The physical functionality of reefs depends on the abundance (or cover), capacity to accumulate CaCO3, and structural complexity of each species present in the system32. The stacked plot represents the functional contributions of four coral groups over time. The pie charts illustrate the proportional contributions of each coral group during three different periods. Acropora spp. and Orbicella spp. contain all the species for each of these genera and are illustrated as a single group, as they are the main reef-building corals in the Caribbean and have dominated shallow-water coral-reef habitats throughout the region in geological times42. The group of massive corals includes important reef framework builders from the Diploria, Pseudodiploria, Colpophyllia, Montastraea, and Dendrogyra genera (many of which were severely affected by SCTLD and were included in the second morpho-functional group from the top in Fig. 1a). The other group includes all other coral species, which are largely classified as weedy, submassive, or foliose-digitate corals (included in the third and fourth morpho-functional groups from the top in Fig. 1a) for which little evidence of declines exists. The black arrows indicate major sources of coral decline widely recognized in the literature. White-band disease resulted in severe population declines of acroporids10. The white-pox epidemic has infected many of the remaining colonies of this genus since the 1990s87. Other coral-disease syndromes (e.g., white plague and Caribbean yellow band) that mainly affect Orbicella and other massive species have increased in frequency and virulence over the last three decades (e.g.,7,88). Coral mortality has also continued to increase in the Caribbean and is associated with warm-water bleaching events and other local-scale anthropogenic impacts13,34,89. The grey-dashed arrows indicate that the source of stress remains, although the effects on widespread coral mortality are unclear.