Genomic data from hundreds of koalas has established that their numbers started falling sharply around 100,000 years ago, well before humans first set foot in Australia. The finding, published on 9 June 2026 in Molecular Biology and Evolution, replaces earlier estimates based on borrowed mutation rates from distant species and offers a clearer separation between prehistoric environmental pressures and the human-driven threats koalas face today.
Researchers calculated the first direct estimate of the koala mutation rate by sequencing genomes from four parent-offspring trios. They arrived at a figure of 0.87 × 10-9 mutations per base pair per year, roughly half the rate seen in humans. Applying this calibrated evolutionary clock to 457 koala genomes sampled across the animal's range produced a revised demographic history.
The analysis shows koala populations entered a prolonged decline during the late Pleistocene roughly 100,000 years ago. Numbers then crashed through a severe genetic bottleneck nearly 60,000 years ago. All living koalas trace their ancestry to a small surviving group in eastern Australia that later expanded when conditions improved.
Climate, not people, drove the ancient collapse
That collapse coincided with major climate upheavals, advancing glacial periods and habitat transformations, including the spread of the arid Nullarbor Plain around 70,000 years ago. The timing places these events firmly before human arrival on the continent. The study therefore attributes the ancient decline to natural environmental changes rather than any human influence.
This distinction matters. Modern koala populations contend with land clearing, historical hunting, bushfires and disease. The species has been listed as endangered in Queensland, New South Wales and the Australian Capital Territory since 2022. Yet the genomic record demonstrates that koalas have endured dramatic natural cycles of contraction and recovery before. Understanding the depth of that resilience, free from assumptions drawn from less precise proxies, equips conservation efforts with firmer empirical ground.
The research team, which included scientists from the University of Sydney and Texas A&M University, was led by Toby Kovacs, a PhD student at the University of Sydney. Their work supplies a mutation rate tailored to the marsupial order Diprotodontia, a group that also encompasses wombats, kangaroos and possums. Previous studies had relied on rates borrowed from humans or mice, which had pointed to a more recent decline potentially linked to human settlement around 65,000 years ago. The new, directly measured rate corrects that picture.
