Phylogenomics of Indo-Pacific Porites

Porites corals are vital components of tropical reef ecosystems worldwide, serving as ecosystem engineers and hubs of biodiversity in shallow water coral reefs. Despite their ecological significance and the widespread use of Porites spp as model for research, the species richness and evolutionary relationships of species within the genus remains elusive. In this study, we analyze genomic data from 330 colonies of Porites from 17 localities across the Indo-Pacific region based on the reduced representation genomic approach ezRAD. We retrieved 41,108 SNPs and provided a phylogenomic hypothesis for 29 nominal species and 10 unknown morphologies, recovering 15 deeply rooted molecular clades. Among these, 12 clades included samples corresponding to single distinct morphospecies. One did not match any described morphology. The remaining two clades comprised species complexes, which included various massive and encrusting morphologies commonly used in experimental biology. Within these complexes, we observed additional geographic or morphological structure, indicating complex evolutionary dynamics, possibly reflecting distinct species, isolated populations or hybridization. Additionally, single divergent samples underscored the importance of more sampling to define species boundaries and refine phylogenomic relationships. We also integrated our findings with previous phylogenetic datasets and their respective sampling localities, challenging traditional notions about Porites species geographic distributions. Overall, our findings indicate a need to revise past synonymies and to formally establish new species. This research holds significant implications for downstream research and conservation. A precise understanding of Porites species and their diversity and distributions will be necessary for effective reef restoration and management.