A lithograph depicting Indigenous Australians and the arrival of Cook and his crew, titled “Captain Cook’s Landing at Botany, AD 1770”. Credit: National Library of Australia

On a hot January day in 1788, 11 British ships commanded by Arthur Philip sailed into Sydney Harbor carrying convicts, sailors, marines and the machinery of a new colony. The location was first charted by British explorer Captain James Cook just a few years ago in 1770.

For thousands of years prior to European settlement, the harbor’s foreshores were inhabited by Indigenous Australian groups, including the Darug, Guringai, and Gadigal peoples. We don’t know what those people thought when they saw this armada land on their shores, but some may not have seen this intrusion as a good omen. Indeed, within little more than a year, their world was struck by something the newcomers recognized and the local people had no immunity against.

Smallpox.

British officers later described bodies in coves, inlets and rock shelters. Paths that had been busy fell silent and camps emptied. “There are a significant number of Aboriginal people perishing in horrible, ghastly circumstances from what sounds like smallpox,” Lynette Russell, a historian at Monash University, told Science. “By 1789, a horrendous depopulation has occurred.”

Now, two new studies investigated where that disease came from and how many lives the British Empire’s colonization of Australia ultimately cost.

The first uses computer models to ask whether smallpox could really have traveled from northern Australia to Sydney, as previously suggested, before colonists noticed the outbreak. The answer, the researchers argue, is no: the 1789 epidemic most likely began in southeastern Australia after the First Fleet arrived.

The second study asks how many people were affected. It estimates that Australia was home to roughly 2.5 million Indigenous people before British invasion, far above older estimates of a few hundred thousand. If that figure is right, colonization and its cascading effects — disease, violence, hunger, displacement and social collapse — caused about 2.4 million excess deaths by 1861.

A Mystery Born From a Delay

The origin of the smallpox epidemic that ravaged Australia’s Aboriginal population has been a point of contention.

If smallpox came with the First Fleet, why did it not appear immediately? One must consider the ships had been at sea for months. Smallpox usually moves fast through susceptible people. Patients die or recover within weeks. If someone had carried an active infection aboard, the outbreak should have burned out long before the ships reached Sydney.

Henry Reynolds, a University of Tasmania historian not involved in the new work, told Science that the voyage itself looked like “the most effective quarantine situation imaginable.”

So, perhaps the disease came from elsewhere. Long before the British arrived in Sydney, Makassan trepang fishers from what is now Indonesia had contact with Aboriginal communities along Australia’s northern coast. Smallpox was also circulating in parts of the Malay Archipelago in the late 18th century. This is why some researchers have proposed that the disease entered Australia from the north, then moved south through trade routes, gatherings and river corridors until it reached Sydney.

It was a plausible story in outline. But the new model tested whether it could actually work.

The researchers divided the continent into hundreds of Indigenous language and cultural groups, then simulated how people might have moved between neighboring regions for trade, ceremony and other types of contact. They then introduced smallpox and its main characteristics, such as its incubation period, infectious stage and high fatality in people with no prior exposure.

The northern route failed.

“No matter how bad we assume the disease to be, it couldn’t have made it from the north to Sydney at the right time,” Corey Bradshaw, a Flinders University ecologist and co-author of both papers, told Science. “It’s beyond a shadow of a doubt” that it came with the fleet.

The Disease Did Not Need to Cross a Continent

Smallpox usually burns through an isolated population, such as those living on a ship, fairly quickly. A person becomes infected, develops symptoms after about 12 days, then either dies or recovers within weeks. The First Fleet had spent months at sea. If smallpox had been spreading among the passengers, British officers almost certainly would have noticed illness and deaths before the ships reached Australia.

The researchers of the new studies instead point to another possibility: the virus may have arrived not in a sick body, but in preserved infectious material.

Before modern vaccination, some doctors practiced variolation. They collected smallpox matter — often dried scabs or fluid from pustules — and introduced it into small cuts in the skin. The goal was to cause a milder infection that would protect a person from a more dangerous one later. It was risky, but in the 18th century it was one of the few tools doctors had against smallpox.

