Genome skimming illuminates hidden species diversity and Symbiodiniaceae associations in east Pacific Pocillopora corals

Biodiversity conservation relies upon accurate species taxonomy to support decision-making. Stony corals in the genus Pocillopora are critical ecosystem engineers in the Eastern Tropical Pacific (ETP), however, Pocillopora species diversity in the region is still unresolved due to high phenotypic plasticity, lack of diagnostic morphological characters, and low-resolution genetic markers used in previous studies. To address this gap, we leveraged low-coverage whole-genome sequencing for 342 Pocillopora coral samples collected from Panamá, Costa Rica, Colombia, Ecuador, and Clipperton Atoll (France). Sequence data were used to recover mitochondrial genomes and barcode loci, ultraconserved elements (UCEs), and genome-wide SNPs for species delimitation. Together, our data revealed the existence of four distinct Pocillopora species in the ETP, corresponding to the nominal species P. effusa (Veron, 2000), P. meandrina Dana, 1846, P. capitata Verrill, 1864 and P. lacera Verrill, 1869. Two P. capitata population sub-clusters with moderate genetic differentiation were separated between offshore islands and continental sites, and individual colonies with signatures of admixture between P. effusa and P. lacera were identified at Isla del Coco, Costa Rica. Additionally, Pocillopora-associated algal symbiont community profiling identified Cladocopium and Durusdinium as dominant genera that varied according to the host species, with P. lacera demonstrating higher specificity for associations with Cladocopium. This study highlights the power of genome skimming as an affordable, high-resolution approach to rapidly assess coral species diversity and algal symbiont associations, thereby empowering marine conservation.