Genetically divergent shallow and mesophotic Stephanocoenia intersepta coral populations across Florida Keys National Marine Sanctuary

Abstract Population genetic analyses can provide useful data on species’ regional connectivity and diversity which can inform conservation and restoration efforts. In this study, we quantified the genetic connectivity and diversity of Stephanocoenia intersepta corals from shallow (<30 m) to mesophotic (30–45 m) depths across Florida Keys National Marine Sanctuary. We generated single nucleotide polymorphism (SNP) markers to identify genetic structuring of shallow and mesophotic S. intersepta populations. We uncovered four distinct genetic lineages with varying levels of depth-specificity. Shallow lineages exhibited lower heterozygosity and higher inbreeding relative to depth-generalist lineages found predominantly on mesophotic reefs. Estimation of recent genetic migration rates demonstrated that mesophotic populations are more prolific sources than shallow populations, particularly in the Lower Keys and Tortugas Bank. Additionally, we compared endosymbiotic Symbiodiniaceae communities among S. intersepta populations using the ITS2 region and SymPortal analysis framework, identifying symbionts from the genera Symbiodinium, Breviolum, and Cladocopium. Symbiodiniaceae communities varied significantly across depth and location and exhibited significant, but weak correlation with host population structure and genotype. Together, these data demonstrate that despite population genetic structuring across depth, mesophotic populations may provide refuge for shallow populations moving forward and remain important contributors to the overall genetic diversity of this species throughout the region. This study highlights the importance of including mesophotic as well as shallow coral populations in population genetic assessments and informs future science-based management, conservation, and restoration efforts within Florida Keys National Marine Sanctuary.