New research using stochastic modeling has resolved a 237-year-old historical mystery: the devastating smallpox outbreak that swept through Indigenous Australian communities in 1789 was almost certainly caused by British colonizers, specifically, vials of dried smallpox scabs carried aboard the First Fleet.
The study, published July 9 in Nature Human Behaviour by researchers from Flinders University and EMM Consulting, combines epidemiological modeling with historical evidence to trace the outbreak’s origin. The conclusion is firm: the variola virus that killed an estimated 220,000 Indigenous people was introduced by the British, not by Indonesian fishermen from the north as some historians had proposed.
A debate settled
For decades, historians debated whether the 1789 smallpox epidemic had arrived with the British First Fleet (which landed at Botany Bay in January 1788) or whether it had trickled south from Makassan (Indonesian) sea cucumber fishermen who visited Australia’s northern coast. The new study’s computer modeling found the northern-origin hypothesis untenable.
“The disease could not have spread from the north coast to the Sydney region,” said Matthew Cody Nitschke of Flinders University, a co-author. The two regions are separated by thousands of kilometers of sparsely inhabited desert, a barrier the variola virus, which requires close human contact, could not have crossed in the time frame observed.
“By contrast, there is very strong evidence that it was the First Fleet,” Nitschke said.
The likely source: dried smallpox scabs that British medics carried for inoculation.
Inoculation, not vaccination
The distinction matters. Edward Jenner’s smallpox vaccine, using the milder cowpox virus, would not be developed until 1796. In 1788, the practice was variolation: deliberately exposing a person to material from a mild smallpox case (often dried scabs) to induce a controlled infection and lasting immunity. It was effective but carried real risk. Variolated individuals could transmit the full disease.
British surgeons on the First Fleet carried dried scabs for this purpose. Some historians previously argued the variola virus could not survive the 8-month voyage from Portsmouth to Botany Bay. The new study notes that the fleet stopped at Cape Town and Rio de Janeiro, both locations where smallpox was endemic, and where fresh scabs could have been obtained just months before the fleet reached Australia.
When terra nullius met smallpox
The outbreak hit in April 1789, about 15 months after the First Fleet’s arrival. For the Indigenous population, which had no prior exposure to the virus and therefore no immunity, the result was apocalyptic.
Henry Reynolds, a historian at the University of Tasmania who was not involved in the study, put it bluntly: “The idea that it came from the north and arrived at exactly the time [as the First Fleet] was always improbable.”
The outbreak was not the result of deliberate biological warfare. 18th-century medicine lacked the germ theory needed for such intent. But whether through accidental contamination or a variolation attempt gone wrong, the result was the same: one of the most deadly epidemics in Australian history, unfolding on a continent the British had claimed under the legal fiction of terra nullius, land belonging to no one.
Rethinking pre-colonial population
A companion study also being prepared for Nature Human Behaviour is re-estimating the Indigenous Australian population before British arrival. The current widely cited figure of approximately 300,000 comes from a 1930s study, a calculation made after a century of disease, frontier violence, and dispossession.
The new estimate, using archaeological and ecological carrying-capacity models, suggests the pre-colonial population may have been as high as 3 million people, with a theoretical upper bound of 5 million, especially in resource-rich coastal and riverine regions.
“By the time people actually sat down and said how many people were here, we had 100 years of disease, frontier violence, and everything else going on,” said Alan Williams of EMM Consulting, a co-author.
Ann McGrath of the Australian National University, a historian not involved in the study, called the interdisciplinary approach “convincing.”
“It refutes this longstanding alternative hypothesis, and it also provides a much expanded estimate of the Indigenous population prior to 1788,” she said.
What the modeling shows
The team used stochastic epidemiological models that simulate disease spread through populations with varying contact rates, travel distances, and immunity levels. The models consistently showed that a southern introduction via Sydney Cove was compatible with the outbreak’s observed timing and reach, while any northern source was unable to propagate the disease to the southeast within the documented period.
The study brings a form of closure to a question that has divided Australian historians for generations, and does so with quantitative tools that were unavailable to earlier generations of researchers. It also recasts the British colonization of Australia in a starker demographic light, a continent that was not empty, but catastrophically depopulated, before most European settlers ever ventured inland.
Reference: Nitschke, M., Williams, A., Ingrey, S., et al. (2026). “Stochastic models indicate rapid smallpox spread and mass mortality of Indigenous Australians after colonial exposure.” Nature Human Behaviour. DOI: 10.1038/s41562-026-02504-6