Syphilis did not jump to humans from a single animal in one dramatic event. The bacterium behind the disease, Treponema pallidum subspecies pallidum, belongs to a family of nearly identical microbes that have been infecting both humans and other primates for thousands of years. The closest animal relatives of the syphilis bacterium are found in wild African primates, particularly baboons and green monkeys, which carry their own strains of T. pallidum. But how the venereal form of syphilis specifically arose in humans remains one of the most contested questions in infectious disease history, and recent ancient DNA discoveries have scrambled assumptions that held for decades.
The Primate Connection
Wild baboons across sub-Saharan Africa have been known for decades to harbor Treponema pallidum, the same species of bacterium responsible for syphilis, yaws, and bejel in humans.1PLOS ONE. Treponema pallidum Infection in the Wild Baboons of East Africa: Distribution and Genetic Characterization of the Strains Responsible These are not just distantly related bacteria that happen to share a name. They are so genetically similar to human strains that they sit on the same phylogenetic tree. When researchers built that family tree using DNA sequences, the strains carried by baboons and other African primates turned out to closely resemble the oldest, most ancestral forms of the pathogen.2PLOS Neglected Tropical Diseases. On the Origin of the Treponematoses: A Phylogenetic Approach
The primate reservoir is not limited to baboons. Surveys across sub-Saharan Africa have found the yaws-causing subspecies (T. pallidum subsp. pertenue) in nonhuman primates broadly.3PubMed Central. Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue In Senegal, researchers documented a venereal form of T. pallidum subsp. pertenue in green monkeys, then watched an outbreak spread to baboons a year later.4PubMed Central. Epidemic of venereal treponematosis in wild monkeys: a paradigm for syphilis origin That observation is striking because it shows the bacterium can shift its mode of transmission within a primate population, moving from skin-to-skin contact to a sexually transmitted pattern. If it can do that in monkeys, it could have done the same thing in our own lineage.
Why the Rabbit Gets Mentioned
If you have read anything about syphilis research, you have probably seen rabbits come up. Rabbits are the primary lab animal used to study syphilis because they can be experimentally infected with the human syphilis bacterium. But rabbits also carry their own natural treponeme: Treponema paraluiscuniculi, the cause of rabbit venereal spirochetosis. Despite being extremely close genetically to the human syphilis strain, sharing roughly 98.6 to 99.3 percent sequence similarity in the regions that have been compared, the rabbit pathogen cannot infect humans.5PubMed Central. Genome differences between Treponema pallidum subsp. pallidum strain Nichols and T. paraluiscuniculi strain Cuniculi A
The reason appears to be genome decay. When scientists sequenced the full genome of the rabbit treponeme, they found it packed with broken genes and gene fragments, far more than the human strains carry.6PLoS ONE. Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay All that damage has apparently stripped away whatever the bacterium once needed to establish infection in a human host. The rabbit treponeme matters for understanding the evolutionary family tree of these bacteria, and it serves as a useful outgroup for comparison, but it is not a source of human syphilis. The real candidates sit on a different branch entirely, among the primate-infecting strains.
How Yaws, Bejel, and Syphilis Relate
Syphilis does not exist in isolation. It is one of at least three human diseases caused by subspecies of the same bacterium. Yaws, caused by T. pallidum subsp. pertenue, spreads through skin contact and produces ulcerating lesions, typically in tropical regions. Bejel, caused by T. pallidum subsp. endemicum, spreads among children through shared eating utensils or casual contact in arid environments. Syphilis, caused by T. pallidum subsp. pallidum, spreads sexually and can ultimately invade the nervous system and cardiovascular system. All three share remarkable similarities in how they cause disease and in their genetic makeup, to the point that no clear biological basis for their differences has been identified.7PubMed Central. The endemic treponematoses
This is important for the “what animal” question because it reframes it. The ancestor of syphilis was probably not a completely different disease that jumped species in a single leap. More likely, a treponeme that was already infecting humans in a non-venereal way, something like yaws, eventually evolved the ability to spread sexually. The phylogenetic evidence supports this: yaws-like strains from central Africa and the South Pacific sit at the base of the family tree, meaning they most closely resemble whatever the original human-infecting treponeme looked like.2PLOS Neglected Tropical Diseases. On the Origin of the Treponematoses: A Phylogenetic Approach The simian strains in African baboons sit close to these basal yaws strains, which strongly suggests the ancestor of all human treponematoses was shared with, or passed between, humans and other primates in Africa deep in prehistory.
