Interacting environmental and evolutionary controls on shifting marine biodiversity hotspots through Cenozoic

Marine biodiversity hotspots are regions characterized by exceptionally high species richness compared to surrounding areas. Fossil and molecular evidence indicate that these hotspots have shifted across space and time throughout the Cenozoic; yet the mechanisms driving their emergence and relocation remain inadequately understood. Here, we examine these dynamics—and their links to environmental change—using genus-level fossil data for molluscs, cnidarians, and foraminifera compiled from the Paleobiology Database and published sources.

Because publicly available fossil occurrence data exhibit strong geographic and temporal sampling inhomogeneities, sampling standardization is essential for robust interpretation of diversity patterns. To reduce sampling biases, we applied Shareholder Quorum Subsampling (SQS) and identified paleo-hotspots as regions where sampling-standardized richness exceeded global confidence intervals. We detected 40 paleo-hotspots exhibiting distinct clade-specific macro-evolutionary signatures. Using models based on Hierarchical Bayesian structural equations reveal that environmental conditions (sea surface temperature, shelf area, sea level) influence hotspot development formation predominantly by modulating macro-evolutionary processes (origination, extinction, immigration), though the strength and direction of these pathways differ among groups. Cnidarian hotspots arise from high evolutionary turnover, where elevated origination rates and expansive shelf area strongly increase hotspot probability. In contrast, for both benthic and planktic foraminifera, no single environmental or macro-evolutionary factor exerts a dominant direct influence; rather, interconnected processes indirectly shape diversity and, ultimately, hotspot formation. Together, these results show that marine biodiversity hotspots arise through distinct, clade-specific macro-evolutionary mechanisms influenced by the environment.