Taxa
Our main goal was to assess long-term changes in the trophic structure of coral reef-associated fishes compared to prehistoric trophic structure before widespread human impacts. As different stressors can affect different components of marine food webs, we analysed otoliths from key taxa representing the most abundant species from different ecological niches. Gobies (Gobiidae) are abundant, small, cryptobenthic fishes that forage in reef crevices. Cardinalfishes (Apogonidae) are cryptobenthic taxa that exhibit nocturnal off-reef foraging29. Silversides (Atherinidae) are small, pelagic planktivores that feed in schools above reefs52 and grunts (Haemulidae) are relatively larger omnivores that forage in both reef and adjacent seagrass and mangrove habitats35. For taxonomic identification based on otoliths, we used a Caribbean otolith reference collection comprised of locally obtained modern specimens22. Owing to the diagnostic limitations of identifying very small otoliths from early life history stages, only a portion (30–100%, depending on the family; Supplementary Table 4) could be identified to the genus or species, whereas the remaining specimens were assigned to family (8–60%).
Study regions
Otoliths were extracted from two coral reef sedimentary deposits that are the only known mid-Holocene otolith-bearing reef sediments in the Caribbean, located in Bocas del Toro, Panama (9° N × 82° W; Fig. 1 and Supplementary Table 3), and the Enriquillo Basin, Dominican Republic (18° N × 71° W). These sites contain well-preserved fossil reef assemblages spanning the mid-Holocene (around 7000 years before present; bp) and modern (around 100 bp) time periods22,53. Multiple sub-localities were sampled in each region (Extended Data Fig. 1). Bulk sediments, around 9 kg per sample, were collected from reef frameworks using different methods depending on the time period as described in ref. 22. At the mid-Holocene sites, sediments were excavated from 3-m-deep trenches, whereas in modern reefs, SCUBA divers collected sediment from 10–15-cm-deep strata adjacent to living corals. Samples were sieved into size fractions (2 mm, 500 µm, 250 µm and 106 µm) and then otoliths were manually extracted under a dissecting microscope.
Dating
Radiometric dating of coral skeletal material using U-Th and calibrated radiocarbon techniques was previously published for Panama4,22,53 and the Dominican Republic54,55,56. For both regions and time periods, fossil samples spanned around 100 years. U-Th dates showed a larger date range than ages obtained from radiocarbon dating, with ages falling between 6345 and 7164 bp (819 y range) for U-Th, and between 6533 to 6638 bp for 14C (105 y range4). Similarly, dates for the modern samples ranged from 1152 to 1984 bp (832 year range3) for U-Th, with the majority of 14C dates between 1926 to 2014 CE for modern (that is, approximately the past 100 years22,53,57).
Otolith specimen selection
We selected otolith and coral specimens across multiple reef sub-localities to capture spatial and temporal variability (Supplementary Table 3). In total, 91 fish otolith specimens were analysed from Panama (42 mid-Holocene, 49 modern) and 42 from the Dominican Republic (21 mid-Holocene, 21 modern). To select otoliths from the collection, a list of sample numbers (specifying a unique combination of locality + depth + bulk bag replicate) were selected on the basis of obtaining samples from a wide distribution of sub-localities in each region. Otoliths were then randomly chosen from each sample number until n = 10–30 otoliths for each taxon from each country and time period were selected (Supplementary Fig. 2 shows the spatial distribution of specimens across different sub-localities). Localities close to banana plantations (for example, Punto Donato) were avoided, as were sites with known time-averaging problems (Airport Point) or distinct exposures (Cayo Adriana, which is oceanographically connected); however, for Atherinidae and Haemulidae, samples were needed from each of these localities for sufficient sample size.
Furthermore, five modern grunts (family Haemulidae) were measured from the reference collection. Other reef fishes (n = 35) were also measured but not included owing to a lack of conspecifics for comparison, including fishes in the Engraulidae (21), Lutjanidae (8), Serranidae (4) and Gerreidae (2) families (Supplementary Fig. 3). These data were not included in the main text owing to a lack of comparisons across time periods or regions.
Coral specimen selection
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