Nature News · Feb 11, 2026 · Collected from RSS
MainCoral reefs are among the most vital marine ecosystems in low-latitude regions. These biodiverse environments provide essential habitats for at least 25% of marine species, including many reef fishes8. Moreover, the health of coral reefs is closely linked to the health, storm protection and nutrition of approximately one billion people—about 13% of the global population—who rely on reefs owing to proximity (that is, living within 100 km of coral reefs)9. Yet global coral cover across reef ecosystems has declined owing to climate change, eutrophication, overfishing and disease1,2. For instance, average stony coral cover in the Caribbean has decreased by 50% since the 1970s3, leading to a shift from coral- to algae-dominated ecosystems.One crucial aspect of coral reef biodiversity and resilience is trophic diversity—the range and specialization of feeding roles within the community. Reef fishes perform critical and varied ecological functions, including ectoparasite cleaning, algae farming, symbiotic relationships with invertebrates and poaching10,11. Even in fishes considered generalists, high-resolution studies show intraspecific prey specialization12,13,14. This wide range of trophic interactions in these ecosystems underpins their extraordinary biodiversity and productivity15,16 and thus supports the services that they provide17.Despite well-documented losses in coral cover and fish biomass, it remains unclear whether the diets of fish communities have been altered by ecological degradation of coral reefs. Many of the impacts leading to coral reef ecosystem change, including overfishing, eutrophication and shifts in coral community composition, began before modern recordkeeping3,4. Thus, reconstructing pre-human trophic structures is critical for understanding whether and how human activities have altered energy flow in these and other marine ecosystems compared to their historical baselines.Stable isotopes are commonly used in modern ecological studies as tracers of trophic structure and energy flow7,18. Recent methodological advancements5,6,19 have enabled isotopic analyses of organic nitrogen in proteins bound within the fossil skeletons of diverse organisms, including fish otoliths, coral, foraminifera and teeth. These innovations make it feasible to reconstruct past marine food web structure and trophic diversity using an ecosystem-based nitrogen-isotope approach, particularly when multiple taxa co-exist at a given fossil reef site. Otoliths—ear stones involved in vestibular function in bony fishes—have taxon-specific shapes and are composed of calcium carbonate (>99.6% by mass) and organic constituents (<0.4%)20 (Supplementary Methods). In fossil and subfossil specimens, the mineral lattice protects the organic constituents from factors leading to poor preservation. The high-sensitivity otolith-bound nitrogen isotope (δ15Noto, where δ15N = [(15N/14Nsample)/(15N/14Nair) – 1] × 1,000) approach enables individual- and community-level δ15N analyses from fossil specimens but has only begun to be applied to study ecosystems5,21. The δ15N patterns in otoliths—as in muscle tissue—convey information about the proportional contribution of food items with distinct isotopic values (Methods).Here we measure the δ15N of fossil-bound organic matter in ~7,000-year-old Caribbean coral reef deposits (Fig. 1), one in Panama (Bocas del Toro) and the other in the Dominican Republic (Enriquillo Basin), to reconstruct coral reef trophic structure before widespread human impacts for comparison with the trophic structure of nearby modern reefs. Fish otoliths and corals are preserved within the coral reef sediments at these sites22, alongside other biogenic hard parts (for example, spines, denticles, teeth, spicules, shells) from diverse organisms such as molluscs, urchins, sharks and sponges4. We focus on coral (Porites furcata; family Poritidae) and four fish families (Fig. 2a), gobies (Gobiidae), cardinalfishes (Apogonidae), silversides (Atherinidae) and grunts (Haemulidae), all of which are important prey fish. As prey fish otoliths are primarily deposited onto reef sediments through predator excretion23, otolith abundances reflect the relative contributions of different fishes to energy flow in the overlying food web averaged over the timescale of sedimentary deposition. These families were therefore chosen for their high abundances in sedimentary deposits as well as their distinct ecological roles. Moreover, apart from grunts, these families are not routinely targeted by fisheries, reducing fishing-driven biases in the dataset24.Fig. 1: Geographic regions and workflow.a, Caribbean regional map and sampling locations within Bocas del Toro, Panama (southwest Caribbean, left) and the Dominican Republic (eastern Caribbean, right) (refer to Extended Data Fig. 1 and Supplementary Table 3 for detailed locality information for modern (red) and fossil (blue) sites). b, Sediment sampling of the coral