The Caribbean was one of the last parts of the Americas to be settled by humans, although scientists don’t agree on when the first settlers arrived or where they came from. Some argue that people probably arrived from the Amazon Basin, where today’s Arawakan languages developed, while others suggest that the first people to settle the islands came from even farther west, in the Colombian Andes.

“The differences in opinion illustrate the difficulty of tracing population movements based on a patchy archaeological record,” wrote archaeologist Hannes Schroeder of the University of Copenhagen, Denmark, and his colleagues. Schroeder’s research team has a new study on the genetics of the long-lost Taino people, which gives some clear indications of their origin and where they went after European colonization.

Complex social networks linked the islands

The Bahamas weren’t settled until 1,500 years ago. The people who settled there are known as the Lucayan Taino, and they and the other Taino communities of the Caribbean were the natives who met the first Spanish colonists in 1492. At the time, the Taino were thriving; Spanish priest Bartolomé de las Casas estimated that about 600,000 people each lived on Jamaica and Puerto Rico, with as many as a million on Hispaniola. That didn’t last long; by the mid-16th century, smallpox and slavery had driven the Taino to the brink of extinction.

Their presence still lingers throughout the islands, in the form of words that run through the heart of Caribbean life, like hurricane and canoe. There are also archaeological remains such as rock art that tell us something of the Taino's spiritual life beyond what comes down to us from the reports of Spanish priests. But the bustling communities and widely flung trade networks that pre-dated European colonization are no more.

It has long been suspected, however, that the Taino didn't die out altogether. Spanish colonists reportedly married Taino wives, and other records say that Taino and escaped African slaves also intermarried and formed communities. Some people in the Dominican Republic, Puerto Rico, and even the mainland US still proudly claim Taino heritage and practice traditions handed down from pre-Colombian times, from cooking to crafting. There has been a larger effort to revive Taino culture and identity in the last century and a half or so, but it has never been clear how directly genetically related modern Caribbean residents are to their vanished ancestors.

But the story, it turns out, is more complicated than simple extinction, and new DNA evidence helps fill in some of the gaps. Archaeologists found three relatively complete skeletons in Preacher’s Cave, a site on the northern end of Eleuthera Island in the Bahamas. Alongside the skeletons, they also found a single tooth, which didn’t clearly belong with any of the three skeletons. Schroeder and his colleagues got permission to sequence DNA from the tooth, which radiocarbon dating showed was more than 1,000 years old. That’s at least 500 years before European contact, meaning the tooth must have belonged to a Lucayan Taino woman who lived on the island between 776 and 992 CE.

The woman was closely related to Arawakan-speaking tribes from the Amazon and Orinoco Basins of South America, such as today’s Palikur people, who live in Brazil and French Guiana. That supports the idea that the Taino’s ancestors came to the islands from a starting point in the Amazon Basin.

Her genome didn’t bear the traces of a recent genetic bottleneck event, which happens when population sizes shrink dramatically and widespread inbreeding leaves a last genetic record—something that could easily happen during a series of migrations among islands. That means the Lucayan Taino had a relatively large population before the Europeans showed up. Schroeder and his colleagues estimate that about 1,600 people on the island were part of the “effective population,” or the pool of people who are actually available to reproduce.

That’s a lot of people for a 320-square-mile island, especially when you consider that a so-called effective population is usually only around a third of the actual population, which includes children, elderly people, and others who aren’t having children.

“It is difficult to imagine how this community was able to sustain such a relatively large effective size without outside contact,” wrote Schroeder and his colleagues. Most researchers think ancient Caribbean societies were very mobile and interconnected, with regional networks of trade and cultural interaction among the islands. The fact that this Taino woman came from such a large population adds support to that picture of the islands’ history.

“We don’t know how far the ‘mating network’ extended. But what we are suggesting is that it’s unlikely to have been restricted to Eleuthera, given the relatively large effective population size,” Schroeder told Ars Technica. And the Europeans’ arrival, 500 years after the unnamed Taino woman’s death, would have disrupted those island-hopping social networks. It’s another possible contribution to the Taino population crash.

Not vanished after all

The recent work also shows that the vanished people of the Caribbean didn’t actually disappear without a trace. Modern inhabitants of the Caribbean islands mostly have a mixture of African and European ancestry, but some have a little indigenous DNA as well. That’s not entirely surprising; Spanish colonists reportedly married Taino wives, and other records say that Taino and escaped African slaves also intermarried and formed communities. Some people have made an effort to revive Taino culture and identity in the last century and a half or so, but it has never been clear how genetically related modern Caribbean residents are to the presumably vanished tribes.

The proportion of indigenous DNA in modern Caribbean genomes varies; in Haiti, the Dominican Republic, and Cuba, Schroeder and his colleagues couldn’t isolate enough Native American sequences in people’s genomes to compare to their Taino sample. But in Puerto Rico, most people have about 10 to 15 percent Native American DNA.

That’s not much, but it’s significant. To put that percentage in context, if you’re of non-African descent, about two to four percent of your genome is actually Neanderthal; about eight percent of the average person’s genome actually came from viruses. So 10-15 percent is nothing to sneeze at. Scientists were aware of its presence but haven’t been sure if most of that DNA was Taino or if it came from Native American populations who later migrated to the islands.

To find it, said Schroeder, “It’s simple. You compare the ancient genome with a modern African and a modern European genome and then mask the sections that match either of those.”

And it turned out that the unmasked Native American sections of modern Puerto Rican genomes are pretty similar to both modern Arawakan Peoples and the ancient Taino woman. The vanished Taino, it appears, live on in today’s Caribbean populations despite the catastrophic effects of European colonization.

“The 1,000-year-old individual from Preacher’s Cave was not a direct ancestor of contemporary Puerto Ricans. In other words, she personally does not have any living descendants in Puerto Rico. But this is perhaps not surprising given that she lived a thousand years ago on a different island,” said Schroeder.

Distant cousins might be a better comparison. “It will be fascinating to see how much ‘Taino’ ancestry has survived in the Caribbean and how this differs across the region,” Schroeder said.

More questions to answer, and more stories to tell

Ancient DNA could have a lot more to tell us about how people first reached the Caribbean, how they interacted, and why their population crashed so quickly when the Europeans arrived. The revelation that Taino DNA closely resembles that of modern Arawakan Peoples also doesn’t rule out the possibility that people reached the Caribbean in earlier waves from places like the Yucatan, for instance. Schroeder says more ancient genetic data could help fill in those gaps.

“It’s unlikely that this one genome tells us the full story of how the Caribbean was first settled by humans,” he told Ars.

DNA studies can also help shed light on the connections and interactions between Caribbean indigenous communities. Little knowledge of the Taino culture is left, but genes can record a history of social interaction that can at least help map out large-scale interactions. And it’s possible that DNA can also help us better understand the eventual extinction of the Taino.

“I feel that ancient DNA can help us better understand the impact of European colonization and what exactly caused the dramatic population declines in the region after 1492,” said Schroeder.

PNAS, 2017. DOI: 10.1073/pnas.1716839115 (About DOIs).