Beneath a rock shelter near present-day Bogotá, a 5,500-year-old skeleton that bore no visible trace of illness has quietly yielded something the living world has long searched for: the oldest known genome of the bacterium behind syphilis and its kin. The find reaches more than three thousand years further back into the genetic record than before, and it suggests that the family of pathogens now known as treponemal diseases was already taking distinct shapes in the Americas long before anyone was keeping written accounts. Whether this ancient strain is an early ancestor of the little-understoo
A 5,500-Year-Old Skeleton From Colombia Reveals a Lost Lineage of the Syphilis Bacterium
The skeleton showed no visible evidence of infection, yet its DNA held the genome
Mark
Why does a skeleton with no signs of disease matter so much here?
Mimi
Because the infection was found in the DNA, not in the bone. Most earlier genomes came from bones that visibly showed disease. This one was a shin bone, rarely used, and it still held the genome.
Luke
Worth noting nobody planned this. The team was studying human population history and found the bacterium during routine screening.
Mark
So the pathogen turned up by accident?
Mimi
Yes, in about 1.5 billion DNA fragments, far more than usual. That depth let them rebuild the genome without enrichment.
Mark
Is this the pinta pathogen?
Luke
Unknown. Malaspinas says they cannot prove it. It's a lead, not a finding.
Mimi
What is firm is that it's T. pallidum and doesn't match any modern form.
Mark
What about the 13,700-year figure?
Luke
That's an estimate from genetic analysis, a divergence date, not a measured age. The skeleton itself is about 5,500 years old.
Mimi
And it doesn't say where syphilis began. Nelson says that debate remains open.
Mark
What else is notable?
Mimi
The team shared results with Colombian communities before publishing, and had the permits.
Le Pouls
- A skeleton that showed no visible sickness has unexpectedly carried the oldest known genome of the syphilis bacterium, upending assumptions about where these infections began.
- The ancient strain matches none of today's disease-causing forms, branching away roughly 13,700 years ago while the modern subspecies only diverged about 6,000 years ago.
- Researchers are racing to determine whether this lineage is an early form of pinta, a poorly understood skin disease, but they cannot yet prove the connection.
- Bacterial DNA made up only a sliver of the sequenced material, so scientists relied on extraordinary sequencing depth to rebuild the genome without special enrichment.
- Further genomic study is the next step, and it is expected to sharpen the picture of how treponemal diseases evolved across the Americas.
Beneath a rock shelter near present-day Bogotá, a 5,500-year-old skeleton that bore no visible trace of illness has quietly yielded something the living world has long searched for: the oldest known genome of the bacterium behind syphilis and its kin. The find reaches more than three thousand years further back into the genetic record than before, and it suggests that the family of pathogens now known as treponemal diseases was already taking distinct shapes in the Americas long before anyone was keeping written accounts. Whether this ancient strain is an early ancestor of the little-understood pinta pathogen remains an open question, as science patiently gathers the evidence needed to answer it.
The skeleton was pulled from a rock shelter near present-day Bogotá, and it is about 5,500 years old. Its bones showed no sign of infection, yet the DNA preserved inside them held the oldest known genome of Treponema pallidum, the spiral-shaped bacterium tied to syphilis, yaws and bejel. The discovery pushes the genetic record of the pathogen back by more than three millennia and hints that these diseases were moving through the Americas far earlier than anyone had documented.
The bacterium was never the original target. Researchers were studying ancient human population history and generated far more genetic data than usual, around 1.5 billion fragments. Teams at UC Santa Cruz and the University of Lausanne independently noticed traces of the pathogen during routine screening and joined forces. Because the sequencing was so deep, they could rebuild the bacterial genome even though it made up a tiny fraction of the material.
The ancient strain belongs to the species but fits none of the forms that cause disease today. It split from other lineages about 13,700 years ago, long before the three modern subspecies diverged around 6,000 years ago. Researchers suggest it may be an early version of pinta, a little-understood skin disease, though they stress that this cannot yet be proven. Experts also caution that the find does not resolve where these diseases first arose, only that their evolutionary story is much older than thought.
