Population structure and gene flow in the endangered Caribbean reef-building coral, Acropora palmata

Abstract Populations of the Caribbean reef-building coral, Acropora palmata , have declined sharply since their genetic structure was first characterized in the early 2000s. Previous analyses comprehensively sampled coral colonies across the Caribbean and western North Atlantic but genomic resolution was limited by the number of loci assayed. These analyses indicated extensive asexual reproduction via fragmentation, high outcrossing at the genet level, and an east–west population split. To advance research and inform management of this endangered species, we present an updated population genomic assessment using a SNPmicroarray to analyze ~ 3,900 samples representing ~ 1,400 genets from 12 regions at 18,898 single nucleotide polymorphism loci. Samples were contributed by over 30 research and restoration groups. Our analysis identified nine spatially structured genetic clusters across 12 regions, with low average pairwise F ST values of 0.01 to 0.125. Interestingly, legacy genets from Florida were admixed between two clusters, one dominant in the Mesoamerican Reef Tract on the western flank and the other found in genets from Cuba to the south. Migration surface analyses highlighted the influence of currents on gene flow. Isolation by distance was evident along the Greater Antilles but weak along the Florida Reef Tract. Kinship among wild genets was low across sites, suggesting limited local relatedness; however, assisted sexual reproduction in restoration efforts resulted in distinct kinship patterns. These findings refine our understanding of A. palmata ’s population structure by resolving additional, weakly diverged genetic clusters. and underscore the benefits of standardized high-resolution genotyping workflows for generating conservation-relevant data.