The first direct measurement of the mutation rate in koalas has changed the timeline of their history. Analysis of 457 genomes shows that the major decline began before humans arrived in Australia, likely due to drying out of the continent, glacial cycles and habitat fragmentation.
Koalas alive today are descendants of an ancient population that survived a severe population decline tens of thousands of years ago. A new genomic study shows that the decline began about 100 years ago and reached a severe bottleneck about 60 years ago—earlier than previous studies suggested, and before or very close to the earliest recorded human arrival in Australia.
Researchers from the University of Sydney and Texas A&M University have concluded after directly measuring the mutation rate of koalas for the first time, Phascolarctos CinereusThey used the new rhythm as a kind of evolutionary clock to analyze 457 complete genomes of koalas from all their distribution areas.
The study, published in the journal Molecular Biology and Evolution, changes the dating of one of the most important events in the history of the species. Previous studies linked the great decline in the koala population to the arrival of humans in Australia about 65 years ago. But these dates were based on mutation rates measured in distant species, including mice and humans.
An evolutionary watch specially calibrated for the koala
Mutations are changes in DNA that are passed down in reproductive cells from generation to generation. Because they accumulate over time, their number can help researchers estimate when populations have diverged, expanded, or contracted.
However, the rate of mutation is not the same in all species. Using a rate measured in another animal could push evolutionary events forward or backward by tens of thousands of years.
To measure the mutation rate in koalas, the researchers sequenced the genomes of four family triplets, each with two parents and an offspring. They looked for genetic changes in the offspring that did not appear in either parent, and therefore created new mutations.
The calculated rate averaged 6.12 mutations per billion DNA letters per generation. This is about half the rate measured in humans per generation. It is one of the first direct measurements in the large group of marsupials known as diprotodontia, which also includes kangaroos, wombats and possums.
After calibrating the genetic clock, the researchers used the hundreds of genomes to reconstruct how the koala population size changed over time.
The collapse began before humans arrived.
The analysis indicated a major decline that began about 100 years ago and a severe bottleneck around 60 years ago. The term “bottleneck” describes a situation in which a population is reduced to a relatively small number of individuals, and as a result loses some of its genetic diversity.
The start of the decline is earlier than the conventional dates for the arrival of modern humans in Australia, so the researchers conclude that humans were not the cause of the early collapse of the koala population.
However, the genetic data do not allow us to identify a single, proven cause. The dating corresponds to a period of widespread environmental changes in Australia in the late Pleistocene: cycles of cold, dry glacial periods and warm, wet interglacial periods, increasing aridity, and changes in the distribution of forests.
Koalas depend on certain eucalyptus species for food and shelter, so deforestation and fragmentation may particularly affect them.
The Nullarbor Plain split the distribution area
Australia has been undergoing a prolonged drying process for millions of years. During the Pleistocene, large areas of the continent became drier and more prone to fires.
The researchers note that the expansion of the semi-arid Nullarbor Plain, about 70 years ago, reduced the habitats suitable for koalas and created a barrier between populations in the east of the continent and those living in the west.
The western population eventually disappeared, while a small eastern population survived the harsh conditions. When the climate improved during the current interglacial period, koalas re-spread across eastern Australia.
Genomic analysis indicates that over the past tens of thousands of years, the population has split into five main genetic groups, which now extend from northern Queensland to Victoria.
According to Toby Kovacs, a doctoral student at the University of Sydney who led the study, koala fossils are not numerous enough to reconstruct the size of ancient populations on their own. The genomes therefore provide an indirect record of periods of decline and recovery.
This is no credit for the influence of man today.
The finding that the ancient collapse began before the arrival of humans does not diminish human responsibility for the state of koala populations today.
Commercial hunting, deforestation and land clearance have caused severe declines in the past. Today, many populations are threatened by habitat loss and fragmentation, urban development, vehicle and dog damage, droughts, heat waves, fires and disease – most notably chlamydia infections.
The combined populations of Queensland, New South Wales and the Australian Capital Territory have been classified as endangered under Australia's federal environmental law since 2022. The classification does not apply equally to all koalas on the continent: in Victoria and South Australia, the status of certain populations is different, and in some areas there is even a recovery.
The new study also found differences in the current trajectories of populations. In Queensland and New South Wales, numbers continue to decline, while some populations in Victoria are showing a recovery.
From the ancient past to nature conservation
Measuring mutation rates is important not only for reconstructing history. It allows us to more accurately estimate the size of populations, the rate of loss of genetic diversity, and their ability to adapt to environmental changes and disease.
Genetic diversity affects the likelihood that a population will have individuals capable of coping with a new pathogen, extreme heat conditions, or a change in vegetation composition. Small, isolated populations may suffer from inbreeding and the accumulation of harmful genetic changes.
Accurate genetic maps can help decide where ecological corridors should be protected, which populations need reconnecting, and which groups hold particularly important genetic diversity.
The researchers are now interested in investigating whether other Australian species also experienced declines before humans arrived. Such results could also influence the broader debate about the reasons for the disappearance of large animals in Australia at the end of the Pleistocene.
The study doesn’t suggest that koalas will necessarily be able to recover from any crisis simply because they survived a previous one. Environmental change is rapid today, and habitats are fragmented by roads, agriculture and cities. But their past survival stories can help researchers understand what conditions allowed for recovery—and how to preserve them in the future.
Questions and Answers
When did the early decline in the koala population begin?
Genetic models indicate the beginning of a decline about 100 years ago and a severe bottleneck around 60 years ago.
How can we know what the population size was without many fossils?
Changes in genetic diversity and mutation patterns make it possible to roughly reconstruct periods in which a population expanded or contracted.
Why did the study change the previous dating?
Previous studies have used mutation rates from humans or mice. The new study measured the mutation rate of the koala itself using four families.
Does the study prove that climate change caused the collapse?
Not absolutely. The dating fits a period of climate change, desiccation, and habitat fragmentation, but the genetic data does not prove a single factor.
Aren't humans responsible for the state of koalas today?
Humans are responsible for many of the current threats, including habitat destruction and fragmentation, urban development, and vehicle impacts. The climate crisis is also increasing droughts, heatwaves, and fire risks.
Toby GL Kovacs et al., “Mutation rate estimate and population genomic analysis reveals decline of koalas prior to human arrival,” Journal Molecular Biology and Evolution, June 2026. DOI: 10.1093/molbev/msag108.
Notes:
The scientific article reports a rate of 6.12×10⁻⁹ mutations per base pair per generation, measured in four parent-offspring triplets, and reconstructs demographic history using 457 complete genomes. The authors date the beginning of the decline to about 100 years ago and the split into five genetic populations to the last tens of thousands of years. (OUP Academic)
The "endangered" status in Australian law applies to the combined populations of Queensland, New South Wales and the Australian Capital Territory, since 12 February 2022. (DCCEEW)
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