Around 40,000 years ago, the giant kangaroo disappeared from Australia. So did Diprotodon (rhinoceros-size wombats) and Palorchestes (tapirlike marsupials) as well as supersize birds, reptiles and some 50 other so-called megafauna—big animals. And now a record of fungal spores pulled from the swamp at Lynch's Crater in the northeastern corner of the continent reveals humans as the culprit.

"The megafauna declined soon after the time that we know people arrived in the region," explains zoologist Christopher Johnson of the University of Tasmania, lead author of the report published March 23 in Science. "We conclude that humans, not climate, caused the extinction."

The basis for the charge rests on two mud cores—one stretching from around 130,000 years ago to 24,000 years ago and the other ranging from roughly 50,000 years ago 3,000 years ago. The long core reveals how the local environment reacted to two previous periods of cooling and drying. Judging by the Sporormiella fungus—which only releases its spores when in the dung of plant-eating animals—big animals fared well during these climatic changes, munching happily on the changing vegetation of the area.

That changed roughly 41,000 years ago, when the number of spores in the core "dropped almost to zero," the researchers wrote. The record in mud also notes an increase in charcoal from large-scale fires and new types of vegetation—eucalyptus trees and the like with grasses beneath, much as seen today. A shift in climate could alter plant populations, but this vegetation change actually precedes by roughly 10,000 years the most recent climate shift within the core's age, to cooler and drier conditions. "Climate change played no role in megafaunal extinction in Australia," Johnson concludes.

Using the second core, the researchers then focused on the period between 43,000 years and 38,000 years ago to try to understand how humans eliminated the megafauna. Humans could have hunted them to extinction or set fires that changed the landscape so much that large herbivores could not survive. But examining the core in 100-year increments showed that the shifts in vegetation happened after the near disappearance of Sporormiella spores—not before as would have been expected if fire-triggered vegetation changes had caused the extinctions. "It could not have been vegetation change due to firing of the landscape, as other people have proposed, because those things followed megafaunal decline," Johnson argues.

In fact, the disappearance of the big plant-eaters seems to have set the stage for fires, allowing the buildup of the dry grasses and other fine fuels that spur burning like the catastrophic wildfires still seen in Australia today. At Lynch's Crater, the disappearance of the large plant-eaters saw an increase in grasses within 300 years, then acacias, eucalyptuses and other hard-leaved plants within 400 years, and, ultimately, a rise in the pollen from forest trees some 1,600 years later. Even today, many of the plants still extant in Australia boast features such as protective spines that would discourage grazing by megafauna or big fruit and seeds that could only be dispersed by large animals that no longer exist—a landscape shaped by ghosts. "These plants are now anachronistic," Johnson observes.

The findings seem to close the case against modern human hunters, although they remain to be confirmed at other sites throughout the continent. And, on every continent except Africa, human arrival and large animal extinctions seem to coincide, so the case may also extend globally. (The reason large animals did not vanish in Africa is perhaps because they co-evolved with us and learned to be wary of this stalking, hairless, upright ape.)

An analysis of ancient DNA from extinct species such as woolly mammoths and rhinoceroses suggests that "climate has been a major driver of population change over the past 50,000 years," according to a 2011 Nature paper that also suggests climate and humans may have colluded to push such species to extinction. (Scientific American is part of Nature Publishing Group.) Johnson, for one, isn't sure climate should be blamed. "Extinctions in other parts of the world were remarkably similar in pattern and severity to those that occurred in Australia," he notes. After all, human hunting wiped out similar species from in neighboring New Zealand less than a millennia ago. "This seems to strengthen the view that human impact—mainly hunting—was the predominant cause in other places as well as in Australia."

As for the specific weapons and techniques, they remain unknown. "It is almost certain that hunting of large animals was one of the things [early Australians] did, but we'll probably never know exactly how they did it," Johnson says. In this case, it wasn't the weapons that fingered the perpetrators but an absence of fungal spores that reveals an ancient human deed.