Ancient DNA Pushes Origins of Syphilis Relatives Back 5,000 Years and Points to the Americas

Few debates in the history of disease have been as persistent or as politically charged as the question of where syphilis came from. One school of thought holds that Spanish sailors carried it back from the Americas after 1492, spreading it through Europe in the epidemic that followed. Another argues it was already present in the Old World before contact. For much of the past century, the evidence - limited mostly to skeletal lesions and historical records - was too ambiguous to resolve the question convincingly.

Ancient DNA is changing that. A study published in Science by Molly Zuckerman, professor of anthropology at Mississippi State University, and graduate student Lydia Bailey synthesizes recent paleogenomic discoveries to argue that diseases closely related to syphilis were present in the Americas more than 5,000 years ago - and that this evidence strongly favors an American origin for at least close relatives of the disease.

What the Paleogenomic Evidence Shows

The study draws on ancient DNA extracted from archaeological remains in Colombia and Mexico. Modern genomic sequencing techniques have advanced dramatically in their ability to recover and analyze degraded DNA from ancient bone and dental material, making it possible to identify pathogen genomes from individuals who lived millennia ago with a precision that was impossible a decade earlier.

The organisms at the center of the evidence are treponemes - a genus of spiral-shaped bacteria that includes the causative agent of syphilis (Treponema pallidum subspecies pallidum) as well as related diseases including yaws, pinta, and bejel. These conditions share evolutionary ancestry and are collectively called treponemal diseases. The ancient Colombian and Mexican specimens carry treponemal pathogen genomes dating back more than 5,000 years, predating any proposed European introduction and pushing the presence of these organisms in the Americas deep into prehistory.

The findings support what researchers call the Columbian hypothesis - the position that syphilis and its relatives originated in the Americas and were introduced to Europe through contact after 1492. The evidence is not absolute; ancient DNA evidence from some regions is still sparse, and the evolutionary relationships among treponemal subspecies involve ongoing debate among specialists. But the depth of the American record now makes an exclusively Old World origin considerably harder to defend.

Why This Matters Beyond the History

Syphilis is not a historical curiosity. Rates in the United States have risen sharply over the past decade - the CDC reported over 200,000 cases in 2022, the highest number in 70 years. Understanding the organism's evolutionary history and its capacity for adaptation is directly relevant to understanding its current resurgence and its potential for future change.

Zuckerman noted that the research "moves us further into understanding the origins and adaptability of a disease that is harmfully resurging in human populations, especially in the U.S., and thus its potential for future change." Long-term genomic data can reveal how the organism has evolved under different environmental and demographic conditions, potentially informing predictions about how current strains might respond to changing patterns of transmission, treatment, and immunity.

Bailey, the graduate student co-author, emphasized a different dimension: examining infectious diseases in deep historical time can shift how we understand the relationship between human mobility, environment, and disease spread - not just in the past but in the present. Publishing these findings in Science, one of the most widely read scientific journals, extends the conversation beyond anthropological specialists into broader public health discourse. Bailey noted this could help "destigmatize infectious disease" by contextualizing it within long patterns of human movement and biological change rather than framing it purely as individual behavior or social failure.

The study also illustrates how ancient DNA technology is reshaping questions that once seemed permanently unanswerable. Paleopathology was limited for most of its history to what could be read from bones. The ability to recover and sequence pathogen genomes from those same bones transforms the field's evidentiary scope fundamentally.