Koala population crash came before humans, genome study reveals

A groundbreaking genomic study in Molecular Biology and Evolution, published by Oxford University Press, has reshaped our understanding of the evolutionary history of the koala (Phascolarctos cinereus). Led by researchers at the University of Sydney and Texas A&M University, the comprehensive analysis reveals that the iconic Australian marsupial experienced severe population declines long before the arrival of human populations on the continent.

Historically, scientists heavily debated the primary drivers of late Pleistocene population contractions in Australia's large mammals. Although evidence for the past population sizes of koalas has been limited, previous whole-genome analyses—relying on mutation rate estimates from distantly related mammals like humans and mice—have suggested that koala populations plummeted rapidly only after modern humans arrived on the continent 65,000 years ago.

By calculating the first-ever species-specific germline mutation rate for the order Diprotodontia, this international research team has corrected the timeline. Sequencing the genomes of parent-offspring trios, the researchers established a precise koala mutation rate. When applied to 457 wild koala genomes sampled across the species’ entire contemporary range, this newly calibrated evolutionary clock shifted the estimated timing of past demographic shifts. The data demonstrate that koala populations began a prolonged reduction around 100,000 years ago, hitting a critical bottleneck nearly 60,000 years ago. It appears that severe population contractions coincided with intense glacial environmental shifts during the late Pleistocene age, long before human contact.

The study points to massive environmental upheaval as the primary catalyst. The continent was dominated by rainforests during the Paleogene Age but went through drastic changes during the Miocene as the Australian tectonic plate drifted northwards. As the continent grew increasingly arid, the emergence of the Nullarbor Plain roughly 70,000 years ago transformed into a semi-arid shrubland, isolating western koala populations from eastern forests and driving a substantial reduction in population size. Following the Last Glacial Maximum, the surviving koala population expanded, splitting into five distinct genetic populations between 16,500 and 6,000 years ago, forming the demographic groups distributed along the east coast of Australia today.

The study also models the genetic paths of recent koala populations over the last 100 generations, demonstrating how previous conservation models using default mammal settings heavily skewed data by pushing population declines entirely into the modern era. While contemporary threats like land clearing, disease, and urbanization remain critical issues that led to the koala being listed as Endangered across Queensland, New South Wales, and the Australian Capital Territory in 2022, understanding their true genetic baseline may help to improve survival strategies.

“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," said the paper’s lead author, Toby 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. By estimating how quickly genetic changes accumulate in koalas, we can better understand how populations changed in the past and how they may respond to future environmental challenges.”

The paper, “Mutation rate estimate and population genomic analysis reveals decline of koalas prior to human arrival,” is available at midnight on June 9^th at https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msag108.

Direct correspondence to:
Toby G. L. Kovacs
School of Life and Environmental Sciences
University of Sydney
Life, Earth, and Environmental Sciences (LEES) Building
Camperdown NSW 2050, AUSTRALIA
toby.kovacs@sydney.edu.au

To request a copy of the study, please contact:
Daniel Luzer
daniel.luzer@oup.com