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

Populations of the Caribbean reef-building coral, Acropora palmata, have declined rapidly since their population genetic structure was first described in the early 2000s. Previous analyses sampled coral colonies across the Caribbean and western North Atlantic but were limited to only 5 to 8 microsatellite loci. These studies concluded that A. palmata reproduces extensively asexually through fragmentation, is generally outbred at the genet level, and is split into an eastern and a western population. To further support basic research and genetic management of this endangered species, we provide an updated assessment of the population genomic structure of A. palmata from over 4000 samples representing ~1500 genets assayed using a coral-algal microarray. These data cover 12 geographic regions and were contributed by >30 groups. Our new analysis identifies nine spatially structured genetic clusters, with low average pairwise FST values of 0.01 and 0.125 within and between them. Interestingly, legacy genets from the Florida Reef Tract were admixed between two clusters, with similarity to genets from the Mesoamerican Reef Tract on the western flank and Bahamas and Cuba to the south and east, respectively. Migration surface analyses support the influence of major current patterns on A. palmata gene flow. Isolation by distance was observed along the Greater Antilles while the Florida Reef Tract showed no such pattern. Relatedness among genets was similarly low across wild sites but assisted sexual reproduction may alter natural patterns of kinship. This updated analysis supports the previous conclusion of a generally outbred, widely dispersing species