For decades, the story of the koala’s decline seemed simple. Humans arrived in Australia, forests were cleared, and koala populations began to fall.
A new study of koala DNA changes that order. It shows koalas were already in deep trouble long before any person reached the continent.
Scientists at the University of Sydney and Texas A&M University traced the koala’s past back about 100,000 years. The real cause, they found, was a changing climate, not us.
Building a genetic timeline
“The study rewrites the timeline for the koala’s genetic history in Australia,” said Toby Kovacs, a PhD student at the University of Sydney who led the research.
Earlier DNA studies had said koala numbers dropped only after people showed up. This new work shows that idea was wrong.
The team looked at how fast koala DNA changes over time. Each generation adds a few small changes, and that steady pace works like a clock.
“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,” noted Kovacs.
Counting mutations in koala families
To set that clock, the team studied four koala families, comparing parents and their young. They counted the brand new changes in each baby koala.
Kovacs notes that fossils are too rare to show how many koalas lived 100,000 years ago, so their DNA is the best way to look back.
Koala DNA picks up new changes about half as often as human DNA does. No one had ever measured this directly for koalas, or for their close marsupial cousins like wombats, kangaroos and possums.
With this koala rate in hand, the team studied 457 koala genomes and tracked how their numbers rose and fell over thousands of years.
Older studies had used rates from humans and mice instead, and those distant animals gave the wrong answer.
Population decline among koalas
The DNA told a clear story. Koala numbers started dropping around 100,000 years ago and reached their lowest point close to 60,000 years ago, during the last ice age.
“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,” Kovacs said.
As Australia dried out, the Nullarbor Plain spread across the south about 70,000 years ago. This wide, treeless land split the western koalas off from the eastern ones.
The western group died out over time. A small group of eastern koalas held on through the worst of the cold.
Five populations along the coast
When the weather warmed again, the survivors spread out and broke into five separate groups between 16,500 and 6,000 years ago.
Those same groups still live along the east coast 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,” said Kovacs.
What this means for conservation
The same DNA clock can also track koalas living now, not just ancient ones. Recent numbers show koalas falling in Queensland and New South Wales while Victorian koalas slowly recover.
Kovacs says that knowing if a group is shrinking helps people protect koalas early, before they lose genetic variety and face bigger risks from inbreeding.
“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,” Kovacs said.
“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.”
Human-caused threats to koalas
The deep past may clear people of that first big decline. The story today is very different.
“It’s important to make clear many of the threats facing modern koala populations are caused by humans, which includes habitat loss and hunting,” Kovacs said.
“Koalas experienced large population retractions in the past, as the climate changed and suitable habitat disappeared.
“The surviving koalas are again experiencing a similar retraction, but this time due to human driven land clearing, bushfires, hunting and disease.”
The koala has been listed as endangered across Queensland, New South Wales and the Australian Capital Territory since 2022.
The study is published in the journal Molecular Biology and Evolution.
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