Ancient DNA Reveals a Vanished Colombian Population

Colombia sits at the gateway between Central and South America, yet until recently, nobody had ever sequenced an ancient human genome from the country. What researchers found when they finally did was a population with no descendants at all.

Colombia’s First Ancient Genomes

An international team led by researchers at the University of Tübingen in Germany and the National University of Colombia sequenced genome-wide data from 21 individuals recovered from five archaeological sites across the Bogotá Altiplano, a high plateau in the Andes. The samples, drawn from bones and teeth, span roughly 5,500 years, from 6,000 years ago up to about 500 years ago. The study, published in Science Advances, represents the first ancient human genomes ever published from Colombia.

A Lineage With No Living Relatives

Seven of the individuals, the oldest in the study, came from the Checua archaeological site and lived around 6,000 years ago, during the Preceramic period. Their genetic makeup turned out to represent a previously undocumented lineage entirely. According to the study, these hunter-gatherers show no closer genetic connection to ancient North American populations, and they didn’t contribute genetically to any known ancient or present-day South American population either. Archaeologist Andre Luiz Campelo dos Santos of Florida Atlantic University, who wasn’t involved in the research, told the Associated Press the finding was unexpected, since researchers hadn’t believed any other distinct lineage of this kind would turn up in South America.

A Complete Population Turnover

Researchers describe the Checua group as descending from the very first wave of people who spread rapidly across South America after arriving from the north. Despite that early presence, their genetic signature disappears entirely from the record within about 4,000 years. Study co-author Kim-Louise Krettek of the University of Tübingen said the team found no descendants of these hunter-gatherers, meaning their genes simply weren’t passed on, and that the area around Bogotá underwent what she described as a complete exchange of population. Researchers aren’t certain why the Checua lineage vanished, whether from environmental pressures, replacement by other groups, or gradual dilution into incoming populations, but co-author Andrea Casas-Vargas of the National University of Colombia said the disappearance raises real questions about both where this population came from and why it disappeared.

A Language Family That Endures Today

By around 2,000 years ago, genetic ancestry in the Altiplano had shifted dramatically toward populations linked to Central America, coinciding with the start of the Herrera period and its associated ceramic technology. Researchers believe this same wave of migration likely introduced Chibchan languages into the region, a family still spoken today across parts of Central America, including Panama and Costa Rica. Later individuals from the Altiplano show closer genetic ties to pre-Hispanic populations in Panama than to other Indigenous Colombian groups, and even some ancient remains from Venezuela carry traces of Chibchan-related ancestry, suggesting this language family may have spread into South America more than once. Harvard anthropologist Christina Warinner, who wasn’t part of the study, said the work highlights Central America’s underappreciated role in shaping the deep history of population movement and mixing across the Americas.

Sources

This report draws on original coverage by Live Science and Smithsonian Magazine of the study published in Science Advances.