Fossil Clues Show Modern Coral Reef Food Webs Have Dramatically Compressed

Isotope evidence from fossil otoliths shows Caribbean reef food chains have shrunk by up to 70%, signaling a major loss of trophic complexity.

Coral reefs across the Caribbean are facing severe decline. Researchers have recorded widespread bleaching, steep losses in coral cover, and significant reductions in fish and shark populations over the past several decades. Yet one important issue has remained unclear: has the basic flow of energy through reef ecosystems also been altered?

New research led by scientists at the Smithsonian Tropical Research Institute (STRI) and published in Nature shows that it has. According to the findings, present-day Caribbean reef food chains are 60-70% shorter than they were 7,000 years ago. Fish that once occupied distinct dietary niches now show far less specialization, weakening the intricate network of energy pathways that previously supported reef life.

To uncover this long-term change, scientists turned to an unusual source of evidence: thousands of microscopic fish ear stones known as otoliths preserved in ancient reef sediments, along with a highly sensitive method for analyzing nitrogen isotopes trapped within them.

Otolith Isotope Analysis Reveals 7,000 Years of Food Web Change

The ratio of nitrogen isotopes in an otolith reflects what a fish consumed during its lifetime, effectively preserving a chemical record of its role in the food web. By examining otoliths and corals from 7,000-year-old fossil reefs and comparing them with samples from nearby modern reefs in Panama and the Dominican Republic, the team reconstructed the structure of reef fish communities before and after centuries of human influence.

The comparison revealed striking changes. Fish that typically fed higher in the food chain, such as grunts and cardinalfishes, are now feeding at lower trophic levels. Meanwhile, species that once occupied lower positions, including gobies, have shifted upward. As a result, the gap between trophic levels has narrowed by roughly 60% in both study regions.

At the same time, differences in diet within fish families have declined by 20–70%, indicating that individuals who once specialized in particular prey types now rely on many of the same food sources as other members of their group.

“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.”

Fossil Reef Excavations Provide Prehuman Baseline

The findings build on more than ten years of field research at STRI in Panama. Starting in the early 2010s, a team led by STRI scientist Aaron O’Dea removed tons of sediment from exceptionally well-preserved fossil reefs in Bocas del Toro, Panama, and the Enriquillo Basin in the Dominican Republic. These 7,000-year-old mid-Holocene reef deposits offer a rare snapshot of Caribbean ecosystems before significant human disturbance. Previous work at these sites has already provided important insights into historical coral communities and the ecological impacts of predator declines.

“Otoliths are incredible structures, and when we first started finding them in our fossil reef samples, I realized 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.

Sorting and cataloguing thousands of otoliths from bulk reef sediment required meticulous effort. Much of this work was carried out by STRI researcher Brígida de Gracia, a Ngäbe paleontologist, along with Chien-Hsiang Lin of Academia Sinica in Taiwan. By building detailed reference collections and refining taxonomic identifications, they established the foundation that made the broader analysis possible.

Nitrogen Isotope Technique Unlocks Ancient Diets

“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 nitrogen isotope method central to the research was developed by Lueders-Dumont in co-author Daniel Sigman’s laboratory at Princeton University. This technique isolates and measures nitrogen preserved within the mineral structure of the otoliths. The organic material has been sealed inside the surrounding calcium carbonate for millennia, protecting it from degradation and allowing scientists to retrieve detailed dietary information long after the fish lived.

Researchers concentrated on four fish families representing a range of ecological roles: gobies (small bottom-dwellers), silversides (pelagic schooling fish), cardinalfishes (nocturnal predators), and grunts (larger omnivores that roam between reef and mangrove habitats). Importantly, most of these species are not directly targeted by fisheries. This suggests that the observed dietary shifts reflect broad changes in ecosystem structure rather than the direct effects of fishing pressure.

Conservation Implications of Shortened Reef Food Chains

These results carry important implications for reef conservation. When all individuals within a population depend on the same limited set of resources (rather than each specializing on different prey), a disruption in food availability can impact the entire group at once. In contrast, prehistoric reefs supported multiple energy pathways that likely helped buffer the system against environmental shocks. The reduction in trophic complexity, therefore, represents a hidden weakness, one that is not easily detected by conventional reef monitoring but could heighten the risk of cascading ecosystem failure.

“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.”

Beyond documenting decline, the research introduces a powerful new approach for evaluating reef health. “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.”

Reference: “Fossil isotope evidence for trophic simplification on modern Caribbean reefs” by Jessica A. Lueders-Dumont, Aaron O’Dea, Erin M. Dillon, Brigida de Gracia, Chien-Hsiang Lin, Sergey Oleynik, Seth Finnegan, Daniel M. Sigman and Xingchen Tony Wang, 11 February 2026, Nature.
DOI: 10.1038/s41586-025-10077-z

Never miss a breakthrough: Join the SciTechDaily newsletter.
Follow us on Google and Google News.