South America’s First Hunter-Gatherers Appeared, Then Unusually Disappeared 2,000 Years Ago

Learn about a previously unknown population of hunter-gatherers in Colombia, whose genetic trail faded away between around 6,000 and 2,000 years ago.

By Sam Walters
Jun 2, 2025 9:40 PM
South America location for missing group of hunter-gatherers
Sopo, Cundinamarca, Colombia (Image Credit: hinterhof/Shutterstock)

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Some of the first hunter-gatherers to arrive in Colombia — and some of the first hunter-gatherers to arrive in all of South America — didn’t stick around. They appeared, then disappeared between 6,000 and 2,000 years ago, only to be replaced by a second population of settlers. That’s what a new study in Science Advances suggests anyway, based on the analysis of 21 ancient genomes from the Altiplano, or high plains, around Bogotá.

“These are the first ancient human genomes from Colombia ever to be published,” said Cosimo Posth, a senior study author at the University of Tübingen, according to a press release.


Read More: New Research Suggests Humans Arrived in the Americas Much Earlier Than Thought


Evidence of Hunter-Gatherers

Recent research has finally started to show how humans first arrived in South America. Indeed, these studies have revealed that humans settled the continent from the north, having reached the region through the Isthmus of Panama — the thin strip of land that connects North and South America.

“Genetic studies on ancient and present-day Indigenous populations have substantially contributed to the understanding of the settlement of the Americas,” the authors of the study stated. “However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America.”

Hoping to learn more about the genetic history of this area, the study authors turned to five archaeological sites from across the Bogotá Altiplano. Pulling genetic material from bones and teeth from all five sites, the team sequenced the genomes of 21 individuals, who lived between 6,000 and 500 years ago.

The results revealed that a previously unknown population of hunter-gatherers had appeared in the Bogotá Altiplano by around 6,000 years ago, and had disappeared by around 2,000 years ago. By then, the genetic traces of these people (which had initially surfaced at the Checua archaeological site near Bogotá) were not detectable.

“Our results show that the Checua individuals derive from the earliest population that spread and differentiated across South America,” said Kim-Louise Krettek, another study author at the University of Tübingen, according to the release. “We couldn’t find descendants of these early hunter-gatherers of the Colombian high plains — the genes were not passed on. That means in the area around Bogotá there was a complete exchange of the population.”


Read More: Humans May Have Settled in North America 16,000 Years Ago, Ready to Hunt


A Sudden Disappearance of Early Settlers

The study authors stress that the disappearance of the early settlers is surprising. “That genetic traces of the original population disappear completely is unusual, especially in South America,” said Andrea Casas-Vargas, another study author from the National University of Colombia, according to the release.

Most Indigenous populations from South America have shown strong genetic continuity, across time periods and cultures. “It was that way, as well, in the populations [that] followed the hunter-gatherers in the Bogotá Altiplano until the arrival of European conquerors,” Casas-Vargas said in the release.

The people that replaced the early hunter-gatherers in Colombia were from Central America, and they brought their culture and language with them, along with a new period of genetic stability that spanned until the arrival of the Europeans.

“In addition to technological developments such as ceramics, the people of this second migration probably also brought the Chibchan languages into what is present-day Colombia,” Casas-Vargas said in the release. “Branches of this language family are still spoken in Central America today.”

As part of their research, the study authors shared their results with the Guardia Indígena Muisca, the representatives of the Muisca people, whose descendants were present in the Bogotá Altiplano when the Europeans arrived around 500 years ago.

“Questions about history and origins touch upon a sensitive area of the self-perception and identity of the Indigenous population,” Posth said in the release. “As scientists addressing questions relevant to the Indigenous communities in Colombia, we respect and value the wealth of community-based knowledge.”


Read More: Early Humans Survived an American Ice Age, Archaeologists Say


Article Sources

Our writers at Discovermagazine.com use peer-reviewed studies and high-quality sources for our articles, and our editors review for scientific accuracy and editorial standards. Review the sources used below for this article:


Sam Walters is a journalist covering archaeology, paleontology, ecology, and evolution for Discover, along with an assortment of other topics. Before joining the Discover team as an assistant editor in 2022, Sam studied journalism at Northwestern University in Evanston, Illinois.

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