Human activity has significantly reduced the resilience of modern coral reefs by limiting the flow of energy through their food chains, according to a new study published in Nature. The research, conducted by an international team that includes scientists from Boston College’s Earth and Environmental Sciences Department, used a novel nitrogen isotope method to analyze fish ear stones, or otoliths, preserved in marine sediments for up to 7,000 years.
Senior Research Associate Jessica Lueders-Dumont led the project and explained that this is the first time ancient reef food webs have been directly reconstructed using such chemical signals. The study compared today’s Caribbean coral reefs with those from before significant human impact and found notable differences: modern food chains are 60-70 percent shorter and fishes are 20-70 percent less functionally diverse than in the past.
“We discovered that on healthier Caribbean reefs, fish communities drew on a wider variety of food sources,” said Lueders-Dumont. “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 leaves present-day coral reef ecosystems more vulnerable to collapse. Coral reefs serve as biodiversity hotspots supporting at least one quarter of marine species but face threats including rising temperatures, overfishing, and nutrient runoff.
The lack of systematic monitoring until recent decades has meant that scientists did not have an accurate baseline for undisturbed reef food webs—a necessary reference point for conservation planning.
Lueders-Dumont and her colleagues developed their approach by examining fossil deposits from Panama and the Dominican Republic—regions where stony coral cover has dropped by more than half in recent decades—and comparing them with modern samples from nearby locations. These deposits contain a wide array of fossil shells, corals, otoliths, sea urchin spines, and other remains representing both ancient and current reef conditions.
Assistant Professor Xingchen (Tony) Wang described how nitrogen isotope analysis on proteins within both fossilized and modern otoliths provided information about each organism’s position in the historical food chain.
“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. “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.”
The research team included scientists from Academia Sinica, Princeton University, Smithsonian Tropical Research Institute (where Lueders-Dumont began this work), and University of California Berkeley. They analyzed 136 fish otoliths along with dozens of corals focusing on prevalent groups such as gobies, silversides, and cardinalfish—the main prey species throughout millennia.
“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 dating back around 7,000 years with those collected recently at corresponding sites, researchers were able to reconstruct long-term changes within reef food chains with high precision. Notably even low-level members saw shifts due to factors such as removal of top predators or declines in habitat complexity—each contributing to altered energy flow across all levels.
“These results show that human impacts such as removing top predators, reducing 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.
She likened reconstructing baselines for marine life thousands of years ago to a form of time travel. The findings suggest that using fossil-based isotope methods can help assess how ecosystems responded historically—which may guide efforts under present climate change conditions.
“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.”
