In the high plains of the Altiplano cundiboyacense, just north of Bogotá, a forgotten chapter of South America’s past has recently been uncovered. For years, this region remained a genetic “white spot” in the larger narrative of South American prehistory. Now, an innovative study has filled in this gap, revealing that a distinct population of hunter-gatherers lived in these rugged plains for thousands of years — only to vanish without a trace.
New Genetic Evidence Sheds Light on Colombia’s Early Inhabitants
The study, led by researchers from the University of Tübingen, the Senckenberg Centre for Human Evolution and Paleoenvironment in Germany, and Colombia’s National University, analyzed 21 ancient genomes extracted from bones and teeth found at five archaeological sites across Colombia. The findings, published in Science Advances on May 28, 2025, provide the first ever genetic data on Colombia’s early inhabitants, offering an unprecedented view into the region’s distant past.
The genetic material, spanning nearly 6,000 years, covers a period from the initial waves of human settlement in South America until just before the arrival of the Spanish. The earliest samples came from Checua, an archaeological site situated about 3,000 meters above sea level, north of Bogotá. The genomes of these early hunter-gatherers revealed a previously unknown genetic lineage that traces back to the very first waves of migration into South America.
A Complete Genetic Replacement
What startled the researchers most, however, was the complete disappearance of this lineage in the region. By around 2000 BCE, genetic traces from these early hunter-gatherers — known to researchers as the Herrera and Muisca periods — were no longer found in the region. Instead, the individuals studied were genetically closer to populations from Panama and Venezuela, marking a complete shift in the genetic landscape.
Kim-Louise Krettek, the study’s lead author, explained that “we did not find any descendants of these first hunter-gatherers in the high plains of Colombia; their genes were not passed on.” This change coincided with the introduction of pottery, maize agriculture, and new social structures, which researchers believe were brought by migrating groups from the north. These new populations, equipped with different cultural practices and technologies, replaced the region’s original inhabitants entirely.
The shift in genetics appears to be linked to the arrival of migrants from Central America, bringing with them new ways of life — and a different genetic heritage. As Krettek emphasized, the transformation points to “a complete replacement of the population around Bogotá.”
Genetic Legacy: The Chibchan Connection
Interestingly, the study also explored the genetic connections between ancient and modern populations. Despite the genetic upheaval in the region, the modern indigenous populations of Colombia do not share the closest genetic ties with these northern migrants. Instead, it is the speakers of Chibchan languages, found in modern-day Panama and Costa Rica, who exhibit a strong genetic affinity with these ancient populations.
This raises intriguing questions about the ebb and flow of genetic influences over time. It suggests that the genetic imprint of the Chibchan peoples, which is less visible in today’s Colombian populations, gradually faded due to subsequent migrations that altered the region’s genetic makeup. The study also underscores the complexity of identity and ancestry, with researchers noting that the “genetic disposition should not be equated with cultural identity.” As Cosimo Posth, one of the study’s co-authors, cautioned, the relationship between genetics and cultural identity is far more intricate than it may first appear.
This research, conducted in collaboration with the Muisca indigenous community — who speak a language within the Chibchan family, extinct since the 18th century — paints a more fluid and complex picture of Colombia’s past than previously imagined. It highlights the significant role of migration and cultural change in shaping the genetic history of South America.
