Rosa Rubicondior: Refuting Creationism - Evolution of Syphilis

The archeological site of Tequendama 1 at the border of the Sabana de Bogotá, Cundinamarca, Colombia.

Ancient DNA pushes back record of treponemal disease-causing bacteria by 3,000 years

Creationists who take the biblical Flood story literally have a problem that rarely features in illustrations of Noah’s floating menagerie: what happened to the infectious diseases? Saving their animal hosts would also have provided opportunities to save their pathogens. Conversely, exterminating the hosts would have threatened the survival of the very organisms that depended on them. A supposedly fresh start for life on Earth would therefore require an explanation for why so many ancient infections apparently came along for the ride.

Many pathogens, including those that infect humans are also host-specific, so that begs the question of which of the human passengers were host to the sexually-transmitted diseases, and how, if they were 'righteous' people, did they acquire them? The authors of the tale knew nothing of microorganisms or the germ theory of disease, of course, so saw no reason to explain all that stuff.

A discovery reported in Science on 22 January 2026 gives that question another uncomfortable historical dimension. An international research team has reconstructed a roughly 5,500-year-old genome of Treponema pallidum from human remains at the Tequendama I rock shelter in Colombia. This is the bacterial species whose recognised subspecies cause syphilis, yaws and bejel. The findings are described in a research paper in Science by Davide Bozzi and colleagues.

The ancient bacterium belonged to a previously unknown branch of the family tree, a sister lineage to all the genetically characterised subspecies of T. pallidum. It should therefore not be described simply as a case of modern syphilis in a prehistoric person. Nevertheless, its presence establishes that this group of pathogens was infecting people in South America long before European contact—and before the date commonly assigned to Noah’s genocidal flood.

The evolutionary history reaches further back still. The researchers’ molecular-clock analysis estimates that the ancient lineage and the other known lineages shared a common ancestor approximately 13,700 years ago. That estimate carries substantial uncertainty, with a range of roughly 6,800–20,600 years, but its central value places this ancestral population well before even the more generous versions of the usual young-Earth creationist chronology. These are estimates reconstructed from genetic evidence, not dates obtained by adding together the supposed lifespans of biblical patriarchs.

The Flood problem deserves careful examination. Genesis is ambiguous on the point. On the one hand it describes the destruction of terrestrial, air-breathing life; on the other hand it specifically refers to all living substance being destroyed. Although the authors were unaware of microorganisms so were not writing a microbiology textbook, a supposedly omniscient, creator god would not have been constrained by the ignorance of primitive pastoralists. But then these obligate parasites would not have survived the destruction of their hosts outside the ark, so the question of what 'life' the Bible is referring to become moot. If you subscribe to the Ark myth, you have to accept that any survivors must have been carried in the Ark.

The discovery of an ancient relative of syphilis does not establish that the particular Colombian lineage survived to the present. But neither qualification explains how the surviving branches of an ancient, host-associated pathogen could have persisted through the alleged destruction of their hosts outside the Ark. Within that narrative, infected passengers or another explicitly justified means of survival would be needed. Simply overlooking the pathogens does not solve the problem.

There appears to be no way to avoid the conclusion that, if the Ark myth were true, Noah and his family must have been carrying the obligate, species-specific sexually-transmitted diseases, syphilis, gonorrhoea and chlamydia as well as pubic lice and an assortment of intestinal worms.

Evolution, meanwhile, supplies the framework that makes the discovery intelligible: common ancestry, branching descent and genetic change over time. The scientists can place an unfamiliar ancient genome within a family tree and investigate when its lineage diverged from its relatives. There is no need to invent a separate creation event for each disease, or a miraculous rescue operation to carry ancient infections across an otherwise universal catastrophe. There is a history to reconstruct—and the evidence is preserved in the DNA.

The treponemal family: related bacteria, different diseases. Treponema is a genus of slender, spiral-shaped bacteria belonging to a group called spirochaetes. Some cause the infections collectively known as treponematoses. Three closely related subspecies of Treponema pallidum cause syphilis, yaws and bejel. Despite their genetic similarity, these infections differ in their usual transmission routes and clinical presentation.

