Chestnut Hill, Mass. (2/11/2026) – Human activity has lessened the resilience of modern coral reefs by restricting the food-fueled energy flow that moves through the food chains of these critical ecosystems, an international team of researchers report in the journal Nature.
Examining otoliths – fish ear stones that are preserved in marine sediments across millennia – the team developed and applied a nitrogen isotope method to 7,000-year-old fossils in order to reconstruct ancient reef food webs directly for the first time, according to Boston College Senior Research Associate Jessica Lueders-Dumont, a lead researcher on the project.
The new analysis highlights underappreciated dimensions of modern coral reef degradation, said Lueders-Dumont, of the Department of Earth and Environmental Sciences' Stable Isotope Biogeochemistry Lab .
Compared to "pristine" coral reef ecosystems from time periods before widespread human impacts, today's Caribbean coral reefs host food chains that are 60-70 percent shorter and fishes that are 20-70 percent less functionally diverse, the study found.
"We discovered that on healthier Caribbean reefs, fish communities drew on a wider variety of food sources," she said. "On degraded reefs, diets have become homogenized—different fish are increasingly eating the same limited set of resources. In the past, individual fish could afford to be choosy; today many are left with whatever is available. It's like going from a vibrant neighborhood of restaurants to a single, stripped-down menu."
This loss of functional diversity means that modern coral reef ecosystems are more prone to collapse. Biodiversity hotspots that support at least a quarter of marine species, coral reefs are being degraded by human-driven factors such as rising temperatures, overfishing, and nutrient runoff.
Because these impacts began long before systematic monitoring, scientists have lacked a clear ecological baseline of an undisturbed reef food web. Such a measuring stick is essential for setting realistic conservation goals.
Lueders-Dumont and colleagues developed a new approach using chemical signals preserved in fossil fish ear stones and corals to estimate trophic level – the position of fishes in the food chain – on Caribbean reefs of the mid-Holocene – about 7,000 years ago – and compare it with today's food web.
The team examined unique fossil deposits in Panama and in the Dominican Republic in the Caribbean Sea, one of the most degraded coral reef ecosystems where stony coral cover has decreased by more than 50 percent in recent decades.
In these coral reef deposits, there is a great diversity of fossil shells, corals, otoliths, sea urchin spines, and many other vestiges of the mid-Holocene coral reefs that fringe Caribbean coastlines. For a comparative fossil record, the researchers sifted through sediments nearby, which contain a similar "modern" record of the same types of shells, corals, otoliths, and other "hard parts" deposited by modern animals, according to the report.
The researchers conducted nitrogen isotope analysis on proteins bound within fossil and modern otoliths and coral skeletons, which can preserve trophic information in the past, said Boston College Assistant Professor of Earth and Environmental Science Xingchen (Tony) Wang, a co-author of the report.
"Because these isotopic signals reflect an organism's position in the food chain, analyzing multiple groups of fish and corals from the same fossil reefs enables us to quantitatively reconstruct reef food-chain structure before major human impacts," said Wang, director of the Stable Isotope Biogeochemistry Lab.
"This approach was previously constrained by the tiny amounts of protein preserved in fossils, but recent advances in our methods now make it possible to apply it to fossil reef assemblages for the first time. It's like ancient DNA, but instead of genes, we're using the chemical signatures locked in ancient proteins."
Using this approach, the researchers – including colleagues from Academia Sinica, Princeton University, Smithsonian Tropical Research Institute, and the University of California, Berkeley – analyzed 136 fish otoliths and dozens of corals.
Otoliths, formed from calcium carbonate, are an important part of the vestibular system that enables hearing and balance in all bony fishes in the teleost group. Otoliths can also preserve well in the fossil record, and have species-specific shapes that allow for taxonomic identification, Lueders-Dumont said.
Lueders-Dumont said the analysis focused on the most abundant fish groups preserved in the fossil record, including gobies, silversides, and cardinalfish.
"These fishes are fundamental prey items on reefs—essentially the 'potato chips of the reef'," said Lueders-Dumont. "Across millenia, they have been eaten and their otoliths excreted to accumulate in the sediment record."
By comparing specimens from fossil archives from reefs dating back approximately 7,000 years in Panama and the Dominican Republic with modern reefs at the same locations, the researchers reconstructed long-term changes in the food chain with unprecedented precision, according to Wang and Lueders-Dumont.
To gain insight into what natural reef food webs were like before human influence and thus learn how human activities have altered modern coral reefs, they measured the trophic levels of ancient and modern fish. Trophic level is a key ecological metric, measuring an animal's role in the ecosystem.
Researchers were surprised to observe changes even among fish at the lowest levels of the food chain.
These results show that human impacts such as removing top predators, reducing the connections between different habitat types, and reductions in coral reef structural complexity – among other factors affecting modern coral reefs – have all altered energy flow to all levels of the food webs," said Lueders-Dumont, who began the project as a postdoctoral fellow at the Smithsonian Tropical Research Institute and has continued the work across multiple institutions.
Reconstructing a baseline of the conditions for marine life thousands of years ago is almost like a form of time travel, said Lueders-Dumont.
The results highlight the promise of fossil-based isotope methods for examining how coral reef ecosystems responded to past environmental change—and what those responses mean for reefs experiencing accelerating climate change today.
"We can now glimpse what pristine coral reef ecosystems looked like before human impacts," she said. "Because our previous benchmarks for conservation have been shaped by already-degraded modern reefs, the ability to reconstruct ancient baselines offers an entirely new perspective on what healthy reef ecosystems are—and how we might restore them."
