Coral reefs are undoubtedly in crisis. Scientists have documented concerning coral bleaching events, dramatic declines in coral cover, fish and shark populations across the Caribbean over recent decades. But a critical question has remained unanswered: has the way energy flows through reef ecosystems also changed? A new study led by scientists at the Smithsonian Tropical Research Institute (STRI) and published in Nature reveals that it has, profoundly. Food chains on modern Caribbean reefs are 60-70% shorter than they were 7,000 years ago, and individual fish have lost the dietary specialisation that once sustained a complex web of energy pathways.
The discovery was made possible by an unlikely combination: thousands of tiny fish ear stones (otoliths) preserved in ancient reef sediments, and a high-sensitivity technique for measuring nitrogen isotopes locked inside them. The nitrogen isotope ratio in an otolith reflects what a fish ate during its lifetime, providing a chemical record of its place in the food chain. By comparing otoliths and corals from 7,000-year-old fossil reefs with those from nearby modern reefs in Panama and the Dominican Republic, the research team reconstructed the trophic structure of Caribbean reef fish communities before and after centuries of human impact.
The results paint a stark picture. Relatively higher-trophic-level fishes such as grunts and cardinalfishes now feed at lower positions in the food chain, whilst low-level fishes like gobies have shifted surprisingly up the food chain. The net effect: the distance between them has compressed by around 60% in both regions. At the same time, the dietary variation within fish families has narrowed by 20–70%, meaning individual fish that once specialised on distinct prey now eat much the same things as their neighbours.
"What struck us is how consistent the pattern is," said Jessica Lueders-Dumont, a postdoctoral marine biogeochemist who led the study. "In every fish family we examined, in both Panama and the Dominican Republic, the dietary diversity has contracted. These reefs have lost an entire dimension of ecological complexity that we didn't even know was missing."
This study builds on over a decade of fieldwork at STRI in Panama. Beginning in the early 2010s, a team led by STRI scientist Aaron O'Dea excavated tonnes of sediment from exceptionally well-preserved fossil reefs in Bocas del Toro, Panama, and the Enriquillo Basin in the Dominican Republic. These beautiful 7,000-year-old, mid-Holocene reef deposits in the Caribbean preserve conditions before human impact: a remarkable archive that has already yielded insights into coral shifts and the ecological consequences of predator loss.
"Otoliths are incredible structures, and when we first started finding them in our fossil reef samples, I realised we had an opportunity to reconstruct not just what corals were like before humans, but also the fishes that live on reefs" said O'Dea.
The painstaking work of sorting, identifying and cataloguing thousands of otoliths from bulk reef sediment was carried out largely by STRI researcher Brígida de Gracia, a Ngäbe palaeontologist, and Chien-Hsiang Lin of Academia Sinica in Taiwan. Their development of otolith reference collections and taxonomic expertise laid the groundwork for the study.
"Picking otoliths from sediment, grain by grain, is challenging but you develop an intimate relationship with these ancient reefs," said de Gracia. "Every otolith tells the story of a fish that lived thousands of years ago. To see those stories come alive through isotope chemistry is incredibly rewarding."
The isotopic technique at the heart of the study was developed by Lueders-Dumont in co-author Daniel Sigman's laboratory at Princeton University. The method extracts and measures nitrogen locked within the mineral structure of the otoliths: organic matter that has been sealed away for millennia, protected from degradation by the surrounding calcium carbonate.
The team focused on four fish families that represent different ecological roles on the reef: gobies (small bottom-dwellers), silversides (pelagic schooling fish), cardinalfishes (nocturnal predators) and grunts (larger omnivores that roam between reef and mangrove habitats). Crucially, most of these species are not targeted by fisheries, meaning the changes reflect broad ecosystem shifts rather than direct harvesting effects.
The findings carry a sobering message for reef conservation. When individual fish within a population all rely on the same pool of resources (rather than each specialising on different prey), a single disruption to food supply can affect the entire population simultaneously. The prehistoric reefs, by contrast, supported a diversity of energy pathways that would have buffered the system against shocks. The loss of this trophic complexity represents a hidden vulnerability: one that is invisible to standard reef monitoring but may increase the risk of cascading ecosystem collapse.
"We already knew that modern Caribbean reefs are home to fewer corals and fewer sharks," said O'Dea. "Now we can see that the fish that remain are feeding and behaving differently too. It strengthens the case that modern Caribbean reefs are not simply diminished versions of what came before; they are potentially functioning in different ways"
The study also provides a new tool for reef assessment. "We now have a way to explore how entire systems function," said Lueders-Dumont. "These tiny ear stones are opening a window into how energy moves through reef ecosystems on time scales previously unimaginable to ecologists".
About the Smithsonian Tropical Research Institute
Headquartered in Panama City, Panama, STRI is a unit of the Smithsonian Institution. Our mission is to understand tropical biodiversity and its importance to human welfare, to train students to conduct research in the tropics and to promote conservation by increasing public awareness of the beauty and importance of tropical ecosystems. Watch our video, and visit our website, Facebook, X and Instagram for updates.