Three closely related pathogens

Disease Causative bacterium Principal transmission routes

Syphilis Treponema pallidum subsp. pallidum Usually through direct contact with infectious lesions during sexual activity. Infection can also cross the placenta during pregnancy, causing congenital syphilis.

Yaws Treponema pallidum subsp. pertenue Usually through non-sexual skin contact with infectious lesions, with bacteria entering through minor skin injuries. It predominantly affects children in warm, humid regions.

Bejel, or endemic syphilis Treponema pallidum subsp. endemicum Usually through non-sexual close contact involving infectious skin or mucosal lesions. Despite its alternative name, it is distinct from the subspecies responsible for sexually transmitted syphilis.

A fourth treponemal disease, pinta, is attributed to Treponema carateum. Its precise evolutionary position remains uncertain: no genome from this organism was available for comparison in the Colombian study.

Where does the ancient Colombian bacterium fit?

The approximately 5,500-year-old genome, designated TE1-3, came from human remains at the Tequendama I rock shelter in Colombia. Genetic analyses place it on a previously unknown branch, sister to the group containing all the genetically characterised T. pallidum subspecies.

A sister lineage is an evolutionary relative sharing a common ancestor. It is not necessarily a direct ancestor. The Colombian organism should therefore not be described as “the ancestor of syphilis”, nor does its discovery establish that the infected person had sexually transmitted syphilis.

What can its DNA tell us?

DNA comparisons reveal evolutionary relationships that cannot be established from bones alone. The researchers also detected sequences corresponding to genes associated with virulence in modern strains, suggesting that the ancient organism possessed genetic machinery relevant to causing infection.

However, those genes do not tell us exactly which symptoms developed, how severe the infection was, or how it spread. Person-to-person transmission is plausible, but transmission from an animal could not be excluded. The skeleton showed no obvious macroscopic signs of treponemal disease—a reminder that infection need not leave recognisable damage on bones.

Two ages, answering different questions

Approximately 5,500 years: the age of the infected human remains, established through radiocarbon dating. This dates an actual occurrence of the ancient bacterial lineage.

Approximately 13,700 years: the estimated age of the common ancestor shared by TE1-3 and the other sampled T. pallidum lineages. This comes from molecular-clock analysis, which combines genetic differences, dated samples and models of evolutionary change. The study’s 95% credible interval was approximately 6,800–20,600 years, so the central estimate should not be treated as an exact date.

The distinction matters: an ancient specimen provides evidence that a lineage existed at a particular time; its ancestry may extend much further into the past.

Glossary

Subspecies

A named subdivision within a species, used to distinguish related populations with characteristic differences.

Genome

An organism’s complete set of genetic material. Ancient genomes are reconstructed from surviving DNA fragments and may have gaps.

Sister lineage

One of two evolutionary branches that share an immediate common ancestor.

Common ancestor

An ancestral organism or population from which two or more lineages descended.

Molecular clock

A method for estimating evolutionary dates from genetic changes, using calibration evidence and models that allow for uncertainty.

Virulence

The degree of harm a pathogen can cause. Finding a virulence-associated gene does not, by itself, establish how severe an ancient infection was.

**Three closely related pathogens**
Disease	Causative bacterium	Principal transmission routes
Syphilis	Treponema pallidum subsp. pallidum	Usually through direct contact with infectious lesions during sexual activity. Infection can also cross the placenta during pregnancy, causing congenital syphilis.
Yaws	Treponema pallidum subsp. pertenue	Usually through non-sexual skin contact with infectious lesions, with bacteria entering through minor skin injuries. It predominantly affects children in warm, humid regions.
Bejel, or endemic syphilis	Treponema pallidum subsp. endemicum	Usually through non-sexual close contact involving infectious skin or mucosal lesions. Despite its alternative name, it is distinct from the subspecies responsible for sexually transmitted syphilis.

