Geomorphic evolution of a Caribbean biological hotspot

Continental shelf archipelagos offer rare opportunities to test island biogeography in a time-resolved, non-equilibrium setting because postglacial sea-level rise drives datable changes in both island area and isolation. Yet most near-shore systems still lack reconstructions that integrate spatial changes in island configuration with duration-weighted histories of fragmentation. Such information is essential for interpreting modern genomic and biodiversity patterns and for evaluating responses to fragmentation such as extinction debt, immigration lag and adaptive responses over time. Here we reconstruct the land-sea geomorphic history of the Bocas del Toro Archipelago, Panama, combining high-resolution bathymetry and topography with a sea-level model corrected for sedimentation and tectonic movement. From this, we quantify multi-scale isolation, historical fragmentation dynamics, and composite metrics that integrate space and time. We show that present-day islands became isolated sequentially from 9.5 to 2.9 ka, with post-isolation area contraction rates varying 20-fold among islands. Over the same interval, shallow marine habitat (0-10 m depth) expanded ninefold as shelf flooding created space for reefs, seagrass, and mangroves. Extending the analyses through the Pleistocene reveals the modern archipelago is atypical and for much of the last million years, the region existed as continuous coastal lowland rather than discrete islands. Projections under moderate emissions scenarios predict [~]5% terrestrial habitat loss but [~]50% expansion of shallow marine habitat by 2150, though whether degraded Caribbean reefs can exploit this expansion remains uncertain. Exploratory correlations between species richness of terrestrial vertebrate groups and geomorphometric predictors reveal that island area, maximum elevation, and cumulative habitat availability since isolation are the strongest correlates of diversity, whilst buffer-zone isolation indices are confounded by covariation between island size and surrounding landmass in this continental shelf context. Overall, Bocas del Toro provides a time-calibrated natural experiment for testing how dynamic connectivity and isolation shaped island and coastal biodiversity.