A 6,000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia

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Ancient DNA from Colombia's Bogotá Altiplano reveals 6,000 years of genetic turnover.

This study sequenced 21 ancient individuals from the Bogotá Altiplano, spanning 6,000 to 500 years ago. It uncovers a previously unknown hunter-gatherer lineage that arrived early, left no genetic legacy, and was later replaced by groups linked to Central American pottery cultures. Surprisingly, these ancient highlanders are more closely related to Chibchan speakers from the isthmus than to modern Colombians, suggesting later migrations diluted that ancestry.

• Pre-ceramic hunter-gatherers formed a previously unknown basal lineage from the initial South American radiation, with no genetic contribution to later populations.
• Around 2,000 years ago, local ancestry was replaced by Central American-related groups associated with Herrera pottery, persisting through the Muisca period.
• Ancient highland individuals show higher affinity to Chibchan speakers from the isthmus than to modern Colombians, indicating dilution of Chibchan-related ancestry in later dispersals.

Sample interpretation

All 21 individuals were from the Bogotá Altiplano. Y-chromosome haplogroups were resolved for 11 males, all belonging to Q lineages, including Q-M3, Q-M848, and Q-L54. Mitochondrial DNA was more diverse, with B2d being the most common (8 individuals), followed by A2 variants and C1c. This genetic profile reflects the region's complex population history.

For genealogy enthusiasts

For ancestry enthusiasts, this study shows that ancient Colombian populations underwent multiple genetic shifts, with early hunter-gatherers leaving no genetic trace. Modern Colombian ancestry is a mix of later arrivals, so ancient DNA is key to understanding the region's deep demographic past.