One species can hide another: high genomic diversity and specific population structures among sympatric Pocillopora corals in the French Natural Park of the Coral Sea

Cryptic species challenge accurate assessments of biodiversity and connectivity. Population genomic analyses using thousands of markers now improve inferences of population structure and, ultimately, management strategies. This is particularly relevant for scleractinian corals, which are declining rapidly, yet whose connectivity remains insufficiently documented and mostly inferred from traditional genetic markers. Here, we aimed to confirm or refine patterns of genetic structure previously identified using microsatellites in four major and partially sympatric Pocillopora coral species from New Caledonia ecoregion, where one of the largest marine protected areas, the French Natural Park of the Coral Sea, has been established. Using single-nucleotide polymorphisms (SNPs) harvested from target-capture data of previously studied colonies, we conducted Bayesian clustering and network analyses to reassess genetic structure within each species and compare it with earlier microsatellite-based results. We detected several sympatric and cryptic genetic clusters, as well as substantial genetic differentiation between both sides of Grande Terre, likely influenced by ocean currents. Despite partial sympatry, species and clusters exhibited distinct and sometimes previously undetected genetic structures, probably shaped by species-specific (e.g., reproductive) traits and environment. These findings improve our understanding of connectivity within New Caledonia ecoregion and provide valuable guidance for effective coral conservation in the region. This deposit contains the command lines, scripts, and analysis files related to Oury & Magalon – One species can hide another: high genomic diversity and specific population structures among sympatric Pocillopora corals in the French Natural Park of the Coral Sea.