The paper in Science, was accompanied by this University of Lausanne news item:

Ancient DNA pushes back record of treponemal disease-causing bacteria by 3,000 years
A recent discovery by an international team, including Unil and CHUV scientists, adds to evidence of extensive pathogen diversity in the Americas long before European contact.
Scientists have recovered a genome of Treponema pallidum – the bacterium whose subspecies today are responsible for four treponemal diseases, including syphilis – from 5,500-year-old human remains in the Sabana de Bogotá, Colombia. The research expands knowledge about the history of this infectious disease and its occurrence in human populations, with findings now published in the journal Science (Jan 22, 2026).

The individual was archaeologically recovered from a rock shelter near Bogotá, Colombia, dating back roughly 5,500 years. The discovery pushes the genetic record of this pathogenic species back by more than 3,000 years, strengthening evidence that these infections have circulated in the Americas far longer than previously known.

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.

Lars Fehren-Schmitz, co-corresponding author
UCSC Paleogenomics
Department of Anthropology
University of California Santa Cruz
Santa Cruz, CA, USA.
What are treponemal diseases?

Treponema pallidum is a spiral-shaped bacterium that exists in three closely related forms today, each responsible for a different disease: syphilis, yaws and bejel. A fourth treponemal disease, pinta, is caused by Treponema carateum or Treponema pallidum subsp. carateum, but no genome for this pathogen has yet been recovered, casting doubts about its phylogenetic relationships and taxonomic classification.

Although the three T. pallidum subspecies are nearly identical genetically, scientists do not know when or how the different disease forms emerged. Some data exists about the evolutionary history of pathogens, but there remain significant gaps between what skeletal remains reveal and what genetics can confirm.

For the study, the research team demonstrated that the ancient DNA recovered belongs to the Treponema pallidum species, but it does not match any of the genetically known forms that cause disease today. The scientists showed that while it is closely related, it diverged early in the evolutionary tree.

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. At this time, we cannot prove this is the case, but it is a lead worth investigating further.

Anna-Sapfo Malaspinas, co-corresponding author
Department of Computational Biology
University of Lausanne
Lausanne, Switzerland.

Scientists estimate this ancient strain split from other T. pallidum lineages about 13,700 years ago. The three modern subspecies, by comparison, diverged much more recently, about 6,000 years ago, which aligns with previous research. These findings shed new light on how diverse these pathogens were in the past and serve as a reference point for understanding when they began branching into different forms.

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.

Elizabeth Nelson, co-corresponding author.
UCSC Paleogenomics
Department of Anthropology
University of California Santa Cruz
Santa Cruz, CA, USA.

A genetic puzzle

Understanding how treponemal diseases emerged and how treponemal pathogens evolved is surprisingly complicated because the bacteria are almost identical genetically, yet they get transmitted differently and can vary in clinical presentation.

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.

Davide Bozzi, first author
Department of Computational Biology
University of Lausanne
Lausanne, Switzerland.

This discovery builds on years of collaborative archaeological and genomic research at the Tequendama 1 site. Archaeologist Miguel Delgado at the Universidad Nacional de La Plata in Argentina and Fehren-Schmitz had previously published work offering detailed context about the skeleton.

The finding emerged unexpectedly. Researchers originally sequenced the individual’s DNA to study human population history, generating 1.5 billion fragments of genetic data—far more than typical studies. While screening the data, teams at the University of California, Santa Cruz and Unil independently detected T. pallidum and joined forces to investigate. The bacterial DNA made up only a tiny fraction of the genetic material, but the unusually deep sequencing allowed researchers to reconstruct the genome without the specialized techniques normally required.

The three diseases caused by T. pallidum (bejel, yaws, and syphilis) can leave marks on bones, but only at certain stages and not in every infected person. Most ancient T. pallidum genomes have been recovered from teeth or bones of people with clear signs of infection, but this skeleton showed none. Researchers sampled a tibia, or shin bone, a skeletal element not typically used for ancient DNA extraction.

The approach paid off, suggesting that even bones without visible signs of disease could be valuable sources of pathogen DNA. The presence of Treponema pallidum in a bone sample can be explained by the fact that treponema can cause bone infections, and that in the initial stage, this type of infection can be asymptomatic - not immediately associated with visible bone lesions.

Gilbert Greub, co-author
Institute of Microbiology
University of Lausanne and University Hospital Center (CHUV)
Lausanne, Switzerland.

