Ancient DNA shows that humans settled in the Caribbean in two distinct waves

When Dr. Juan Aviles went to school in Puerto Rico, teachers taught him that the island’s original people, the Taino, disappeared shortly after Spain colonized it. Violence, disease and forced labor exterminated them, destroying their culture and language, the teachers said, and the colonists repopulated the island with slaves, including Indians from Central and South America and Africans.

But at home, Dr. Aviles heard another story. Your grandmother would tell you that they were descendants of Taino ancestors and that some of the words they used were also descended from the Taino language.

“But, you know, my grandmother had to drop out of school in second grade, so I didn’t trust her initially,” said Dr. Aviles, now a doctor in Goldsboro, NC

Dr. Aviles, who studied genetics in graduate school, became active in using it to help connect people in the Caribbean with their genealogical history. And recent research in the field has led him to recognize that his grandmother was right.

A study published on Wednesday in the journal Nature, for example, shows that about 14 percent of people in Puerto Rico can trace their ancestry back to the Taino. A smaller number of people in Cuba (4%) and the Dominican Republic (6%) can say the same.

These results, and similar ones based on DNA found in ancient Caribbean skeletons, are providing new insights into the region’s history. They show, for example, that the islands of the Caribbean were populated in two distinct waves from the continent and that the human population of the islands was also smaller than previously thought. But those who lived on the islands before colonial contact were not entirely extinct; millions of people living today have inherited their DNA, along with traces of their traditions and languages.

Before the advent of Caribbean genetic studies, archaeologists provided most of the clues about the origin of people in the region. The first human residents of the Caribbean seem to have lived mainly as hunter-gatherers, fishing on the islands and fishing in the sea, while maintaining small plantations.

Archaeologists have discovered some tombs of these ancient people. Beginning in the early 2000s, geneticists were able to fish a few bits of DNA preserved in their bones. Significant advances in recent years have made it possible to extract entire genomes from ancient skeletons.

“We went from zero complete genomes two years ago to more than 200 now,” said Maria Nieves-Colón, an anthropological geneticist at the University of Minnesota who was not involved in the new study.

The genes of the oldest known residents of the Caribbean link them to the first populations that settled in South and Central America.

“It’s a Native American population, of course, but it’s a very distinct deep lineage,” said David Reich, study co-author and geneticist at Harvard Medical School.

But it is still unclear exactly where on the continent these first American Indians left in canoes to reach the islands of the Caribbean.

“I don’t think we’re as close as we thought we would be to an answer,” said Dr. Nieves-Colón, co-author of another large-scale genetic study in July.

Part of the problem is that scientists have yet to find ancient DNA in the Caribbean more than 3,000 years old. The other problem is that ancient DNA is still scarce on the continent’s Caribbean coast. “There is a lot that we can’t see because we don’t have ancient DNA,” said Dr. Nieves-Colón.

About 2,500 years ago, the archaeological record shows, there was a drastic change in the cultural life of the Caribbean. People began to live in larger settlements, intensively growing crops such as corn and sweet potatoes. His ceramics became more sophisticated and elaborate. For archaeologists, the change indicates the end of what they call the Archaic Age and the beginning of the Ceramic Age.

Dr. Nieves-Colón and other researchers found that the DNA of the Caribbean islanders also changed at the same time. The skeletons of the Ceramic Age widely shared a new genetic signature. Their DNA links them to small tribes that still live today in Colombia and Venezuela.

It is possible that migrants from the Caribbean coast of South America brought with them the languages ​​that were still spoken when Columbus arrived, 2,000 years later. We don’t know much about these languages, although some words have survived. Hurricane, for example, comes from hurakán, the Taino name for the god of storms.

These words have a striking resemblance to words from a South American language family called Arawak. The DNA of the Ceramic Age Caribbean is more similar to that of living Arawak speakers.

In the Ceramic Age record, it is difficult to find people with many archaic ancestors. They seem to have survived in some places, like western Cuba, until they disappeared about 1,000 years ago. People with ancestors from the Ceramic Age came to dominate the Caribbean, with almost no cross between the two groups.

“It looks like archaics were simply dominated by pottery,” said William Keegan, an archaeologist at the Florida Museum of Natural History and co-author of the new study.

Dr. Keegan, who has studied Caribbean archeology for more than three decades, said the new DNA discoveries have surprised him in many ways, giving him a series of new questions to investigate.

Throughout the Pottery Age, for example, surprisingly new pottery styles emerged every few centuries. Researchers have long guessed that these changes reflect the arrival of new groups of people to the islands. The old DNA does not support this idea, however. There is a genetic continuity through these drastic cultural changes. It seems that the same group of people in the Caribbean has gone through a series of major social changes that archaeologists still need to explain.

Dr. Reich and his geneticist colleagues also discovered family ties that spanned the Caribbean during the Ceramics Age. They found 19 pairs of people on different islands who shared identical segments of DNA – a sign that they were very close relatives. In one case, they found long-distance cousins ​​from the Bahamas and Puerto Rico, more than 800 miles apart.

This discovery runs counter to influential theories of archeology.

“The original idea was that people would start in one place, establish a colony in another place and then cut all ties to where they came from,” said Keegan. “But the genetic evidence is suggesting that these ties have been maintained for a long time.”

In other words, instead of being made up of isolated communities, the Caribbean was a busy long-distance network that people regularly traveled in a canoe. “Water is like a road,” said Dr. Nieves-Colón.

Genetic variations also allowed Dr. Reich and his colleague to estimate the size of Caribbean society before contacting Europe. Christopher Columbus’ brother, Bartolomeu, sent letters to Spain putting the number in the millions. DNA suggests that this was an exaggeration: genetic variations imply that the total population reached tens of thousands.

Colonization caused a major shock in the Caribbean world, drastically changing its genetic profile. But the people of the Ceramic Age still managed to pass their genes on to future generations. And now, with a population of about 44 million, the Caribbean may contain more Taino DNA than in 1491.

“Now we have this evidence to show that we were not extinct, we just mixed up and are still around,” said Dr. Aviles.

His fascination with Caribbean DNA research recently led him to help found the Council of Native Caribbean Heritage. The organization helps people find their own links to the Caribbean’s distant past. Dr. Aviles and his colleagues consulted Dr. Reich and other researchers, both to discuss the direction of the research and to use it to understand their own stories.

Dr. Aviles and his colleagues uploaded the ancient Caribbean genomes to a genealogical database called GEDMatch. With the help of genealogists, people can compare their own DNA with ancient genomes. They can see the corresponding stretches of genetic material that reveal their relationship.

Sometimes Dr. Aviles imagines explaining all of this to his late grandmother. “But first, I would apologize for not believing her,” he said, “because she was right.”