Fossil otolith assemblages reveal millennial-scale changes in reef fish biomass and trophic structure across the Isthmus of Panama

Human activities have disrupted food webs across ecosystems, but opportunities to quantify pre-impact baselines are rare. Here, we present a novel approach to reconstruct per-capita fish biomass and trophic structure over millennia using the size of otoliths (ear stones) preserved in fossil assemblages. Using this approach, we compared fish energetics on modern (past ~100 years) and mid-Holocene (~7-4 ka) coral reefs along the Caribbean and Pacific coasts of Panama-two adjacent regions with distinct oceanographic conditions and human impacts. Estimated mean per-capita fish biomass at mortality was around twofold higher in the highly productive Pacific compared with the more oligotrophic Caribbean. Reefs in Pacific Panama also supported relatively more top-heavy trophic structures, consistent with enhanced pelagic subsidies. This interoceanic difference has widened over time: while reefs in Caribbean Panama experienced predator loss and declining per-capita fish biomass, Pacific reefs showed increasing per-capita biomass, principally explained by piscivorous fish. These contrasting millennial-scale shifts highlight how environmental context can shape ecosystem responses to anthropogenic impact. The approach we develop demonstrates how otolith assemblages can serve as a tool to explore long-term energetic dynamics in fish communities, offering unique insights into reef resilience and recovery potential. This article is part of the theme issue 'The biosphere in the Anthropocene'.