A rock shelter near Bogota once looked like a calm archaeology site, with tools, bones, and lots of open questions.
Then scientists took a closer look at the DNA inside ancient remains, and the results pointed to a group of people who did not match any known population, living or ancient, in the Americas.
A surprise under the altiplano
The research team studied remains from the Bogota altiplano (high plateau), including individuals who lived about 6,000 years ago, and published the work in Science Advances in late May 2025.
The dataset included genome-wide data, meaning DNA from across the whole genome, from 21 individuals, ranging from about 6,000 to 500 years ago, giving a long timeline instead of a single snapshot.
In 1992, researchers first found the Checua remains near the town of Nemocon, and later digs and projects added more material collected between 1987 and 2003.
Some of the oldest individuals came from a place linked to Checua, and their genetic profile looked unlike anything else in current databases.
Andrea Casas Vargas, a researcher at the Universidad Nacional de Colombia and a co-author, told CNN that the team did not expect to find a lineage not reported in other populations.
How ‘ancient DNA’ works
DNA is like a cookbook inside cells, and time is not kind to it; heat, humidity, and microbes can rip pages apart.
That is why researchers often use dense bones or teeth, which can protect tiny scraps of genetic material better than softer tissue.
Colombia’s warm and humid environments have made ancient DNA harder to recover than in colder, drier regions, which is one reason the country stayed underrepresented in big genetic maps for so long.
In the lab, those scraps get read like a shredded document; lots of small pieces are scanned, then software helps line them up to rebuild a useful genetic picture.
It is slow work, and it can fail, so getting full genomes from ancient remains in Colombia was a milestone for research in the region.
The ‘ghost lineage’ idea
The strangest part was what the oldest Checua individuals did not show: No close link to later ancient Colombians in the same region, and no clear match to any modern Indigenous group studied so far.
One clue still connected them to Native American ancestry; their Y chromosome markers fit a broader Native American line, but the rest of their genome stood apart.
A lineage is basically a branch on the human family tree, so calling it “unknown” means it was a branch that scientists had not seen before when comparing many populations.
A good way to think about it is a family surname with no living relatives; the label exists, but the branches that carried it seem to have ended.
Researchers suggested several possible reasons, such as isolation, environmental stress, or later population movements that replaced earlier groups over time.
Why Colombia mattered here
Scientists have long called Colombia a key corridor into South America, because people traveling south had to pass through this region.
Around 20,000 years ago, people were already moving south from the north, and Reuters reported that later Colombian remains showed genetic similarities with Panama, supporting the idea of repeated movement through the isthmus area.
Christina Warinner of Harvard University told CNN that Colombia had been a blank spot in ancient DNA studies of the Americas, which made these genomes especially valuable.
The same study also reported that later Altiplano individuals, from about 2,000 to 500 years ago, shared a more similar genetic makeup with each other than with the older group.
That pattern hinted at big population changes over time, and it supported the idea that South America’s human story was shaped by more than one movement and more than one community.
Where this mystery could lead
The team said follow-up work had already begun in other regions of Colombia, aiming to add more ancient genomes and see if this lost lineage appeared elsewhere.
For now, the Bogota Altiplano find reads like a missing chapter, proof that people lived, traveled, and disappeared in ways history never recorded, leaving only bone, stone tools, and a few fragile strands of DNA.