Scientists have reconstructed the genome of Treponema pallidum from a 5,500-year-old skeleton in Colombia, marking the oldest known instance of this bacterium linked to syphilis and related diseases. The ancient strain diverged early in the pathogen's evolution, suggesting treponemal infections were diversifying in the Americas millennia before European contact. This discovery extends the genetic history of these diseases by over 3,000 years.
The remains, excavated from a rock shelter in the Sabana de Bogotá region near present-day Bogotá, date to approximately 5,500 years ago. Researchers sequenced the individual's DNA to explore ancient human population history, generating about 1.5 billion genetic fragments. During analysis, teams at the University of California, Santa Cruz, and the University of Lausanne detected traces of Treponema pallidum in the tibia sample, which showed no visible signs of infection.
This bacterium causes diseases like syphilis, yaws, and bejel today, with a related form responsible for pinta. The reconstructed genome belongs to Treponema pallidum but does not match modern subspecies, indicating it split from other lineages around 13,700 years ago—far earlier than the 6,000-year divergence of current forms. "Our findings show the unique potential of paleogenomics to contribute to our understanding of the evolution of species, and potential health risks for past and present communities," said Lars Fehren-Schmitz, a geneticist at the University of California, Santa Cruz.
The study, published in the journal Science, highlights the long evolutionary history of treponemal pathogens in the Americas. "Current genomic evidence... does not resolve the long-standing debate about where the disease syndromes themselves originated, but it does show there's this long evolutionary history of treponemal pathogens that was already diversifying in the Americas thousands of years earlier than previously known," noted Elizabeth Nelson, a molecular anthropologist at Southern Methodist University.
One hypothesis suggests this could be an ancient form of the pinta pathogen, endemic to Central and South America. "One possibility is that we uncovered an ancient form of the pathogen that causes pinta, which we know little about," said Anna-Sapfo Malaspinas of the University of Lausanne.
The research involved international collaboration, including archaeologist Miguel Delgado and others, with ethical engagement of Colombian communities before publication to respect the site's cultural significance. This work at the Tequendama 1 site underscores how ancient DNA can reveal hidden disease histories, aiding predictions of future pathogen evolution.