We know the First Fleet carried surgeons and the authors argue that at least one of them may have had access to variola matter, either before leaving Britain or during stops in Rio de Janeiro or Cape Town. Earlier historians doubted this because heat can damage the virus, but the paper notes that previous research has shown smallpox material could have survived the temperatures recorded during the voyage.

This would explain the long delay. The virus did not need to circulate among sailors or convicts in 1788. It only needed to remain viable somewhere in the colony until Aboriginal people were exposed.

The researchers then modeled what happened after that exposure. The 1789 epidemic did not sweep across the whole continent. It most likely began around the Sydney region, then spread through southeastern Australia along the places where people moved: coastal corridors, harbor communities and major river systems such as the Murray and Lachlan.

In those areas, the toll was enormous. Using a 60 percent fatality rate, based on global smallpox data, the researchers estimate that the first epidemic killed between 40,000 and 240,000 Indigenous people. That range is wide because no one counted the dead at the time, and because the model has to estimate population density, movement and transmission from incomplete evidence. But even the low end would have devastated communities.

The study stops short of answering the most explosive question: whether anyone in the colony exposed Aboriginal people to smallpox on purpose.

That would be impossible to answer with such a model. Still, the question of intent hangs over the findings because smallpox had already been discussed as a weapon in other colonial settings. In North America, British commanders had considered spreading the disease among Indigenous communities through contaminated blankets. The researchers point to Dharawal oral traditions that describe disease arriving through tainted goods.

“It would be devastating to find out it was intentional,” Ann McGrath, an Australian National University historian not involved in the study. “But the whole colonial project was intentional and damaging enough without proving smallpox was intentionally spread.”

Counting the People Who Were There

To measure the scale of the disaster, historians first need to know how many people lived in Australia before it began.

For much of the 20th century, common estimates placed the precolonial Indigenous population at a few hundred thousand. Many of those estimates relied on colonial observations made after disease, displacement and violence had already transformed Aboriginal societies.

“There’s been an assumption that Aboriginal populations were quite low and their activities were ephemeral and transient,” said Alan Williams, an archaeologist and co-author.

The second study takes a different approach. It compares several lines of evidence that do not depend mainly on late colonial counts, such as archaeological radiocarbon dates, genetic reconstructions and models of how many people different landscapes could support.

Those methods converge on a much larger number. The paper estimates a median precolonial population of 2.51 million people, with a wide uncertainty range. For that population to fall to the levels recorded in the 19th century, the authors estimate about 2.39 million excess deaths between 1788 and 1861.

“We’re saying previous estimates are out by a factor of 10,” Russell told Science.

That figure does not mean smallpox alone killed millions. The first epidemic was one blow. Later outbreaks, measles, influenza, tuberculosis, frontier killings, loss of land and starvation compounded the damage.

A Different Picture of Australia Before 1788

A larger population of natives changes how readers should imagine precolonial Australia.

It was not an empty continent dotted with isolated bands. It was a continent of many nations, languages and systems of knowledge. Archaeology has already shown that some Indigenous communities built and maintained sophisticated landscapes. At Budj Bim in southeastern Australia, Gunditjmara people created channels, weirs and ponds for eel aquaculture over at least 6,600 years, now recognized by UNESCO as a World Heritage cultural landscape.

Smallpox was declared eradicated by the World Health Organization in 1980, the only infectious disease to receive that distinction. But in 1789, among people with no immunity, it could move through families and communities with terrifying force.

The present-day Aboriginal and Torres Strait Islander population has been estimated at 984,000 in 2021, according to the Australian Bureau of Statistics. But if the new estimates are right, it also means the population has still not returned to its preinvasion size.

For Shane Ingrey, a Dharawal molecular biologist and co-author, the point is deeply personal.

“The smallpox story was a way that the British could say that there were no more of us in those early times, that everybody was wiped out,” Ingrey told Science. “We want to undo the myth” of an empty continent.