The evolution and systematics of corals have been difficult to unravel despite being the fundament of one of the world\u27s most charismatic ecosystems. Coral diversity and diversification processes are not well understood due to morphological plasticity, potential hybridization and generally high rates of dispersal. Both geographically and methodologically extensive studies are needed to improve our understanding of coral ecology and evolution, including spatial biodiversity processes involving hosts and their associated symbionts. This dissertation investigates coral evolution in three complementary studies using the genus Galaxea L. as a model. First, I ask whether endosymbiotic community composition differentiate among morphologically cryptic genetic lineages in G. fascicularis. The Symbiodinium ITS2-sequence was metabarcoded using next generation sequencing (NGS) and community assembly was analyzed with joint distribution models. Symbiodinium communities were found to cluster into three regular community types that cannot be explained by environment or host genotype, potentially indicating species interactions between Symbiodinium types. Second, I assessed how spatial connectivity between geographic populations corresponds to neutral differentiation on the subspecies level using population genomic methods. Coral populations from the Ryukyu archipelago, the Daito islands, and the Ogasawara Islands were characterized by restriction site-associated DNA sequencing (RAD) to investigate whether the Daito Islands could be a stepping stone between Ryukyu and Ogasawara. The Ogasawara population was found to be highly differentiated and to have diverged under little amounts of continuous gene flow since the early Pliocene. No stepping stone role of the Daito Islands was found and the Ogasawara population may receive most migrants from the Ryukyu Islands, which was consistent with the dispersal patterns predicted by a oceanographic dispersal model. Lastly, I investigated the evolutionary history in the genus Galaxea taking a phylogeographic approach. I asked whether the genetically well-differentiated and sympatric lineages within G. fascicularis in Okinawa maintain their separation over geographic space and to what extent their spatial distributions overlap in the genus distribution range. Galaxea field collections were gathered from across the Indo-Pacific, and complemented by museum specimens to increase geographical coverage. At the same time the relationship between genetic lineages and taxonomic species was evaluated based on five out of seven currently accepted species (G. fascicularis, G. astreata, G. cryptoramosa, G. paucisepta, G. horrescens). The genus Galaxea clustered into three highly divergent clades; one Indo-Pacific, one Pacific, and one basal small clade found in Chagos. All morphological species were part of the Pacific clade. Overall this study indicates spatial rather than ecological or symbiosis-related processes to drive diversification and that the current taxonomy does not reflect biological species in this genus.Okinawa Institute of Science and Technology Graduate Universit
