Larval dispersal is one of the most complex phenomena that connects populations when larvae migrate over long distances from their native reefs to a new one. Dispersal outcomes are largely variable among individuals, even siblings, and the factors that drive this variability are not understood, making it challenging to create protection plans for marine species. Clownfish, Amphiprioninae, are among the most important coral reef species economically. Thus, creating protection plans for clownfish is necessary, especially as they are under habitat loss threat. Clownfish are considered an optimum model of organisms for studying larval dispersal and population connectivity mainly due to their relatively short larval dispersive phase and ease of breeding them in captivity. Since dispersal traits are influenced by genes, transcriptomic studies can reveal insights into larval dispersal. Thus, the variation in dispersal outcomes could be better understood if the differential expression of genes related to dispersal, such as swimming abilities, are considered. However, there is a lack of knowledge in the basics of gene expression in clownfish larvae. The aim in this thesis is to explore the ontogenic variability in RNA quantities across development in clownfish larvae as a first step of understanding the nature of their gene expression and optimizing RNA extractions and quantifications methods using clownfish as a model organism. We performed an RNA quantification study using larvae of Amphiprion bicinctus clownfish reared at KAUST SeaLabs. This thesis provides some insights regarding the pooled and individual quantities of RNA across time. The optimal pool size and age for various transcriptomic studies was determined. It was concluded that extracting RNA from young larvae is difficult. Depending on the research, it might be necessary to use older larvae or other techniques. The results from this thesis will build the foundation needed as a first step to perform differential gene expression studying the causes of variability in dispersal traits in A. bicinctus and the link between these traits and transcriptomics.

The relationship between clownfish and sea anemones is a beloved and iconic example of marine symbiosis. However, ecological information in the eastern Red Sea about the endemic Red Sea clownfish, Amphiprion bicinctus, and its host sea anemones remains relatively incomplete. For example, previous studies report that A. bicinctus forms mutualistic relationships with three to five host anemone species in the Red Sea. But the reported number and combination of host anemone species varies substantially among sources and little is known about host anemone distributions at different scales on the eastern coastline. To better understand the ecology of A. bicinctus and its host sea anemones, we conducted 70 surveys in three regions of Saudi Arabia and one region in Djibouti. We then analyzed distribution patterns for all anemone species observed in these regions, to attain deeper knowledge of anemone habitat usage and relative abundance. We recorded six host sea anemone species associated with A. bicinctus in the Red Sea, one of which represents a new case of symbiosis, and we identified differences in species composition and abundance across different reef scales. We noted patterns of decreasing anemone diversity with increasing latitude, beginning at 20° N, and greater overall anemone abundance in the central Red Sea. We also used field and laboratory observations to examine anemonefish abundance, survival, and fecundity on different species of anemones at different life history stages. In sum, this thesis collectively identifies eastern Red Sea anemone hosts for A. bicinctus, evaluates their regional and fine-scale distributions, and assesses how different anemone species impact their anemonefish occupants on different levels.