The Columbian Hypothesis and Where Syphilis Emerged
For over a century, the dominant story went like this: Columbus’s crew encountered syphilis in the Americas in the 1490s and brought it back to Europe, where it exploded into a devastating epidemic. This is the Columbian hypothesis, and it has some powerful circumstantial evidence behind it. Syphilis first appeared in European medical records in the mid-1490s, right after Columbus returned. The epidemic’s speed and severity suggest a population with no prior exposure.
The alternative, the pre-Columbian hypothesis, argues that syphilis already existed in Europe and was simply not recognized as a distinct disease before the 1490s. For years, proponents pointed to skeletal remains from medieval Europe that seemed to show syphilis-like bone damage. But when these cases have been subjected to rigorous review, the evidence has generally not held up well. A careful reanalysis of supposed pre-Columbian syphilis cases in Europe found that the evidence did not withstand scientific scrutiny.8PubMed Central. The science behind pre-Columbian evidence of syphilis in Europe: research by documentary That said, a small number of cases remain intriguing. A skeleton from a Spanish necropolis dated to the 9th through 11th century, studied using a combination of pathological and histological techniques, showed signs consistent with third-stage acquired syphilis.9Anthropological Science. Treponemal disease in the Old World? Integrated palaeopathological assessment of a 9th–11th century skeleton from north-central Spain Such cases have never been confirmed by recovering actual treponemal DNA, however, so they remain contested.
In the Americas, the picture is clearer. Skeletal evidence of treponemal disease in the New World predates Columbus by centuries. One striking case involves a pre-Columbian individual from northern Chile, dated to around 210 BC, whose remains show bone damage consistent with a thoracic aortic aneurysm. The researchers argue this aneurysm had a syphilitic cause, based on the specific blood vessels involved and the fact that syphilis was the leading cause of such aneurysms before antibiotics were available.10PubMed. Thoracic aortic aneurysm in a pre-Columbian (210 BC) inhabitant of Northern Chile: Implications for the origins of syphilis Phylogenetic modeling has been broadly consistent with an American origin scenario, with molecular clock estimates placing the divergence of treponeme subspecies well before Columbus.11PLoS Neglected Tropical Diseases. Syphilis at the Crossroad of Phylogenetics and Paleopathology
Ancient DNA Scrambles the Story
Bones can only tell you so much. The bone changes caused by syphilis overlap with those caused by yaws, bejel, and even some non-treponemal conditions. For decades, paleopathologists argued over ambiguous skeletons. Ancient DNA has begun to resolve these arguments, and the results have been surprising.
In 2023, a team recovered treponemal genomes from nearly 2,000-year-old human remains in Brazil. These are among the oldest treponeme genomes ever sequenced, and they did not match what anyone expected. The ancient pathogen was most closely related to the bejel-causing subspecies, T. pallidum endemicum, not to syphilis or yaws. Bejel today is associated with dry, arid climates, yet here it was in prehistoric tropical Brazil. The finding directly contradicts the assumption that you can identify a treponeme subspecies based on the climate zone where the infected person lived.12PubMed Central. Redefining the treponemal history through pre-Columbian genomes from Brazil The high-quality genome from this study also allowed better molecular clock estimates, pushing the divergence of modern T. pallidum subspecies firmly into pre-Columbian times.
A follow-up study published in 2025 went further, analyzing five pre- and peri-contact ancient treponemal genomes from the Americas. These represented ancient relatives of all three modern subspecies: syphilis, yaws, and bejel. The results pointed to previously unexplored diversity and supported the conclusion that T. pallidum emerged in the Americas, with the ancestor of all currently characterized strains tracing back to the New World.13PubMed Central. Ancient genomes reveal a deep history of Treponema pallidum in the Americas Meanwhile, when researchers examined 16th-century remains from Europe, they found a surprisingly high diversity of T. pallidum strains circulating in early modern Europe, consistent with multiple introductions or a rapid diversification after arrival.14Current Biology. 16th-Century Materials Document a Variety of Treponema pallidum Strains in Early Modern Europe
These genetic findings have complicated the old framing. If all characterized T. pallidum lineages trace to the Americas, but the oldest yaws-like strains in living primates are African, something does not add up neatly. One possibility is that the earliest treponeme crossed into humans from African primates, traveled with human migrations into the Americas, diversified there over thousands of years, and then one branch evolved venereal transmission and was carried back to Europe. Another possibility is that we simply have not yet recovered ancient treponemal DNA from Africa or Asia to fill in the gaps. Researchers openly acknowledge that the mystery may be partly a product of where they have been able to look so far.
