Syphilis is often framed as a relatively modern disease, one linked to dense cities, global trade, and the upheavals of European contact. New genetic evidence from ancient human remains in Colombia suggests that narrative is incomplete.
Researchers have reconstructed the genome of Treponema pallidum, the bacterium responsible today for syphilis and several related diseases, from the 5,500-year-old skeleton buried in the Sabana de Bogotá. Published in Science, the finding pushes the confirmed genetic record of this pathogen back more than 3,000 years and places its presence in the Americas long before urbanization or European arrival.
“Our results push back the association of T. pallidum with humans by thousands of years, possibly more than 10,000 years ago in the Late Pleistocene,” said researcher Davide Bozzi, in a press release.
Tracing a Syphilis Genome in Ancient DNA
The ancient genome came from a human skeleton excavated at a rock shelter near Bogotá. The individual lived roughly 5,500 years ago, a time when people in the region moved frequently and relied on hunting and foraging. The remains showed no clear signs of disease.
That absence matters because infections caused by T. pallidum only sometimes leave marks on bone, and most previously recovered ancient genomes have come from teeth or skeletal elements showing visible damage. In this case, researchers analyzed a tibia, or shin bone, a skeletal element rarely targeted in ancient pathogen studies.
The pathogen was detected during sequencing, originally designed to reconstruct human population history. Because the dataset was unusually large, traces of T. pallidum became visible without targeted pathogen screening, suggesting that ancient pathogen DNA may be detectable even in remains that show no outward signs of disease.
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A Previously Unknown Branch of the Syphilis Bacterium
Comparisons with modern genomes revealed that the ancient strain does not belong to any known T. pallidum subspecies. Today, nearly identical forms of the bacterium cause several distinct diseases, including syphilis, yaws, and bejel, while pinta remains genetically uncharacterized.
Phylogenetic analysis placed the ancient genome on a previously unknown branch of the T. pallidum family tree. The lineage appears to have split from other strains roughly 13,700 years ago, well before the emergence of the modern subspecies, which diverged closer to 6,000 years ago.
“One possibility is that we uncovered an ancient form of the pathogen that causes pinta, which we know little about, but is known to be endemic in Central to South America and causes symptoms localized to the skin,” said coauthor, Anna-Sapfo Malaspinas.
Despite its age, the genome contained genes associated with virulence in modern T. pallidum, indicating that the bacterium had already evolved the capacity to cause disease long before large, sedentary populations or urban centers existed.
"Current genomic evidence, along with our genome presented here, 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,” said coauthor Elizabeth Nelson.
Reshaping Ideas About Disease and Stigma
The findings complicate long-standing assumptions that diseases such as syphilis emerged only after agriculture, population crowding, or global trade created favorable conditions for transmission. Instead, the ancient genome suggests T. pallidum circulated among small, mobile groups shaped by close social contact and high mobility.
“Reframing syphilis, alongside other infectious diseases, as products of both localized and highly specific evolutionary, ecological, and biosocial conditions and globalization may represent critical steps toward reducing stigma and improving public health,” said coauthors Molly Zuckerman and Lydia Ball.
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