A groundbreaking study published on May 28 in Science Advances has unveiled a previously unknown genetic lineage of hunter-gatherers who lived near present-day Bogotá, Colombia, around 6,000 years ago. This enigmatic group, identified through ancient DNA analysis, disappeared approximately 2,000 years later, leaving no genetic trace in later populations. The findings offer fresh insights into the cultural and population shifts that shaped South America during the Early and Middle Holocene (11,700 to 4,000 years ago).
A Lost Lineage in the Colombian Highlands
The study, led by researchers including Cosimo Posth and Kim-Louise Krettek from the University of Tübingen, sequenced genomes from the bones and teeth of 21 skeletons across five archaeological sites in the Altiplano, a high plateau near Bogotá. These samples spanned 5,500 years and included seven genomes from the Checua site (6,000 years ago), nine from the Herrera period (around 2,000 years ago), three from the Muisca period (1,200 to 500 years ago), and two from Guane populations (530 years ago). These are the first ancient human genomes from Colombia to be published, marking a significant milestone in understanding the region’s prehistory.
The Checua genomes revealed a small, distinct group of hunter-gatherers whose DNA showed little similarity to Indigenous North American groups or other ancient and modern Central or South American populations. “Our results show that the Checua individuals derive from the earliest population that spread and differentiated across South America very rapidly,” Krettek explained. This group likely descended from the first Americans who crossed the Bering Land Bridge from Asia at least 23,000 years ago, as evidenced by trackways at White Sands National Park in New Mexico. While the timing of human arrival in South America remains debated, sites like Monte Verde II in Chile confirm human presence by 14,550 years ago.
A Mysterious Disappearance
Remarkably, the Checua population vanished around 4,000 years ago, with no genetic descendants detected in later groups in the Altiplano. “We couldn’t find descendants of these early hunter-gatherers of the Colombian high plains — the genes were not passed on,” Krettek noted. This suggests a complete population replacement in the Bogotá region, a rare and significant event in human history.
The disappearance of the Checua people coincides with major cultural changes during the Herrera period, which began around 2,800 years ago. This era saw the emergence of ceramic pottery in the Altiplano, a technological development whose origins have long puzzled researchers. The new genetic evidence points to an influx of migrating groups from Central America between 6,000 and 2,000 years ago, who likely introduced these innovations.
Newcomers and the Spread of Chibchan Languages
The study suggests that these Central American migrants brought more than just ceramics. “In addition to technological developments, the people of this second migration probably also brought the Chibchan languages into what is present-day Colombia,” said co-author Andrea Casas-Vargas, a geneticist at the National University of Colombia. Chibchan languages, still spoken in parts of Central America today, became widespread in the Altiplano by the time of European contact. Genetic markers linked to Chibchan-speaking populations first appeared in the region around 2,000 years ago.
The genetic profile of later Altiplano inhabitants shows stronger similarities to pre-Hispanic groups from Panama than to Indigenous Colombians, indicating significant mixing. Ancient remains from Venezuela also carry some Chibchan-related ancestry, though less closely related to ancient Colombians, hinting at multiple waves of Chibchan language expansion across South America.
Unraveling South America’s Ancient Past
The findings challenge previous assumptions about the continuity of Indigenous populations in the Altiplano and highlight the dynamic nature of human migration in South America. The complete replacement of the Checua population underscores the scale of demographic shifts that accompanied technological and linguistic changes in the region.
To further unravel these mysteries, the researchers propose sequencing additional ancient genomes from the Altiplano and neighboring areas. Such studies could clarify the timing of Central American migrations and the extent of Chibchan influence. For now, the discovery of this lost Colombian lineage offers a tantalizing glimpse into a forgotten chapter of human history, distinct from the well-known Maya or Inca, and a testament to the power of ancient DNA to resurrect vanished worlds.