Biodiversity of coral reefs is higher than in any other marine ecosystem, and significant research has focused on studying coral taxonomy, physiology, ecology, and coral-associated fauna. Yet little is known about symbiotic copepods, abundant and numerous microscopic crustaceans inhabiting almost every living coral colony. In this thesis, I investigate the genetic diversity of different groups of copepods associated with reef-building corals in distinct parts of the Indo-Pacific; determine species boundaries; and reveal patterns of biogeography, endemism, and host-specificity in these symbiotic systems. A non-destructive method of DNA extraction allowed me to use an integrated approach to conduct a diversity assessment of different groups of copepods and to determine species boundaries using molecular and taxonomical methods. Overall, for this thesis, I processed and analyzed 1850 copepod specimens, representing 269 MOTUs collected from 125 colonies of 43 species of scleractinian corals from 11 locations in the Indo-Pacific. The genetic assessment of the most abundant copepod morphotypes associated with hermatypic corals in Lizard Island (Great Barrier Reef) revealed a large number of species previously unknown for this region. Analyses of diversity and patterns of biogeographical distribution of copepods associated with Galaxea corals throughout the Indo-Pacific showed that the species diversity of this group is high and appears to be regionally specific, an uncommon pattern in most coral reef-associated invertebrates. Results for the symbiotic copepod fauna of Red Sea pocilloporid corals, a family of corals with a high level of morphological variability within and among its members, showed that the majority of the discovered poecilostomatoid copepods belong to the genus Spaniomolgus, which demonstrated a significant genetic diversity of morphologically-similar species. Assessment of the diversity of copepods associated with the Red Sea mushroom corals revealed several undescribed species and showed no evidence of specificity to the hosts neither on species nor on the family level, which contradicts a modern assumption of high host-specificity of copepods. Overall, this dissertation is a first study of genetic diversity of copepods associated with invertebrates, and it provides substantial insight into the diversity of coral-associated microcrustaceans and insight to patterns of their host-specificity as well as distribution around the Indo-Pacific.
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