Ancient DNA Pushes Syphilis' Roots Back 5,500 Years — New Genome From Colombia Rewrites Timeline

Archaeologists and geneticists have recovered DNA from the spiral-shaped bacterium Treponema pallidum in a 5,500-year-old skeleton unearthed in Colombia, providing the oldest direct genomic evidence of a treponemal infection to date.

What the Genome Reveals

The ancient strain, designated TE1-3, does not match any strains circulating today. Genomic analysis places TE1-3 on a deep branch described by the authors as an "early-diverging sister lineage" of T. pallidum. Based on calibrated molecular dates, the team estimates TE1-3 split from other T. pallidum lineages about 13,700 years ago — a timing that pushes documented treponemal genomic evidence back roughly 3,000 years.

Transmission and Virulence

It remains unclear whether TE1-3 was transmitted mainly through sexual contact (as with modern syphilis) or by skin-to-skin routes associated with yaws, bejel and pinta. The genome, however, contains virulence genes found in modern strains, indicating the bacterium was capable of infecting humans and causing disease.

Audition now for ScienceAlert's Casting Call

Broader Implications

The findings strengthen genetic support for an American origin hypothesis for the lineage that eventually gave rise to syphilis-like diseases, but they do not prove exclusivity. Some researchers argue, controversially, that related treponemal infections occurred in Europe before Columbus. The new genome instead highlights how ecological, social and demographic contexts — mobility of hunter-gatherers, later agricultural settlement, and local environments — likely shaped how treponemal infections emerged and spread.

'Far from static or specific to a human population or environment, pathogens are tethered to mobile hosts and shaped by biosocial and environmental conditions,' note anthropologists Molly Zuckerman and Lydia Bailey in a related perspective.

The study, led by evolutionary genomics researcher Davide Bozzi and colleagues, was published in Science. Researchers emphasize that additional ancient genomes and archaeological context are needed to resolve how transmission modes and disease expression changed over time.

Takeaway

TE1-3 demonstrates that treponemal bacteria were present in the Americas thousands of years before the first recorded European outbreaks of syphilis, complicating simple 'Old World vs New World' origin stories and underscoring the need for more ancient DNA to map the pathogen's complex history.