know that La Salle did have two North American Indigenous people with him when he returned to France after claiming the Mississippi basin. But only one, Nika, is documented in the ship’s log for the return expedition. Nika is recorded, along with La Salle, as being a victim of the mutiny.

So who was the mystery person whose bones were discovered in the ship’s cargo hold?

Indigenous people often salvaged wrecked colonial vessels, says Jones, so it’s possible that a local Indigenous man, possibly exploring the wreck for cargo, became trapped while diving. “The Spanish expedition that found and described La Belle in 1687 said that the deck was only partially above water, meaning that the holds would have been underwater,” explains Jones.

That explanation, says genetic anthropologist Theodore Schurr at the University of Pennsylvania, seems plausible. Schurr, who was not involved in the project, is amazed the study was even possible. “That any DNA survived being immersed in seawater for many centuries is remarkable.”

“The ability to extract the wealth and richness of DNA data was a wonderful surprise,” Jones says. “We plan to further investigate regional DNA databases, archival records, and genealogies to again try and identify who the people are.”