Ancient DNA Reveals Mysterious New Group of Humans in Colombia With No Genetic Ties to People Today

two skeletons in an excavation site in the ground
These skeletons of two hunter-gatherer individuals excavated at the Checua archaeological site north of Bogotá, Colombia, helped uncover the genetic details of a mysterious population. Ana María Groot / Universidad Nacional de Colombia

Scientists have found genetic evidence of an ancient group of people in Colombia with no modern-day descendants. It’s as if they simply vanished from the face of the Earth. What’s more, they’re also not closely related to the ancient Native American populations that scientists had thought would be their ancestors.

“This is unexpected,” Andre Luiz Campelo dos Santos, an archaeologist from Florida Atlantic University who did not participate in the research, tells Adithi Ramakrishnan at the Associated Press. “Up to this point, we didn’t believe there was any other lineage that would appear in South America.”

An international team of researchers described the discovery in a study published in late May in the journal Science Advances. They analyzed DNA from the bones and teeth of 21 individuals found at five archaeological sites in the Altiplano—the high plains around Bogotá—dating to between 500 and 6,000 years ago. The analyses represent Colombia’s first ancient human genomes ever to be published.

Need to know: What is ancient DNA?

Ancient DNA is genetic material recovered from old biological remains. Often extracted from cells in bones, teeth or preserved tissues, the DNA might have degraded over time—but it can offer researchers a window into the genetics of populations that lived a long time ago.

Seven of the individuals belonged to the mysterious population—a previously undocumented lineage of people. These were the oldest remains analyzed in the study, and they were unearthed at the Checua excavation site north of Bogotá at an elevation of about 1.86 miles. While this group was present 6,000 years ago, they had disappeared by 4,000 years later.

“These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations,” the researchers explain in the study. “By 2,000 years ago, the local genetic ancestry is replaced by populations from Central America.”

The new findings raise questions “as to where they came from and why they disappeared,” Andrea Casas-Vargas, co-author of the study and a researcher at the National University of Colombia’s Genetics Institute, tells CNN’s Jack Guy.

Panoramic view of the Altiplano, the high plains around Bogotá.
A panoramic view of the Altiplano, the high plains on a vast plateau around Bogotá. William Usaquen / Universidad Nacional de Colombia

The first people to reach the Americas came from Siberia via the Bering Land bridge at least 15,000 years ago (though some studies suggest they crossed thousands of years earlier). These people split into a northern Native American lineage and a southern Native American lineage. Populations belonging to the latter group would eventually settle in Central and South America, as reported by Popular Mechanics’ Elizabeth Rayne, though scientists don’t know the exact timeline. A paleontological site in Chile, however, suggests people first arrived in South America at least 14,550 years ago, per Live Science’s Skyler Ware.

The small Checua population examined in the study derived from the first migration wave to reach South America, which passed through Colombia before populating the rest of the continent. But to the researchers’ surprise, their genes were seemingly not passed on. “That means in the area around Bogotá there was a complete exchange of the population,” Kim-Louise Krettek, first author of the study and an archaeologist at the Senckenberg Center for Human Evolution and Paleoenvironment at the University of Tübingen in Germany, says in a statement.

Archaeologists speculate the Checua population could have disappeared due to environmental changes or been replaced by other groups. They might have also just mixed into other local populations to the point that their unique DNA was diluted out of the gene pool.

Either way, the Altiplano populations looked very different by 2,000 years ago, when people from Central America had replaced the Checua population, bringing ceramics, technology and likely also the Chibchan languages into present-day Colombia. In fact, the Altiplano individuals from less than 2,000 years ago were found to have greater genetic ties to Chibchan speakers from Panama than to Indigenous Colombians.

The genetic disappearance of the Checua people is unusual for South America, where researchers have found regions with strong genetic continuity, according to the statement.

Colombia “is a key region for understanding the peopling of South America… but until now, it has been a blank spot in ancient DNA studies of the Americas,” Christina Warinner, an anthropologist from Harvard University who was not involved in the study, explains to CNN. “This study highlights the deep history of population migration and mixing in the formation [of] today’s populations and points to Central America as a key region that influenced the development of complex societies in both North and South America.”

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