New research demonstrates that fossilized bones, which preserve physical records of ancient life, can also retain chemical traces of the metabolism of those life forms.
The discovery, detailed in a new study in Nature led by scientists at New York University, opens the door to studying what ancient animals ate, the diseases they carried, and the environments they lived in millions of years ago.
The recent study reports that fossil bones as old as 3 million years still contain thousands of preserved metabolic molecules. Upon analysis of these chemicals, researchers pieced together ancient diets, found signs of disease, and uncovered evidence of warmer, wetter environments in parts of Africa where early humans once lived.
Why Fossils Rarely Reveal Day-to-Day Biology
Metabolomics, the study of small molecules made during digestion and other metabolic processes, has changed modern medical research by connecting chemistry to health, nutrition, and the environment. However, scientists have rarely used metabolomics on fossils because they thought bone changes too much over time to retain useful chemical signals.
“I’ve always had an interest in metabolism, including the metabolic rate of bone, and wanted to know if it would be possible to apply metabolomics to fossils to study early life,” said Timothy Bromage, a professor of molecular pathobiology at NYU College of Dentistry and lead author of the study. “It turns out that bone, including fossilized bone, is filled with metabolites.”
How Bone Can Trap Chemistry for Millions of Years
The idea came from earlier discoveries that collagen, the protein that gives bones their structure, can survive in ancient fossils, including those of dinosaurs. Bromage thought that if collagen can last, other biomolecules might survive too.
Bone is not a solid block. Its porous structure has tiny channels made by blood vessels that once carried oxygen and nutrients. Bromage suggested that metabolites circulating in the bloodstream could become trapped in these small spaces as bone grew, with surrounding minerals protecting them from breaking down.
“I thought, if collagen is preserved in a fossil bone, then maybe other biomolecules are protected in the bone microenvironment as well,” Bromage said.
To test this idea, the researchers used mass spectrometry, a method that ionizes molecules to identify them. When they tested modern mouse bones, they found nearly 2,200 different metabolites, showing that bone can retain a detailed chemical record of metabolism.
Testing Fossils From Early Human Landscapes
The team then used the same technique on fossilized animal bones dating back 1.3 to 3 million years. The samples came from sites in Tanzania, Malawi, and South Africa, regions known for their connection to early human evolution.
The fossils belonged to animals with modern relatives still living in those areas, including rodents such as mice, ground squirrels, and gerbils, as well as larger mammals like antelope, pigs, and elephants. Thousands of metabolites emerged from the fossil samples, many of which closely matched those found in living species.
These chemical signatures reflect everyday biological processes, like the metabolism of amino acids, carbohydrates, vitamins, and minerals. Some markers were linked to estrogen-related genes, which let the researchers figure out the biological sex of some fossilized animals.
Disease, Diet, and a Parasite Still Alive Today
One of the most significant findings came from a ground squirrel bone recovered from Olduvai Gorge and dated to about 1.8 million years ago. The researchers detected a metabolite unique to Trypanosoma brucei, the parasite responsible for African sleeping sickness in humans and spread by tsetse flies.
“What we discovered in the bone of the squirrel is a metabolite that is unique to the biology of that parasite, which releases the metabolite into the bloodstream of its host,” Bromage said. “We also saw the squirrel’s metabolomic anti-inflammatory response, presumably due to the parasite.”
The team also found plant-based metabolites that showed what ancient animals ate. While plant metabolite databases remain limited, the researchers identified compounds associated with plants such as aloe and asparagus.
“What that means is that, in the case of the squirrel, it nibbled on aloe and took those metabolites into its own bloodstream,” Bromage explained. “Because the environmental conditions of aloe are very specific, we now know more about the temperature, rainfall, soil conditions, and tree canopy.”
Reconstructing Ancient Ecosystems
At every site studied, the metabolic evidence indicated warmer, wetter environments than those in the same regions today. These findings match earlier geological and ecological studies, supporting the new method.
“Using metabolic analyses to study fossils may enable us to reconstruct the environment of the prehistoric world with a new level of detail, as though we were field ecologists in a natural environment today,” Bromage said.
Austin Burgess is a writer and researcher with a background in sales, marketing, and data analytics. He holds a Master of Business Administration, a Bachelor of Science in Business Administration, and a Data Analytics certification. His work combines analytical training with a focus on emerging science, aerospace, and astronomical research.