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To persist in oligotrophic waters, reef-building corals rely on nutritional interactions with their intracellular symbionts: photosynthetic dinoflagellates of the genus Symbiodinium. This relationship is threatened by increasing environmental stress, which can stimulate loss of these symbionts from coral tissues (‘coral bleaching’). Members of the genus Symbiodinium display high levels of genetic diversity, and demonstrate a corresponding diversity in physiological responses to environmental change. However, the true diversity and potential for genetic adaptation in this genus remain poorly characterised.  This thesis aimed to further the understanding of symbiont diversity and adaptive potential by conducting assessments of Symbiodinium at Atauro Island and the neighbouring Timor-Leste mainland. These sites have previously been shown to be of outstanding conservation value, with extremely high levels of coral diversity. Atauro Island also possibly hosts the highest diversity of reef fish in the world. However, the Symbiodinium communities at these sites have never been assessed. Two specific objectives were therefore addressed here. The first was to measure Symbiodinium diversity at Atauro Island (four sites) and Timor (three sites), using direct sequencing of three gene regions: cob gene, mitochondrion; ITS2 region, nucleus; and psbAncr region, chloroplast; in addition to Next Generation Sequencing of the ITS2 region. The second objective was to establish evidence for Symbiodinium hybridisation, a potentially rapid evolutionary mechanism that may facilitate adaptation to environmental stress, by looking for genetic incongruences between Symbiodinium organelles.  Coral symbionts of Timor-Leste were found to be similar to those from other coral reefs of the Indo-Pacific, with several host generalist and multiple host specific types observed. However, there were also several novel Symbiodinium types found (C15p, C15q, C1x, C1z). Despite their geographic proximity, there were strong differences observed between the symbiont communities of Atauro Island and mainland Timor. In particular, the coral genus Pocillopora hosted clade C symbionts exclusively at Atauro Island, while it hosted clade D exclusively at Timor sites. Other symbiont types also showed geographic partitioning, and diversity was 1.25 times higher at Atauro Island, a figure consistent for the cob and ITS2 regions. While Timor sites have comparable Symbiodinium diversity to other reefs globally, Atauro has noticeably elevated Symbiodinium diversity. Next Generation Sequencing affirmed these patterns, with Atauro Island sites having much more diverse cryptic populations of Symbiodinium, largely driven by symbionts in clade C. The exception was clade D symbionts, which were proportionally far more diverse at Timor, a pattern consistent in multiple coral genera.  There was strong evidence of genetic incongruence at two Atauro Island sites, with all testing procedures identifying genetic discordance between organellar and nuclear genomes, consistent with theoretical predictions of hybridisation. This study therefore presents strong evidence for Symbiodinium hybridisation, and its corroboration by multiple loci is significant. Putative hybrid Symbiodinium always had a common type as one of the possible parents, with a rarer symbiont as the other. For example, one putative hybrid had organellar genes of the common generalist Symbiodinium C40, while it was identified as the rare type C3z with the ITS2 region. Both of these Symbiodinium types were also found in congruent relationships, which strongly supports the possibility that they sexually reproduced to produce the incongruent putative hybrid.   Environmental stressors, such as increased temperature, turbidity and sedimentation, are suggested reasons for lowered Symbiodinium diversity at Timor, as they may impose a selection pressure on corals to only keep highly beneficial symbionts. This reduction in diversity likely limits the potential for adaptive change through methods like hybridisation, and highlights the need to assess and conserve symbiont diversity to the same extent as coral diversity.

Symbiodinium diversity and potential hybridisation on the highly biodiverse coral reefs of Timor-Leste