Community reorganization without collapse in a warming world: Habitat-contingent, trait-mediated biodiversity change within a conserved multi-scale structure

Biodiversity change under sustained environmental pressure is increasingly understood as a process of long-term reorganization across spatial scales rather than uniform loss or gain. Estuarine ecosystems, which experience strong environmental gradients and frequent short-term extreme disturbances, provide an ideal context for evaluating how local (), spatial ({beta}), and regional ({gamma}) diversity reorganize across habitat domains and functional guilds through time. Here, we examined four decades of fish and invertebrate community data from a coastwide, ecological monitoring program, spanning multiple estuarine systems along the Texas coast. We asked three main questions: whether habitat context modifies the direction of trait-mediated biodiversity responses across the full -{beta}-{gamma} structure; whether spatial homogenization is detectable through dominance-weighted {beta}-diversity metrics and how they relate to richness-based metrics; and whether the pace of reorganization has intensified over time. Functional traits related to dispersal capacity and thermal affinity structured the magnitude of biodiversity change within habitat domains, but habitat context determined its direction, the same guilds exhibited opposite diversity trajectories across gear-defined habitat domains despite broadly similar functional composition, demonstrating that trait-based forecasting frameworks will mispredict reorganization direction when habitat context is ignored. Spatial homogenization proceeded undetected by richness-based {beta}-diversity metrics but was revealed through dominance-weighted measures, indicating that dominance-weighted homogenization operates through two distinct habitat-dependent mechanisms: convergence on shared warm-adapted dominant taxa in shallow assemblages, and convergence toward impoverished assemblages as dominant taxa declined in deeper habitats, both processes invisible to richness-based metrics. Despite a measurable intensification in the pace of local and regional diversity change after approximately 2000, spatial turnover among bays remained stable and -{beta}-{gamma} scaling relationships were preserved across all diversity orders, demonstrating that rapid reorganization can proceed without destabilizing fundamental metacommunity structure. Across all findings, biodiversity change was persistent, directional, and strongly habitat dependent, following a chronic rather than episodic trajectory consistent with sustained environmental processes as the primary driver.