7,000 years of change: How humans reshaped Caribbean coral reef food chains
Using a novel nitrogen isotope method they developed, researchers reconstructed ancient reef food chains for the first time in order to gauge the health of modern reefs
Boston College
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A new analysis published in the journal Nature highlights the dimensions of modern coral reef degradation, according to an international team of researchers, including scientists from Boston College's Department of Earth and Environmental Sciences’ Stable Isotope Biogeochemistry Lab.
view moreCredit: Michael Aw, Ocean Image Bank
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.”
Journal
Nature
Method of Research
Experimental study
Subject of Research
Not applicable
Article Title
Fossil isotope evidence for trophic simplification on modern Caribbean reefs
Article Publication Date
11-Feb-2026
Ancient fish ear stones reveal modern Caribbean reefs have lost their dietary complexity
A study of 7,000-year-old fossils and cutting-edge isotope chemistry shows that food chains on today's Caribbean coral reefs are 60% shorter than before human impact, with fish diets becoming strikingly uniform: a hidden dimension of reef degradation with
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A secretary blenny (Acanthemble maria) from Panama.
view moreCredit: Tim Treuer
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 BrÃgida 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.
Journal
Nature
DOI
Collecting sediments from a 7,000-year-old fossil reef exposed in the Dominican Republic. When sieved, 10 kilograms of this reef matrix can yield hundreds of tiny fish ear stones (otoliths), each one a chemical record of what a fish ate on a reef that existed thousands of years before human impact.
Credit
Sean Mattson
Elkhorn coral and school of blue-striped grunts in the Caribbean.
Credit
Michael Aw, Ocean Image Bank
A pristine 7,000-year-old coral reef, preserved intact in a storm-cut gully in the Dominican Republic's Enriquillo Basin. Sediments within reef frameworks like this one contained thousands of microscopic fish ear stones whose nitrogen isotopes revealed how energy flowed through Caribbean reef food webs before human arrival.
Credit
Sean Mattson
First author of the scientific paper and former STRI post-doctoral fellow Jessica Lueders-Dumont.
Credit
Jorge Alemán
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