[Gilbert Greub is] also director of Unil's Institute of microbiology and Davide Bozzi's thesis co-supervisor.

The researchers believe understanding how infectious diseases emerged and evolved in the past could help scientists predict how they may change in the future and help societies prepare for what lies ahead.

Before publishing, the researchers shared their findings with communities in Colombia, recognizing the discovery's significance to the country's medical history. They consulted with local scholars, students and community members, and connected with stakeholders through presentations and interviews. The team also obtained all necessary permits for exportation and study.

This process was essential because the findings are deeply connected to Colombia's medical and cultural history. Engaging scholars, students, and Indigenous and non-Indigenous community members ensures the results are ethically communicated and interpreted in partnership with local communities. This approach builds trust, supports responsible stewardship of sensitive discoveries, and reinforces local ownership of knowledge.

Miguel Delgado, co-author.
División Antropología
Facultad de Ciencias Naturales y Museo
Universidad Nacional de La Plata
La Plata, Argentina.

In addition to Nelson, Bozzi, Malaspinas, Delgado, Greub, and Fehren-Schmitz, Nasreen Broomandkhoshbacht, now at the University of Vermont, also co-led the research, working with Kalina Kassadjikova of the University of California, Santa Cruz; Jane Buikstra of Arizona State University; Carlos Eduardo G. Amorim of California State University, Northridge; Melissa Estrada Pratt of the Instituto Colombiano de Antropología e Historia in Bogotá, Colombia; Nicolas Rascovan of the Institut Pasteur in Paris; and David Šmajs of Masaryk University in the Czech Republic.

Publication:
Davide Bozzi et al.
A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia.
Science 391, eadw3020 (2026). DOI: 10.1126/science.adw3020

Structured Abstract

INTRODUCTION
The origins and early diversification of Treponema pallidum subspecies, which cause syphilis, yaws, and bejel, remain poorly resolved despite paleopathological evidence for treponemal disease in pre-Columbian populations. Sparse genomic data from ancient, precolonial contexts create a multimillennial disconnect between osteological evidence of treponematosis and its molecular record.

RATIONALE
To better resolve the evolutionary history of T. pallidum, we performed genomic reconstruction and analysis of pathogen DNA detected in shotgun-sequenced DNA data for a human population genomics project. Although the skeleton showed no macroscopic signs of treponematosis, our metagenomic screening identified T. pallidum in an individual who died ~5500 years ago [5464 to 5309 calendar years before the present (cal yr B.P.), 2σ] and was excavated from Middle Holocene contexts of the Tequendama I rock shelter in Sabana de Bogotá, Colombia. We applied multiple methods (competitive mapping, phylogenetics reconstructions, genome-wide average nucleotide identity statistics, and patristic distance) to confidently identify this pathogen as T. pallidum, reconstruct the genome (TE1-3), and evaluate its relationship to other genomically characterized Treponema. With this genome, we inferred divergence estimates of TE1-3 from other T. pallidum to reconstruct the early diversification of T. pallidum subspecies.

RESULTS
Our analyses place TE1-3 as an early-diverging sister lineage to all modern T. pallidum subspecies, unveiling a previously unknown subspecies. Bayesian molecular clock analyses estimate the divergence between TE1-3 and other T. pallidum lineages to ~13,700 years ago [95% highest posterior density (HPD): 6768 to 20,592 cal yr B.P.]. This suggests that the divergence between TE1-3 and the modern, genomically characterized T. pallidum subspecies occurred during the Late Pleistocene to Early Holocene, closely following the peopling of the Americas, whereas the diversification of the known subspecies themselves took place more recently, within the Holocene ~6000 cal yr B.P. (3622 to 9452 cal yr B.P. 95% HPD). After assessing the breadth of coverage, we determined that TE1-3 likely possessed virulence-associated genes found in modern T. pallidum strains, suggesting similar genetic potential for virulence.

