It’s surprising how easy it is to see a koala every day in Australia’s major cities.
The cute, grey marsupial can be found on t-shirts, hanging off people’s bags and pencils, and decorating any decent souvenir shop. But seeing a real koala in the wild has become increasingly tricky in some parts of the country. The iconic marsupial is now listed as endangered in Queensland, New South Wales and the Australian Capital Territory.
But koalas have been in a similar situation before.
As my new study published in the journal Molecular Biology and Evolution shows, koalas experienced a population crash about 100,000 years ago. This finding rewrites our understanding of the genetic history of koalas in Australia – and overturns previous theories about what caused their decline in ancient times.
Turning to the genome
Fossil records of koalas are extremely rare. This makes it difficult to estimate how many koalas were present in the past.
Instead, genomes provide important clues about their evolutionary history. The genome acts as a historical record. It preserves genetic information from ancestral populations that can be used to determine their population size.
Previous genomic studies of koalas have estimated koalas experienced a major population decline roughly 40,000 years ago. This was shortly after the arrival of humans in Australia, suggesting this may have been a contributing factor.
Yet the impact of human arrival on Australian fauna is hotly debated. Some researchers use it to explain the widespread extinction of megafauna during this period.
My new study challenges this theory.
dcla/iNaturalist, CC BY-NC
Pushing the timeline back 60,000 years
My colleagues and I set out to construct the first estimate of the koala mutation rate. This is simply the number of mutations that appear in each generation.
Estimating the historical population sizes that have shaped mutation patterns in the genome relies heavily on knowing how often new mutations arise. The problem is that each species has its own unique mutation rate.
To estimate the mutation rate in koalas, we sequenced the genomes of 12 koalas from three families, comprising seven parents and five offspring. This allowed us to count the number of new mutations over each generation.
The whole koala genome has about 3.4 billion sites where changes could occur. We found only 25 mutations per offspring. That’s the equivalent of searching for 25 wrong letters scattered across more than 1,000 copies of The Lord of the Rings trilogy.
We then applied this mutation rate to 457 koala genomes sampled across their entire range. This allowed us to investigate how koala populations have changed over time – including when their numbers crashed.
We found koala population declines occurred around 100,000 years ago – well before humans arrived in Australia. This effectively rules out humans as a cause of the population crash.
Although the mutation rate is a fundamental evolutionary concept, we surprisingly have very few estimates for Australian species. Our estimate is the first from Diprotodontia, the marsupial order which also includes wombats, kangaroos and possums.
Previous studies estimating historical population sizes in koalas have had to rely on mutation rate estimates from distantly related placental mammals such as humans and mice. Applying the koala mutation rate has rewritten the genetic timeline for koalas.
So, what caused the crash?
The koala population crash 100,000 years ago matches a period of intense environmental change across Australia.
The Pleistocene (2.5 million to 11,700 years ago) saw repeated glacial periods, characterised by cold and dry conditions, as well as repeated interglacial periods, characterised by warmer and wetter conditions.
As Australia became drier, the expansion of the Nullarbor Plain established a vast semi-arid shrubland across southern Australia, shrinking suitable koala habitat and separating eastern and western koala populations.
Unfortunately, the population west of the Nullarbor Plain (which was recently described as a distinct species from the modern koala) went extinct around 28,000 years ago.
Although eastern populations were restricted to a small patch of forest on the east coast, they persisted through harsh glacial conditions. Over the last 17,000 years, as conditions became warmer and wetter, they expanded and formed the five genetic groups that are now distributed along the east coast of Australia.
Given our 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.
Craig Manners/Unsplash
Koalas are back to hard times
Koalas are once again experiencing population declines across Australia.
One similarity between modern and ancient declines is they are both largely driven by reductions in the amount of suitable habitat. The ancient decline was driven by global glacial cycles – an unavoidable result of Earth’s orbit.
However, recent declines have generated a similar bottleneck over a much shorter time window, due to the historical and continued removal of suitable koala habitat. This is made worse by other threats such as hunting, disease, vehicle strikes, feral dog attacks and bushfires.
Fortunately, most koala populations have only recently started losing genetic diversity, and rapid population recovery can prevent further loss and inbreeding.
Hopefully the eastern koala will persist once again.
