Unlocking Ice Age secrets through ancient proteins

Fifty thousand years ago, Ice Age Australia was home to enormous, now-vanished animals. Hippo-sized marsupials grazed among forests, giant kangaroos stood taller than people, and strange clawed browsers roamed the wetlands. These were Australia’s megafauna, the continent’s great beasts that disappeared long before recorded history.

For decades, scientists have tried to understand what caused their extinction. Did early humans hunt them? Did climate change alter their habitats beyond repair? Or was it a mix of both? The challenge lies in the incomplete fossil record, often just fragments of bone too small to identify.

But now, a study published in Frontiers in Mammal Science offers a powerful tool to help solve the mystery. The study was conducted by Carli Peters of the Max Planck Institute of Geoanthropology in Germany, Annette Oertle (University of Vienna), Richard Gillespie (Australian National University), Nicole Boivin (University of Queensland and Griffith University), and Katerina Douka (University of Vienna). The research realized by the team introduces a molecular fingerprinting method that can spot the identities of extinct megafauna using the proteins in their bones. The paper, titled “Collagen peptide markers for three extinct Australian megafauna species” may sound highly technical, but its implications are thrilling. It gives scientists a new way to recognize and study Australia’s lost giants, even from the tiniest fossil fragments.

When most people think of ancient DNA, they imagine genetic blueprints locked away in fossils. But DNA is fragile. In Australia’s warm and humid environments, it rarely survives beyond a few tens of thousands of years. Proteins, on the other hand, especially collagen, the main structural protein in bone, can be surprisingly durable.

That’s where palaeoproteomics comes in: the study of ancient proteins. One technique, called Zooarchaeology by Mass Spectrometry (ZooMS), works a bit like forensic science. Scientists extract collagen from a bone, break it into peptides (short chains of amino acids), and run them through a machine that measures their masses. Different species have slightly different collagen “fingerprints,” and those unique markers can reveal which animal the bone came from.

Until recently, though, ZooMS had a major limitation. It relied on having reference data, protein fingerprints from known animals, for comparison. Most of these references came from European or North American species. Australia’s megafauna, by contrast, had been largely left out of the database. That meant that if you picked up a mystery bone fragment in Tasmania or Victoria, ZooMS couldn’t always tell you which extinct giant it belonged to.

The new study fills in that gap by providing collagen markers for three iconic, but very different, extinct Australian animals. The first one is the Zygomaturus trilobus. Imagine a cross between a wombat and a hippo, weighing up to 700 kilograms. Zygomaturus was a bulky, plant-eating marsupial that grazed in forests and wetlands across mainland Australia. Fossils show it had wide jaws suited for chewing tough vegetation. The second one is the Palorchestes azael. Nicknamed the “marsupial tapir,” this bizarre browser was about the size of a rhino. It had powerful front limbs with sharp claws, perhaps used to strip bark or pull down branches. Reconstructions make it look like something out of a fantasy novel. The third one, which sounds like it's named after a Pokemon, is the Protemnodon mamkurra. A giant kangaroo, but not like the red kangaroos we see today. Protemnodon was a forest dweller, heavier and built differently, weighing around 100–150 kilograms. Some species of Protemnodon may have survived until humans first set foot in Tasmania, making them among the last of the megafauna.

By analyzing collagen from fossil bones housed in Australian museum collections, Peters and her colleagues identified unique peptide markers for each of these creatures. That means future researchers can now take even a tiny bone shard, run it through ZooMS, and know whether they’re looking at a giant kangaroo, a marsupial tapir, or something else entirely.

This research has big implications for our understanding of Australia’s deep past. First, it helps scientists reconstruct ancient ecosystems. By identifying which animals were present in a site, even from the most fragmentary remains, researchers can piece together food webs, migration patterns, and habitats. Second, it opens doors to studying extinction events. One of the biggest debates in Australian archaeology is whether humans arriving around 65,000 years ago triggered the downfall of the megafauna, or whether climate shifts played the bigger role. To answer that, scientists need accurate timelines: who was living where, and when. These protein markers allow more precise identification of specimens that can then be radiocarbon dated. Third, it helps ensure that valuable fossils are used wisely. Traditional analyses often required destructive sampling. In this study, the team cleverly used leftover collagen from earlier radiocarbon dating projects, making the most of rare material without drilling into new specimens.

One of the most interesting results from the study is the dating of Protemnodon mamkurra fossils from Tasmania to about 42,000–43,000 years ago. That overlaps with the earliest evidence for humans crossing into Tasmania. In other words, giant kangaroos and humans may have shared the island for a brief window of time. Did humans hunt them? Compete with them for food? Or simply witness their last days? The protein data doesn’t give all the answers, but it provides a sharper tool for asking the right questions.

With peptide markers now available for four extinct Australian megafauna species (the three in this study plus a giant kangaroo identified earlier), researchers are building a reference library that can be used across the continent, and even into Papua New Guinea, which was once connected to Australia as part of the supercontinent Sahul.

Future discoveries may reveal late-surviving populations, new species, or unexpected connections between ancient animals and people. Every new collagen fingerprint adds another puzzle piece to the story of life and extinction on Earth’s driest inhabited continent.

At first glance, protein fingerprints from fossil bones might seem like a small technical advance. But step back, and it becomes something bigger: a way to bring vanished creatures back into focus. Instead of faceless bones, we get to meet the heavyset Zygomaturus, the clawed and mysterious Palorchestes, and the forest-dwelling Protemnodon, not just as names in a museum catalog, but as animals that once shaped Australia’s landscapes. By unlocking these molecular time capsules, the researchers behind the study have given us a sharper lens for peering into the Pleistocene, a time when humans were newcomers and megafauna still roamed free. And with every discovery, we get a little closer to answering one of the great mysteries of prehistory: how and why Earth’s giants disappeared. Who would have known that in addition to keeping our bodies together, proteins can hold together the stories of entire lost worlds?

If you want to learn more, read the original article titled "Collagen peptide markers for three extinct Australian megafauna species" on Frontiers in Mammal Science at http://dx.doi.org/10.3389/fmamm.2025.1564287.