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The Pacific coast of the Southern Central American Isthmus is a highly productive and biodiverse region with a rich human history. Although the interaction of the oceans, climate, biodiversity and early human systems has shaped the region’s ecology, research has remained largely disconnected, arising independently from discrete disciplines. To unite this disparate research, we reviewed and synthesized the historical ecology of the Isthmus from the Last Glacial Maximum to the rise of industrial fishing in the 1950s. Our findings reveal a complex interplay between environmental changes, human adaptations and resource use patterns. We identify three major transitions that influenced resource use: the shift to agriculture, the stabilization of rising sea levels and the arrival of Spanish colonists. Each transition marked a significant shift in human–environment interactions, yet we find that the ocean consistently played a central role. This interdisciplinary synthesis offers insights into the region’s socio-ecological past, emphasizing the importance of ocean–land connections for Isthmian peoples and the critical need for research and conservation efforts to ensure its future sustainability. A Spanish language version of the abstract is provided as electronic supplementary material. This article is part of the theme issue ‘Shifting seas: understanding deep-time human impacts on marine ecosystems’. 

Understanding how humans have altered coral reef food webs remains challenging due to the absence of prehistoric baselines. Here, we use fish remains preserved in fossil and archaeological deposits from Panamá and the Dominican Republic to explore how Caribbean reef fish mortality patterns have changed over millennia. By quantifying accumulation rates of shark dermal denticles (scales) and bony fish otoliths (ear stones) in reef sediments, we assess relative fish abundance, while otolith size serves as a proxy for body size at death. Comparisons of these death assemblages suggest a 75% decline in shark-derived material and a 22% reduction in the sizes of human-targeted fishes—consistent with historical exploitation. This evidence of decline in large-bodied, higher trophic level fish remains coincided with a doubling in prey fish otolith accumulation and a 17% increase in their reconstructed body sizes. These patterns in time-averaged death assemblages align with effects of release from predation, documenting an often assumed (but rarely shown) cascading effect. In contrast, otoliths of predator-sheltered cryptobenthic fishes showed no change in either accumulation or size, suggesting that ‘‘bottom–up”environmental factors were not responsible for the observed changes. Together, these data indicate that pre-exploitation predator communities strongly controlled exposed prey fishes, but this “top–down” effect diminishes rapidly toward the food chain base, especially in predator-resistant groups. Understanding trophic cascades on Caribbean reefs requires studying systems before predator depletion.