reef framework in modern and fossil coral reefs. c, Assorted specimens of coral reef matrix-sourced fossil fish otoliths viewed under a dissecting microscope and inset showing example scanning electron microscopy (SEM) images of the cleaned otoliths and coral skeletal material. From top to bottom in the inset we show representative otoliths from each family (Fig. 2a) in the current study: grunts (Haemulidae), cardinalfishes (Apogonidae), silversides (Atherinidae) and gobies (Gobiidae), with the bottom-most image showing fragments of branching finger coral (Poritidae). Scale bars, 1 mm. Fossil and modern reef images in b and images of assorted specimens and otolith SEM in c reproduced from ref. 22; PLoS, under a CC0 1.0 Creative Commons license.Full size imageFig. 2: Coral- and otolith-bound δ15N for fossil (~7 ka) and modern (0.1 ka) time periods.a, Descriptions of the taxa analysed in both time periods to generate an ecosystem nitrogen isotope distribution for coral reef trophic reconstruction. Top row: larger reef-associated fishes; middle rows, smaller reef-associated fishes; bottom row, primary consumers. b, Measurements of otolith- and coral-bound nitrogen isotopes (δ15N) for each fish family, where each symbol denotes an individual coral fragment or fish otolith. Each symbol represents the mean ± 1 s.d. of replicate measurements from individual otoliths or coral fragments. The n value below each category reflects the number of biologically independent individuals (coral fragments or fish) measured for each family, time period and region. c, Family-level patterns in δ15N (trophic level) for fossil and modern time periods (where n is the same as for b). Statistical tests for whether mean δ15N has changed since the mid-Holocene are shown below each fish silhouette (Wilcoxon, two-sided; *P < 0.05, **P < 0.01, ***P < 0.001). δ15N declined for Dominican Republic cardinalfishes (P = 2.5 × 10−4, W = 100, r = 0.873) and grunts (P = 0.048, W = 20, r = 0.82) (Extended Data Table 2). Data from Bocas del Toro, Panama, are shown on the left; data from the southeast Dominican Republic are shown on the right for b and c. d, Regional and family-level patterns in isotopic niche width (diet-driven δ15N diversity), calculated as the 1 s.d. of the individual-level measurements in b. The percent decline compared with the mid-Holocene niche width is shown above each modern bar. Statistical tests for whether the variances have changed since the mid-Holocene are shown below each fish silhouette (F-test, two-sided; *P < 0.05, **P < 0.01, ***P < 0.001). Panama gobies (P = 0.043, F = 3.0), silversides (P = 0.0042, F = 8.53) and grunts (P = 0.0004, F = 10.22) declined significantly (Extended Data Table 4). Grey arrows (from b, pointing towards c and d) indicate that the metrics shown in c (trophic position) and d (dietary diversity) are calculated from all data shown in b. Insets in each of c and d illustrate how each metric was calculated. Fish silhouettes in a–d reproduced from ref. 51, GitHub, under a GPL-2 license.Full size imageWe use δ15N to quantify three complementary metrics: mean trophic level (MTL; the mean of δ15Noto measurements for a family or the whole community), isotopic niche width (as reflected by the standard deviation of δ15Noto measurements for a given family or the whole community25) and food chain length (FCL; the range in mean family δ15Noto) (Supplementary Fig. 1). Below, population refers to individual otoliths within a family, whereas community refers to the assemblage of the studied families. Together, these metrics trace fish behaviour, dietary diversity and energy-flow pathways across individuals (each otolith), families (means and variance across individuals within each family) and the partial communities (mean and variance across the families). As diets are averaged within individual fish, high levels of specialization—each fish relying on a distinct subset of prey—can yield relatively large within-family δ15N variance compared with prey δ15N variance14,25. For example, a large isotopic niche width within a given family, in this context, indicates dietary specialization at the level of individual fish. If fish engage in more generalist foraging, or if resource diversity (that is, the ‘menu’) has become more homogenous, then we would observe greater trophic similarity among individuals and a narrow within-family isotopic niche width12,25. On modern reefs, we predicted that coral loss, predator depletion and habitat fragmentation would reduce resource diversity and promote generalist foraging, leading to greater trophic similarity among individuals. If fish diets also become more similar among families, then FCL is expected to decrease. Ecological theory also predicts that decreased habitat connectivity should lead to decreased FCL26,27.We analysed 136 fish otoliths and co-occurring corals from both fossil (mid-Holocene, 7,000 years ago; ka) and modern Caribbean reefs to reconstruct prehistoric and contemporary reef fish t