The work was shared with Colombian communities before publication, with local scholars, students and residents invited to discuss the findings. Researchers see this as a way of building trust and keeping the knowledge tied to the country's own history. The next phase will bring more genomic analysis, which may confirm whether this lineage is an early pinta pathogen and reveal how these infections took shape in the Americas.
The skeleton came out of a rock shelter near present-day Bogotá, and it is about 5,500 years old. Its bones showed no visible sign of infection. Yet the DNA inside them has now yielded the oldest known genome of Treponema pallidum, the spiral-shaped bacterium tied to syphilis and its relatives.
The find extends the known genetic record of the pathogen by more than 3,000 years. It also adds weight to the idea that treponemal diseases were circulating in the Americas far earlier than the record had shown. Today T. pallidum exists as three closely related subspecies, each causing a different illness: syphilis, yaws and bejel. A fourth disease, pinta, is caused by Treponema carateum, also classed as T. pallidum subsp. carateum. No complete genome has yet been recovered for the pinta pathogen, which leaves its place in the family tree uncertain.
The researchers confirmed that the ancient DNA belongs to the species T. pallidum, but it matches none of the forms that cause disease now. It is closely related to modern strains, yet it branched off early. Genetic analysis puts its separation from other T. pallidum lineages at about 13,700 years ago. The three modern subspecies appear to have diverged much later, around 6,000 years ago. Both timelines support earlier research.
Anna-Sapfo Malaspinas, of the University of Lausanne and the SIB Swiss Institute of Bioinformatics, raised one possibility: the genome could be an ancient form of the pinta pathogen. Pinta is little understood, endemic from Central to South America, and causes symptoms confined to the skin. "At this time, we cannot prove this is the case," she said, but she called it a lead worth pursuing. Elizabeth Nelson, a molecular anthropologist and paleopathologist at SMU, was careful about the limits. The evidence, she said, does not settle the long-running debate over where the disease syndromes originated. It does show a long evolutionary history of treponemal pathogens already diversifying in the Americas thousands of years earlier than known. Davide Bozzi of Lausanne and the SIB said the results push the association of T. pallidum with humans back by thousands of years, possibly beyond 10,000 years ago, in the Late Pleistocene.
The pathogen was not the original target. Researchers sequenced the individual's DNA to study ancient human population history and produced about 1.5 billion fragments of genetic data, far more than is typical. During routine screening, teams at the University of California, Santa Cruz and the University of Lausanne each spotted traces of T. pallidum independently, and they decided to investigate together. Bacterial DNA was a tiny share of the total, but the depth of sequencing let them reconstruct the genome without specialized enrichment techniques.
The sampling choice matters too. Most ancient genomes of this bacterium have come from teeth or bones that plainly showed disease, since these infections mark the skeleton only under certain conditions and not in every case. Here the team sampled a tibia, the shin bone, which is not commonly used for ancient DNA work. That it worked suggests bones without obvious disease markers can still hold useful genetic information.
The work builds on long-running archaeological and genetic study at the Tequendama 1 site, including earlier research by archaeologist Miguel Delgado of the Universidad Nacional de La Plata in Argentina and by Lars Fehren-Schmitz of UC Santa Cruz. Before publication, the team shared its findings with communities in Colombia, consulting local scholars, students and community members through presentations and interviews. All permits for export and study were obtained. Delgado said the process builds trust and reinforces local ownership of knowledge, given how closely the findings are tied to Colombia's medical and cultural history.
The research was co-led by Nasreen Broomandkhoshbacht, now at the University of Vermont, with colleagues from institutions in the United States, Colombia, Switzerland, France and the Czech Republic. The next step is more genomic work, which may show whether this lineage is an early pinta pathogen and clarify how these diseases evolved in the Americas.
Citations marquantes
At this time, we cannot prove this is the case, but it is a lead worth investigating further.— Anna-Sapfo Malaspinas, University of Lausanne and SIB
The genome does not resolve the debate over where the disease syndromes originated, but shows a long evolutionary history already diversifying in the Americas.— Elizabeth Nelson, SMU (paraphrased)
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