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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. 

Nitrogen is a major limiting element for biological productivity, and thus understanding past variations in nitrogen cycling is central to understanding past and future ocean biogeochemical cycling, global climate cycles, and biodiversity. Organic nitrogen encapsulated in fossil biominerals is generally protected from alteration, making it an important archive of the marine nitrogen cycle on seasonal to million-year timescales. The isotopic composition of fossil-bound nitrogen reflects variations in the large-scale nitrogen inventory, local sources and processing, and ecological and physiological traits of organisms. The ability to measure trace amounts of fossil-bound nitrogen has expanded with recent method developments. In this article, we review the foundations and ground truthing for three important fossil-bound proxy types: diatoms, foraminifera, and corals. We highlight their utility with examples of high-resolution evidence for anthropogenic inputs of nitrogen to the oceans, glacial–interglacial-scale assessments of nitrogen inventory change, and evidence for enhanced CO 2 drawdown in the high-latitude ocean. Future directions include expanded method development, characterization of ecological and physiological variation, and exploration of extended timescales to push reconstructions further back in Earth's history. 

Abstract We investigated the biogeography of benthic foraminifera in a highly urbanized tropical seascape, i.e. Hong Kong, in order to assess their utility as bioindicators relative to other marine fauna. Hong Kong is one of the largest coastal cities on the planet and studies of other benthic fauna in the region are available for comparison. We found that: (1) turbid, muddy habitats host a unique foraminiferal fauna; (2) areas with intermediate levels of eutrophication have the highest foraminiferal species diversity; (3) semi-enclosed and heavily polluted environments host a distinct foraminiferal fauna, characterized by low taxonomic diversity and/or high dominance, and that is acclimated to stressful marine conditions. Biodiversity patterns of foraminifera in Hong Kong are generally consistent with those of other soft-sediment macro- and meio-fauna (e.g. polychaetes, molluscs and ostracods); however, foraminifera may be more sensitive than these other groups to eutrophication and associated changes in coastal food webs. The tolerance of some, but not other, species to eutrophic and hypoxic conditions means that foraminiferal faunas can serve as bioindicators across a wide array of environmental conditions, in contrast with corals whose sensitivity to eutrophication results in their absence from eutrophied settings. The well-known autoecology of foraminifera taxa can help to characterize environmental conditions of different habitats and regional environmental gradients. Although the use of fauna as bioindicators may be most robust when data are compared for multiple taxonomic groups, when such broad sampling is not available, benthic foraminifera are particularly well suited for environmental assessments due to their ubiquity, interspecific environmental breadth, and the well-understood environmental preference of individual taxa.