CONCLUSION
Our results show the presence and previously unknown diversity of T. pallidum from a Middle Holocene hunter-gatherer context in Sabana de Bogotá, Colombia, extending the genomic record of treponematoses by more than three millennia. TE1-3’s early divergence supports models in which treponemal pathogens had already diversified in the Americas during the Holocene. The availability of this ancient South American genome provides a rare calibration point for reconstructing the early diversification of T. pallidum subspecies. This study also underscores the value of metagenomic screening of ancient remains to uncover previously undetectable infectious disease histories in deep time. These findings open new questions about the timing, routes, and drivers of treponemal spread, and on the longstanding interplay among Treponema pallidum, human hosts, and the broader socioecological landscapes in which these diseases have evolved, persisted, and spread to affect human populations.

Deeply divergent Treponema pallidum lineage in the Americas and implications for pathogen evolution.
We identified and reconstructed a ~5500-year-old 1.7× T. pallidum (TE1-3) from a Middle Holocene individual at Tequendama I rock shelter in Colombia. Phylogenomic analysis reveals that TE1-3 is an early-branching sister lineage to all extant T. pallidum subspecies, with divergence dating to ~13,700 years ago (95% HPD: 6768 to 20,592 cal yr B.P.) and coinciding with early human migration and ecological shifts in the Americas. Despite its antiquity, TE1-3 possesses the T. pallidum virulence-associated genes, suggesting conserved pathogenic capacity. TE1-3 provides the earliest molecular evidence of T. pallidum in the Americas to date, bridging a multimillennial gap between skeletal signs and genomic data and offering a rare glimpse into the long-term evolution of treponemal pathogens. [Figure created in BioRender]

Abstract Treponematosis, a bacterial infection caused by Treponema pallidum subspecies and T. carateum (yaws, bejel, syphilis, pinta), has afflicted humans for millennia. Despite paleopathological evidence and emerging genomic data, little is known about the evolutionary history of these pathogens. We report a 5500-year-old Treponema genome (TE1-3) from Middle Holocene hunter-gatherer contexts of the rock shelter Tequendama I in Colombia. Our analyses place TE1-3 as a sister lineage to all known T. pallidum subspecies, positioning this pathogen in the Americas millennia before European contact and before diversification of the subspecies causing syphilis, yaws, and bejel. This discovery broadens the known diversity of T. pallidum while extending the genomic record of treponemal pathogens by millennia, providing molecular support for a deep history of T. pallidum in the Americas.

Davide Bozzi et al.
A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia.
Science 391, eadw3020 (2026). DOI: 10.1126/science.adw3020

© 2026 American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

The significance of this discovery extends beyond adding another ancient infection to the medical history books. Here is physical evidence of a treponemal pathogen infecting a person in South America some 5,500 years ago, together with genetic evidence of a much older evolutionary ancestry. The precise timing of that ancestry remains open to refinement, but the relationships are intelligible in terms of branching descent and genetic change. Evolution provides the framework for investigating the evidence; biblical mythology provides a chronology into which that evidence must somehow be squeezed.

For those who insist on a worldwide flood that exterminated terrestrial life outside the Ark, ancient pathogens present an awkward question. How did the surviving lineages persist when their hosts were supposedly destroyed? This particular Colombian branch need not have survived, but its modern relatives still require an explanation. Invoking infected passengers merely turns the Ark into a means of preserving infections alongside their hosts. Invoking miraculous protection adds another unsupported intervention, apparently necessary to ensure that disease remained available to afflict the descendants of the chosen survivors.

Intelligent design offers no improvement. If the biological machinery that enables these bacteria to infect their hosts is evidence of deliberate engineering, then its harmful consequences belong in the assessment of the supposed engineer. Calling beneficial biological features “designed” while treating pathogenic ones as somebody else’s responsibility is special pleading. Evolution requires neither benevolent intentions nor malevolent ones: inherited variations persist when they favour survival and reproduction, even when that success comes at another organism’s expense.

Meanwhile, the scientists are doing what science does best: recovering evidence, testing relationships, acknowledging uncertainty and revising our understanding of the past. Their discovery reveals another part of the long, unplanned history shared by humans and their pathogens. No foresight, no special creation and no supernatural rescue operation are needed to explain why that history takes the form of an evolutionary family tree.

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