So Did an Animal Actually “Give” Us Syphilis?
The honest answer is that syphilis is not really a zoonotic disease in the way most people imagine. When people ask “what animal did syphilis come from,” they tend to picture something like a bat giving us rabies or a civet giving us SARS: a clean, one-time jump from an animal host to a human one. The treponeme story does not work that way. Humans and nonhuman primates in Africa appear to have been sharing closely related treponemes for a very long time, possibly since before the split between yaws-like and syphilis-like strains even existed. The primate strains are not the direct ancestor of syphilis; they are more like cousins on a shared family tree.
Yaws, not syphilis, is the likely original human treponematosis. It spread through skin contact in warm, humid environments, and its closest relatives are found in African primates. At some point, a lineage of this skin-contact pathogen adapted to survive in a new niche, one that relied on sexual transmission rather than casual skin-to-skin contact. That adaptation is what we call syphilis. Whether it happened in Africa, the Americas, or somewhere along the human migration route between them remains unclear. What is increasingly clear is that it happened within human populations over thousands of years, not in a single dramatic leap from an animal.
Why Primate Reservoirs Still Matter
Even though syphilis is not a recent animal-to-human spillover, the fact that wild primates carry closely related treponemes has real implications. The outbreak documented in Senegalese green monkeys showed how quickly the bacterium can spread through a primate population and shift its transmission route.4PubMed Central. Epidemic of venereal treponematosis in wild monkeys: a paradigm for syphilis origin Researchers have flagged the risk of cross-species transmission in areas where humans and wild primates are in close contact, particularly in national parks and research stations where baboons and people overlap.15bioRxiv. Risk Factors and Patterns of Treponema Infection Affecting Olive Baboons in Gombe National Park
The concern is not that baboons will “re-infect” humans with syphilis. Humans already have syphilis; it circulates among us without any animal reservoir needed. The concern is more subtle. Primate treponemes represent a pool of genetic diversity. If a primate strain were to recombine with or swap genetic material with a human strain, it could theoretically produce something new, perhaps something with different antibiotic susceptibilities or different tissue preferences. This has not been documented, and the risk is speculative. But as deforestation and human encroachment push people and primates into closer proximity, researchers argue it is worth monitoring.
What the Llama and Sheep Myths Get Wrong
Popular accounts have sometimes blamed syphilis on llamas, sheep, or cattle. These claims have no scientific support. They tend to originate from either early colonial-era speculation, which blamed Indigenous peoples and their livestock for European diseases, or from confused readings of early Spanish accounts. No livestock species has ever been found to carry Treponema pallidum or any closely related treponeme. The bacterium’s entire known natural range is limited to humans, nonhuman primates, and rabbits, and the rabbit treponeme, as noted earlier, cannot infect people.
The llama hypothesis specifically seems to trace to a 1994 book that proposed Columbus’s sailors contracted syphilis from llamas. There is no genetic, microbiological, or veterinary evidence for llamas serving as a treponeme reservoir. Llamas were never common in the Caribbean islands where Columbus’s crew spent their time, which makes the story geographically implausible on top of being biologically unsupported. The persistence of these myths says more about our desire for a simple origin story than about the actual biology.
What Ancient DNA Might Settle Next
The recovery of ancient treponeme genomes is still in its early years. Almost all the ancient DNA work so far has come from the Americas and Europe, for the simple reason that those are the regions where archaeological collections have been systematically screened. Africa, where the nonhuman primate reservoir is richest and where the oldest yaws-like strains exist in living populations, has yielded almost no ancient treponemal DNA. The same is true of Asia and the Pacific Islands. If researchers can recover ancient treponeme genomes from African archaeological sites, the phylogenetic picture could shift dramatically.
One possibility that cannot be ruled out is that the treponemes found in the Americas descend from an African ancestor that arrived with the first human migrations across Beringia more than 15,000 years ago. If so, the “American origin” supported by current genomic data would really mean “American diversification” of a pathogen whose ultimate roots are African. Alternatively, there may have been multiple independent introductions of treponemes into human populations from primate hosts at different times and places, with the one that happened to evolve venereal transmission becoming the lineage we now call syphilis. These are not just academic questions. Understanding how and where the bacterium gained the ability to spread sexually could help explain why syphilis behaves so differently from yaws and bejel despite being caused by a nearly identical organism, an answer that after more than 500 years of asking, we still do not have.