Researchers at Flinders University have extracted and sequenced DNA from fossilised megafauna remains in South Australia, revealing that some species persisted until about 35,000 years ago, significantly later than the widely accepted 45,000-year extinction timeline.

The findings, based on remains from several cave sites in the Flinders Ranges, complicate the debate about what caused Australia’s megafauna extinctions. If humans arrived around 65,000 years ago but some megafauna survived until 35,000 years ago, that suggests a more complex extinction process than rapid human-caused overkill.

Professor Jeremy Austin, who leads ancient DNA research at Flinders, said the results surprised the team. “We found well-preserved DNA from giant kangaroos and marsupial lions in deposits dated to 37,000-35,000 years ago. That’s after most researchers thought these animals were extinct.”

Australia’s megafauna, which included giant wombats, marsupial lions, and kangaroos standing three metres tall, disappeared sometime after humans arrived on the continent. Exactly when and why has been debated for decades.

The traditional explanation focused on human hunting as the primary cause, with rapid extinctions occurring within a few thousand years of human arrival. More recent theories emphasise climate change and habitat modification through Aboriginal fire management practices as contributing factors.

Dating megafauna extinction has always been challenging. Radiocarbon dating becomes unreliable beyond about 50,000 years, and many fossil sites have complex depositional histories where remains from different time periods get mixed together.

Ancient DNA provides an independent line of evidence. DNA degrades over time, but under favorable conditions like cool, dry caves, it can preserve for tens of thousands of years. By extracting and sequencing DNA from fossils, researchers can directly verify that an animal existed at a particular time rather than relying solely on associated materials for dating.

The Flinders team used new extraction techniques that recover tiny fragments of degraded DNA that older methods missed. These fragments are only 30-50 base pairs long, compared to hundreds or thousands of base pairs in fresh DNA, but modern sequencing technology can still identify them.

The cave sites where the remains were found likely served as predator dens where marsupial lions and other carnivores brought prey. This created accumulations of bones that became buried and preserved over time.

Some of the DNA came from coprolites, fossilised feces, which preserve DNA from prey species even when bones don’t survive. This is a relatively new research area that’s revealing information about extinct species’ diets and ecosystems.

The research builds on Australia’s growing capabilities in ancient DNA analysis. Australia has unique challenges for this field because the hot climate causes faster DNA degradation than in the Northern Hemisphere where most ancient DNA research has focused.

Finding sites with good DNA preservation required surveying dozens of cave systems and testing hundreds of samples. Most yielded no useable DNA, highlighting how rare preservation conditions are.

The research received funding from the Australian Research Council and the Australian Heritage Council, totaling about $850,000 over four years. Ancient DNA research is expensive because it requires clean room facilities to prevent contamination and sophisticated sequencing and bioinformatics analysis.

The extinction timing debate has implications beyond academic interest. Understanding what caused megafauna extinctions informs conservation efforts for surviving Australian species, many of which face threats from habitat loss, introduced predators, and climate change.

If Australia’s megafauna survived human presence for 30,000 years before declining, that suggests ecosystems were relatively resilient until some tipping point was reached. That could have been climatic, such as the Last Glacial Maximum around 30,000 years ago when conditions became particularly harsh.

Or it could have been cumulative effects of thousands of years of human impacts through hunting and landscape modification that eventually exceeded ecosystems’ capacity to sustain large-bodied species.

Some Indigenous Australian groups have oral histories mentioning large animals that might be megafauna. These stories have sometimes been dismissed by researchers as mythological, but if some megafauna survived until 35,000 years ago, humans and megafauna coexisted for longer than previously thought, making it more plausible that cultural memories could persist.

The research team is now working on extracting DNA from additional sites to verify the findings and hopefully narrow the extinction timing further. They’re also analyzing DNA from smaller animals that survived the extinctions to understand how ecosystems changed.

One interesting aspect is genetic diversity. By comparing DNA from megafauna remains at different time periods, researchers can estimate population sizes and detect whether populations were declining gradually or collapsed suddenly.

Preliminary analysis suggests the giant kangaroo populations were already genetically depleted by 40,000 years ago, indicating small population sizes even before final extinction. That pattern is more consistent with gradual decline than catastrophic collapse.

The ancient DNA techniques developed for this research have applications beyond megafauna. They’re being used to study indigenous plant species, understand how Aboriginal land management shaped ecosystems, and track the spread of dingoes and other introduced species.

Australia’s archaeological and paleontological records are increasingly providing insights into long-term ecosystem dynamics that are relevant for managing contemporary biodiversity. Understanding baselines before European colonisation helps identify what ecosystems might look like in a more natural state.

Whether the revised extinction timeline changes the broader debate about human responsibility for megafauna extinctions is unclear. Humans were still present throughout the period when extinctions occurred, but the extended timeline weakens arguments for rapid overkill and strengthens arguments for complex interactions between human activities, climate change, and ecosystem dynamics.

Additional research results are expected throughout 2026 as analysis of samples from other sites continues. The findings will likely continue generating debate about extinction causes and timing for years to come.