Genes of ‘extinct’ Caribbean islanders found in living people

Jorge Estevez grew up in the Dominican Republic and New York City hearing stories about his native Caribbean ancestors from his mother and grandmother. But when he told his teachers that he is Taino, an indigenous Caribbean, they said that was impossible. “According to Spanish accounts, we went extinct 30 years after [European] contact,” says Estevez, an expert on Taino cultures at the Smithsonian Institution’s National Museum of the American Indian, who is based in New York City.

Many scientists and historians continue to believe the Taino were wiped out by disease, slavery, and other brutal consequences of European colonization without passing down any genes to people in the Caribbean today. But a new genetic study of a 1000-year-old skeleton from the Bahamas shows that at least one modern Caribbean population is related to the region’s precontact indigenous people, offering direct molecular evidence against the idea of Taino “extinction.”

“These indigenous communities were written out of history,” says Jada Benn Torres, a genetic anthropologist at Vanderbilt University in Nashville who studies the Caribbean’s population history and has worked with native groups on several islands. “They are adamant about their continuous existence, that they’ve always been [on these islands],” she says. “So to see it reflected in the ancient DNA, it’s great.”

The skeletal remains come from a site called Preacher’s Cave on Eleuthera, an island in the Bahamas. Archaeologists began excavating there in the early 2000s to probe the Bahamas’ first European arrivals: Puritans who took refuge in the cave after a shipwreck. As they dug, they also found older artifacts associated with the island’s precontact indigenous culture, including a handful of well-preserved burials.

At the time, Hannes Schroeder, an ancient DNA researcher at the Natural History Museum of Denmark and the University of Copenhagen, was on the lookout for skeletons from the Caribbean he could test for DNA—even though he knew success was a long shot. DNA deteriorates faster in hot, humid environments than it does in cold, dry ones. Hunting for ancient DNA in the Caribbean “was uncharted waters,” he says. He tested teeth from five of the Preacher’s Cave burials, and in the end just one had DNA intact enough to sequence. But by the standards of ancient DNA from the tropics, that tooth was a bonanza.

It belonged to a woman who lived about 1000 years ago, according to radiocarbon dating. Schroeder’s team sequenced each nucleotide base of her genome an average of 12.4 times, providing the most complete genetic picture of a precontact Taino individual to date, they report this week in the Proceedings of the National Academy of Sciences . “It’s a feat of working with tropical samples,” says Maria Nieves-Colón, a geneticist who studies ancient and modern Caribbean populations at the National Laboratory of Genomics for Biodiversity in Irapuato, Mexico, and at Arizona State University in Tempe.

The Taino woman’s DNA shores up archaeological evidence about her ancestors and her culture. When Schroeder’s team compared her genome to those of other Native American groups, they found she was most closely related to speakers of Arawakan languages in northern South America. Early Caribbean ceramics and tools are strikingly similar to ones found in excavations there, archaeologists have long argued.

The two lines of evidence suggest that about 2500 years ago, the woman’s ancestors migrated from the northern coast of South America into the Caribbean, rather than reaching the islands via the Yucatán Peninsula or Florida. It seems that once people arrived, they didn’t stay put. Archaeologists know that ceramics and other goods were traded between islands, indicating frequent trips. Moreover, the Taino woman’s genome doesn’t contain long repetitive sequences characteristic of inbred populations. Her community, therefore, was likely spread out across many islands and not confined to 500-square-kilometer Eleuthera. “It looks like an interconnected network of people exchanging goods, services, and genes,” says William Schaffer, a bioarchaeologist at Phoenix College who helped excavate the remains in Preacher’s Cave.

Genetic studies of modern populations have found that many people from Puerto Rico, Cuba, and several other Caribbean islands carry significant indigenous ancestry, in addition to genes inherited from European and African populations. Still, it’s possible that these living people descend not from the Taino, but rather from other Native Americans who, like many Africans, were forcibly brought to the islands as slaves. But when Schroeder compared the genomes of modern Puerto Ricans to the ancient Taino woman’s genome, he concluded that they descend in part from an indigenous population closely related to hers. “It’s almost like the ancient Taino individual they’re looking at is the cousin of the ancestors of people from Puerto Rico,” Nieves-Colón says. Growing up in Puerto Rico, she, like Estevez, was always told that the Taino died out. “You know what? These people didn’t disappear. In fact, they’re still here. They’re in us.”

Estevez, who founded the cultural organization Higuayagua Taino of the Caribbean, didn’t need an ancient DNA study to tell him who he is. Thanks to his family’s oral history and cultural practices, he says, he has always had a strong connection to his indigenous ancestry. But he hopes the new study will convince skeptics that Taino people are alive and kicking. “It’s another nail in the extinction coffin,” he says.