There has been long-running debate over how the smallpox outbreak that devastated the indigenous population in Australia began in 1789. Now, a new modeling study has a possible answer: It was brought to Australia by the “First Fleet” of British ships to settle in 1788.
The finding is based on mathematical modeling of the disease’s impact on Indigenous Australians and rejects the contrary idea that the outbreak originated through contact with Indonesian islanders fishing in the country’s far north.
allan williams — An archaeologist at the private firm EMM Consulting and co-author of the study, published July 9 in the journal nature human behavior – told Live Science that the likely source of the outbreak were vials of dried smallpox scabs that British doctors kept to administer inoculations (a precursor to smallpox vaccines, which were not) Invented by Edward Jenner until the 1790s).
Some historians had argued that live smallpox virus could not have survived the eight-month ship voyage from Portsmouth, England, to Botany Bay, now the modern city of Sydney, where British ships first landed.
But investigation revealed that the smallpox scab vials may have been refilled during the voyage, when the fleet stopped in Cape Town, South Africa, or Rio de Janeiro, Brazil, just a few months earlier, Williams said.
Smallpox outbreaks devastated indigenous communities and contributed to the rapid demise of indigenous Australian culture, he said. Studies estimate that approximately 220,000 people died from the disease, and Australian officials in the early 20th century did not understand the true extent of the indigenous population when attempting to document historical accounts.
wrath of mystery
Within a few decades of British Royal Navy officer James Cook charting Australia, the British sent ships to settle the continent. The British “First Fleet” to Australia consisted of 11 ships: two naval ships, six convict transports and three ships for provisions. The British claimed that Australia did not legally belong to anyone. They soon left Botany Bay because the land and water there were poor, and moved to Sydney Cove in Port Jackson, now part of modern Sydney. There, he raised the British flag, claiming the entire continent.
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There was no sign of smallpox spreading in nearby indigenous communities when the First Fleet arrived, but in the decades that followed the disease had a devastating impact. Since there were no recorded cases of smallpox in the fleet, it was argued that the disease may have reached Australia through contact with islanders from the Makassar region of Sulawesi, on the tropical north coast of the continent, now part of Indonesia.
But new computer modeling of the proposed north coast outbreak showed the disease could not have spread from there to Australia’s southeast. Williams said that, among other issues, the two regions were separated by thousands of miles of uninhabited desert. Meanwhile, researchers found that modeling of smallpox outbreaks in indigenous communities near Port Jackson indicated that the outbreak originated there.
co-author Matthew Cody NitschkeAn expert in computer modeling at Flinders University in Adelaide told Live Science that it is now clear that the outbreak had a very low probability of originating in the north; On the contrary, “there is very strong evidence that this was the First Fleet.”
In those days, disease theory was not knownSo the spread of smallpox may have been accidental, Williams said.
An Indigenous Australian man holds traditional weapons during a ceremonial dance at the Laura Quincan Dance Festival in Cape York, Australia. New estimates place Australia’s theoretical population capacity of up to 5 million indigenous people before British arrival.
(Image credit: Chameleon via Getty Images)
modifying earlier ideas
The new study in Nature Human Behavior refers to another study by the same researchers that is now being prepared for publication by the same journal. It is proposed that there were up to three million Indigenous Australians at the time of the arrival of the First Fleet – up from the 300,000 or more proposed in some earlier studies.
A second study based on archaeological investigation of early indigenous Australian communities suggests that Australia had a theoretical population capacity of up to 5 million people before British arrival, particularly in the resource-rich areas of the north and southeast.
The earlier estimate of approximately 300,000 Indigenous Australians appears to have come from a study in the 1930s based only on their declining numbers. “By the time people really sat up and pointed out how many people were here, we had 100 years of disease, frontier violence and everything else going on,” Williams said.
Historians at the University of Tasmania henry reynoldsThose who were not involved in the study told Live Science that the research rejects the longstanding idea that the smallpox outbreak began on the North Coast. “The idea that it came from the north and arrived at exactly the same time [as the First Fleet] Was always impossible,” he said.
Ann McGrathA historian at the Australian National University in Canberra, who was not involved in the work, agreed. “The strong interdisciplinary approach of this latest research strongly refutes this, and it also provides a greatly expanded estimate of the Indigenous population before 1788,” he said in an email.
Nitschke, M., Williams, A., Ingre, S., Griffiths, B., Pitt, N., Russell, L., Ulm, S., Beller, K., Bird, M., Fatima, S., McNiven, I., Saltre, F., Bashford, A., Wilson, C., and Bradshaw, C. (2026). Stochastic models indicate rapid smallpox spread and mass death of Indigenous Australians following colonial exposure. nature human behavior. https://doi.org/10.1038/s41562-026-02504-6