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Abstract The abundance of many Caribbean corals has declined over the past few decades, yet nowPorites astreoidesis more common on many shallow reefs than in the 1980s and shows evidence of local adaptation. We compare the small‐scale (1–8000 m) genetic structure of this brooding species and the broadcasting coralOrbicella annularison reefs (<14 m depth) in St. John, US Virgin Islands, to examine how larval dispersal and asexual propagation contribute to the retention of genotypes within reefs. Populations ofP. astreoideshave genetic structure across reefs separated by a few 100 m, increased relatedness within reefs, and parthenogenetic larval propagation confirmed by parent–offspring genotyping. Within reefs,P. astreoidescolonies <1 m apart are more related, independent of clonal reproduction, than corals at greater distances. In contrast,O. annularislacks across‐reef genetic structure, has low relatedness within and among reefs, and does not produce asexual larvae. Small‐scale genetic structure and high relatedness inP. astreoidesare evident even without considering asexual propagation, but asexual reproduction enhances these differences. Neither species shows the genetic signature of inbreeding or reduced genotypic diversity despite the high within‐site relatedness ofP. astreoides. Monitoring on these reefs from 1987 indicates thatPoriteshas increased in abundance whileOrbicellahas decreased in abundance. The success ofPoritesis due to greatly increased settlement and recruitment compared withOrbicella. Together these results indicate that high numbers of locally retained and successful genotypes might explain the relative success ofPoriteson shallow, present‐day reefs in the Caribbean. 

In 1983 to 1984, a mass mortality event caused a Caribbean-wide, >95% population reduction of the echinoid grazer, Diadema antillarum . This led to blooms of algae contributing to the devastation of scleractinian coral populations. Since then, D. antillarum exhibited only limited and patchy population recovery in shallow water, and in 2022 was struck by a second mass mortality reported over many reef localities in the Caribbean. Half-a-century time-series analyses of populations of this sea urchin from St. John, US Virgin Islands, reveal that the 2022 event has reduced population densities by 98.00% compared to 2021, and by 99.96% compared to 1983. In 2021, coral cover throughout the Caribbean was approaching the lowest values recorded in modern times. However, prior to 2022, locations with small aggregations of D. antillarum produced grazing halos in which weedy corals were able to successfully recruit and become the dominant coral taxa. The 2022 mortality has eliminated these algal-free halos on St. John and perhaps many other regions, thereby increasing the risk that these reefs will further transition into coral-free communities.