As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef-building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region. Populations are generally well-mixed throughout the basin (FST = 0.038), although notable patterns of substructure arise at local and regional scales. Eastern and western populations appear segregated with a genetic break around the Mona Passage in the north, as has been shown previously in other species; however, we find evidence for significant connectivity between Curaçao and Mexico, suggesting that the southern margin of this barrier is permeable to dispersal. Our results also identify a strong genetic break within the Mesoamerican Barrier Reef System associated with complex oceanographic patterns that promote larval retention in southern Belize. Additionally, the diverse genetic signature at Flower Garden Banks suggests its possible function as a downstream genetic sink. The findings reported here are relevant to the ongoing conservation efforts for this important and threatened species, and contribute to the growing understanding of large-scale coral reef connectivity throughout the wider Caribbean.

Microsatellite genotype dataGenotype information for each sample is displayed on a single line. Labels for diploid loci are organized as column headers along the top. Dataset includes 369 individuals collected from 10 geographic locations. This file is formatted for input in GenAlEx v.6.502OfavCarib_allSites.xlsxSTRUCTURE individual output fileSTRUCTURE output file with inferred population assignment probabilities for individual samples (K=5). Burn-in period of 300,000 followed by 1,000,000 MCMC repetitions.K5.indfile.txtSTRUCTURE population output fileSTRUCTURE output file with mean assignment probabilities for each of ten populations, pre-defined by sampling location (K=5). Burn-in period of 300,000 followed by 1,000,000 MCMC repetitions.K5.popfile.txt