A groundbreaking genomic study has reshaped our understanding of the evolutionary history of the koala (Phascolarctos cinereus), revealing the iconic Australian marsupial experienced a severe population decline around 100,000 years ago, before the arrival of humans on the continent.

All modern koalas are descended from a single, struggling ancestral population that survived harsh climate upheavals, such as glacial periods, and fluctuating cold and dry periods as the Australian tectonic plate moved.  

However, modern koala populations are now facing a new combination of threats, including hunting, land clearing, bushfires and disease. The koala has been listed as endangered across Queensland, New South Wales, and the Australian Capital Territory since 2022.

Led by researchers at the University of Sydney and Texas A&M University, the findings overturn earlier studies that suggest koala populations declined only after humans arrived. The findings were announced in Molecular Biology and Evolution, published by Oxford University Press.

“The study rewrites the timeline for the koala’s genetic history in Australia,” says PhD student Toby Kovacs, who led the research.

“By calculating the mutation rate of modern koala populations, we can estimate and build the genetic timeline backwards all the way to 100,000 years ago to get a glimpse of genetic diversity and the sizes of ancient koala populations.”

“Fossil records are too sparse to know exactly how big koala populations were 100,000 years ago, so studying their genomes offers vital clues to their evolutionary history,” said Mr Kovacs.

“Genomic analyses show that koalas have experienced major population declines in the past due to climate change and habitat loss. When environmental conditions improved, their populations recovered and expanded across much of eastern Australia.

“It’s important to make clear many of the threats facing modern koala populations are caused by humans, which includes habitat loss and hunting.

“Understanding how koala populations responded to past declines and recoveries can help guide the science-based conservation strategies needed to protect the species into the future.”

How scientists rebuilt the koala’s genetic history

The researchers meticulously reconstructed the genetic history of the koala by homing in on the ‘mutation rate’ in its genome (an organism’s genetic information).

For every organism, with each generation and offspring, new mutations (genetic changes) will appear naturally in their genome. The ‘mutation rate’ is the number of new mutations per generation. Each species has a unique mutation rate, with genomes mutating more quickly in some organisms than others.

The researchers sequenced the genomes of four parent-offspring trios and counted the mutations. These were used to calculate a precise koala mutation rate, which was approximately half that seen in humans.

This new mutation rate was a powerful genetic tool that was applied to 457 koala genomes, allowing researchers to investigate changes in koala populations over time.

This is the first study to estimate mutation rates for koalas directly or any species in the marsupial order Diprotodontia, which also includes wombats, kangaroos and possums.  

Previous studies suggested that koala populations plummeted after modern humans arrived on the continent 65,000 years ago. But this relied on mutation rate estimates from distantly related mammals like humans and mice.

Environmental upheaval the biggest reason for population drop

The study found koala populations began a major decline around 100,000 years ago, hitting a critical bottleneck nearly 60,000 years ago.

The timing of the severe population drop matches a period of intense environmental change, coinciding with the most recent glacial period during the late Pleistocene age, long before human contact.

The continent which would eventually become Australia was dominated by wet forests during the Paleogene (23 - 66 million years ago) but went through drastic changes during the Miocene (5- 23 million years ago) as the Australian tectonic plate drifted northwards.

During the Pleistocene (2.5 million to 11,700 years ago), repeated glacial periods, characterised by cold and dry conditions, and interglacial periods, characterised by warmer and wetter conditions, drove further environmental change across Australia, contributing to increasingly arid and fire-prone landscapes.

As Australia became drier, the expansion of the Nullarbor Plain, roughly 70,000 years ago, established a vast semi-arid shrubland, shrinking suitable koala habitat and separating eastern and western koala populations.

While the western population would eventually go extinct, a small population of eastern koalas persisted through the harshest glacial conditions.

As conditions became more favourable during the current interglacial period, the surviving koala population expanded, splitting into five genetic populations between 16,500 and 6,000 years ago. This formed the current groups distributed along the east coast of Australia today.

“Given these results, we’re now curious to see if other Australian species, including the closest relatives of extinct megafauna, also experienced population declines before humans arrived,” says Mr Kovacs.

The new mutation rate for koalas not only reconstructs the species’ ancient genetic history but could be used to examine modern koala populations to help conservation.

Estimates for the last few generations of koala populations found in Queensland and New South Wales have been steadily declining while Victorian populations have been recovering.

“Our team is generating enormous genomic resources for koalas, but to fully understand what these datasets can tell us, we also need to know how quickly new genetic changes arise in the species,” says Mr Kovacs.

“Estimating the mutation rate improves our ability to reconstruct koala population history, understand their capacity to adapt, and make more informed conservation decisions for the future.” 

Declaration: The authors declare no competing interests