If this were correct, there should be some genetic evidence to back it up. But the only way of finding it would be to examine the DNA of the pre-colonization populations. On this tropical island, ancient DNA, which degrades rapidly in heat and humidity, is hard to come by. But Nieves-Colón has spent the past decade looking for it, and her work backs up the counter-narrative.

There was already some genetic evidence to support the idea of Taíno survival. In 2001, Juan Carlos Martínez-Cruzado of the University of Puerto Rico analyzed modern Puerto Ricans and found substantial amounts of Native American ancestry in their mitochondrial genomes—a subset of DNA that’s inherited from mothers. “The Taíno contribution to the current population is considerable,” he wrote.

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But such ancestry can be hard to interpret because European colonizers moved people around. “In contemporary populations, when indigenous ancestry is found, you can only say that it’s indigenous to the Americas,” says Jada Benn Torres of Vanderbilt University, who studies the genetic ancestry of indigenous Caribbean peoples. “It’s hard to pinpoint it to one particular area.” That’s why the ancient DNA is necessary.

Over the past 10 years, Nieves-Colón has been working to wrest tiny fragments of DNA from ancient remains. From three archaeological sites on the island, she and her colleagues acquired 124 skeletal remains, which all dated between A.D. 500 and 1300. They then searched teeth, bones, and dental plaque for genetic fragments—a difficult task, since DNA breaks down quickly and readily in tropical conditions.

Still, the team managed to completely decipher the mitochondrial genomes from 45 precontact people, and partial nuclear genomes from two of them.

These hard-won sequences confirmed that indigenous Puerto Ricans were strongly connected to Amazonian groups from Venezuela and Colombia, and likely originated from that region. They also contained genetic evidence connecting pre-colonial populations with modern ones.

The team found that the 45 ancient mitochondrial genomes fell into 29 distinctive clusters. Most of these have never been detected in modern-day people across the Caribbean, and may well have disappeared. But three of them did survive: They’re still around in the genomes of today’s Puerto Ricans, and only in Puerto Ricans.

“We wouldn’t have expected that if the ancient narrative [of extinction] was completely true,” says Nieves-Colón. “These people didn’t disappear.”

“This shows that there really are ties to populations that are indigenous to the island, and survived through colonization, and are present in modern peoples,” adds Benn Torres. “This is something that some people have said all along, based on their oral histories and other ways of knowing.”