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 population 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 a distinct east–west population split. To advance basic research and inform genetic management of this endangered species, we present an updated population genomic assessment using a species-specific microarray to analyze over 4,000 samples representing ∼1,500 genets from 12 geographic regions. Data were contributed by more than 30 research and restoration groups. Our analysis identifies nine spatially structured genetic clusters, with low average pairwise FST values of between 0.01 to 0.125. Interestingly, legacy genets from the Florida Reef Tract were admixed between two clusters, one dominant in the Mesoamerican Reef Tract on the western flank and the other cluster appearing in genets from Cuba to the south. Migration surface analyses highlight the influence of major current systems 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 may disrupt natural kinship patterns. These findings refine our understanding of A. palmata’s genetic architecture and underscore the importance of incorporating genomic data into conservation strategies. Competing Interest Statement The authors have declared no competing interest. Footnotes Table S1: metadata was corrected and led to minor changes in the migration surface analysis (Fig 2b). An error in the color coding of populations in Fig 2a was corrected. As a result, language describing the Structure results was clarified throughout the manuscript. A new table displaying the number of migrants was included (Table S2).