Population Replacement In Pre-Columbian Columbia

UPDATE: I previously blogged this same paper closer to when it came out in 2025.

The "old world" is full of examples of hunter-gatherers being demographically replaced by farmers. The pre-Columbian New World was no different. The paper below explores a specific example of this happening in what is now the country of Columbia around 0 CE. In the "old world" this generally happened at the time that the Neolithic Revolution reached a region, and sometimes again when a civilization transitioned to the Bronze Age.

Also, to be clear, the extinct population is not outside the overall range of New World genetic diversity, it just doesn't correspond to any particular population that survived to the present that had been previously sampled. As the ancestry model chart below illustrates, it is within the range of South American specific ancestry.

Geographically, however, the location is notable. The modern DNA samples sometimes described as having Papuan affinity come from an area in the Amazon more or less due south of the highlands areas where the deceased subjects in this study, shown in the map below, were found. 

It is so geographically close, indeed, that the absence of any Papuan-like DNA in the hunter-gatherer samples in this study is itself notable, and tends to contradict the hypothesis that Papuan-like DNA seen in relict populations of living subjects nearby has a source older than the main New World founder population of ca. 14,000 years ago. I summed up a lot of the Paleo-Asian DNA in the New World discussion in a 2021 post, although I have made more posts since then on the subject.

Genetic studies on Native American populations have transformed our understanding of the demographic history of the Americas. However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America. Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. 

We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation. These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations. 

By 2000 years ago, the local genetic ancestry is replaced by populations from Central America associated with the Herrera ceramic complex and survives through the Muisca period despite major cultural changes. These ancient Altiplano individuals show higher affinities to Chibchan speakers from the Isthmus of Panama than to Indigenous Colombians, suggesting a dilution of the Chibchan-related ancestry through subsequent dispersal events.

Krettek, K. L., Casas-Vargas, A., Mas-Sandoval, A., & Posth, C. "A 6000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia." 11(22) Science Advances (May 28, 2025) (open access). https://www.science.org/doi/10.1126/sciadv.ads6284