Supplementary material from "Insidious shifts in a putative climate change coral refugium"

Tropical reefs are under rapid decline due to a combination of impacts, such as pollution, overfishing and climate change. Coral loss has been overlooked in the Southwestern Atlantic (SWA) turbid-zone reefs, prompting a climate change refugia hypothesis that was largely based on the region's relatively low bleaching levels and stable total coral cover. Here, using a novel functional classification, we examine coral reef cover dynamics in Abrolhos, SWA’s largest reef complex. Monitoring was carried out over 18 years (2006-2023) and across three heatwaves. Results show insidious shifts in coral assemblages, including the collapse of branching corals and the replacement of previously dominant massive endemic forms by fast-growing, small, and typically brooding species. Unexpectedly, coral decline occurred regardless of protection levels and herbivorous fish biomass. Macroalgae declined alongside corals, albeit with higher spatial heterogeneity. These trends signal a loss of structural complexity and ecological functions, highlighting the need for robust sampling design for long-term monitoring, improved environmental licensing to reduce pollution and sedimentation near coral reefs, and effective climate policy to address greenhouse gas emissions.