Climate change poses a serious threat to species that demonstrate temperature dependent sex determination (TDS), including marine turtles. Increased temperatures can result in highly female skewed sex ratios and decreased hatchling success. In situ sand temperature data was collected from the nesting depth of hawksbill and green turtles at five study sites along the coast of the Red Sea. The sand temperature profile at four of the sites exceeded the pivotal temperature of 29.2°C (commonly cited in literature) throughout the study duration, which suggests feminization of turtles could be occurring, but further studies need to identify the pivotal temperature in this region. The percentage of days exceeding the commonly cited maximum thermal threshold (33 and 35°C) was calculated for each site at 30 and 50 cm. Sand temperature recordings were as high as 36.0°C at 30 cm depth, and 35.3°C at 50 cm. This suggests that the turtle hatchlings in some areas of the Red Sea could already have high mortality rates due to high temperatures, unless they are locally adapted to these high temperatures. The Red Sea is home to five out of the seven extant species of marine turtles in the world, but not much is known about these populations. The Red Sea is an understudied region of the world, but it has the potential to provide insight on how species might adapt to future climate change due to its high and variable water temperatures (range of 20°C to 35°C) and high salinity (40 PSU). Sites with lower sand temperatures (and lower risk of feminization) may represent priority areas for conservation efforts, particularly in regions facing imminent coastal development.

The Red Sea is one of the warmest, saltiest, and most oligotrophic seas in the world that supports a healthy and extremely diverse coral reef ecosystem. Increasing development along the Saudi Arabian coast may increase eutrophication due to impacts of human population and also oil pollution from increased shipping traffic and refinery activity. The risk of oil pollution combined with increased eutrophication due to coastal development provides a clear stressor interaction which is vastly understudied. Individually, these stressors are known to negatively impact coral reproduction, recruitment, and growth. This study focuses on reef settlement and recovery following experimentally-simulated disturbance scenarios. Carbonate recruitment tiles were placed on the reef and exposed to four treatments: control, nutrient enrichment with slow-release fertilizer, tiles soaked in crude oil, and a combination treatment of nutrient enrichment and oil-coated tiles. At periods of 3, 6, 9, 14, and 17 weeks, tiles were collected to classify the settled community and measure oxygen production. Oil, nitrate, and phosphate were the biggest determining factors predicting settlement and oxygen production of the different treatments. The oil treatment had the least overall settlement and oxygen production, whereas the nutrient treatment had the most turf algal recruitment and oxygen production. The combination treatment had an antagonistic effect on algal growth: the nutrients facilitated growth on the otherwise toxic oiled tiles.

Sponges have important ecological functions on coral reefs because they are regionally abundant, competitively dominant, and process large volumes of seawater. The sponge loop hypothesis proposes that sponges consume dissolved organic carbon (DOC) and then releases the carbon as shed cellular detritus back to the reef benthos. Within this context, we examined the carbon flux mediated by the giant barrel sponge, Xestospongia testudinaria, on reefs in the Red Sea, where sponge abundance is comparatively low relative to coral reefs elsewhere, such as the Caribbean. Seawater samples were collected from the incurrent and excurrent (In-Ex) flow of 40 sponges from inshore, mid-shelf, and offshore reefs between 18° and 22°N latitude off the coast of Saudi Arabia. Concentrations of DOC and living particulate organic carbon (LPOC) were significantly higher in incurrent (ambient) seawater on inshore reefs than mid-shelf and offshore reefs. Consistent with studies of X. muta in the Caribbean, the diet of X. testudinaria is comprised primarily of DOC; mean values of the nutritional components across all sites were 60.5% DOC, 35.7% detritus, and 3.8% LPOC. Taking into account the specific filtration rates of nutritional components and oxygen consumption of sponges across the inshore-offshore gradient, there is evidence (1) of a threshold concentration of DOC below which sponges cease to be net consumers of DOC, and (2) that sponges on offshore reefs are food-limited. Contrary to the sponge loop hypothesis, there was no evidence that X. testudinaria, returned DOC to the benthos in the form of detritus, but was, instead, a net consumer of detritus from the water column. Unlike the cryptic, interstitial sponges that were studied to advance the sponge-loop hypothesis, emergent sponges may have an alternate pathway for returning DOC to the benthos by converting it to sponge biomass rather than sponge detritus.

Knowledge of biodiversity within an ecosystem is essential when trying to understand the function and importance of that ecosystem. A challenge when assessing biodiversity of reef habitats is cryptobenthic fishes, which encompass many groups that have close associations with the substrate. These fishes can be behaviorally cryptic, by seeking refuge within the reef matrix, or visually cryptic, using cryptic coloration to match the surrounding habitat. These factors make visual surveys inadequate for sampling these fishes. One such group of cryptobenthic fishes are the gobies, family Gobiidae, which currently represent over 1600 species, although new species are continually being discovered. Gobies are often small (less than 5 cm), and many species will be associated with a very specific microhabitat type. Due to the understudied nature of the Red Sea, little is known about habitat preferences of gobies within the region. In order to determine the differences in goby community structure within the central Red Sea, fishes were sampled at one reef using 1 m² enclosed rotenone stations from three distinct microhabitats: hard coral, rubble, and sand. Following collection, specimens were photographed and sequenced using COI, to aid in species identification. 232 individuals were collected representing 31 species of goby. Rubble microhabitats were found to host the majority of collected gobies (69%), followed by hard coral (20.6%), then sand (9.9%). Goby assemblages in the three microhabitats were significantly different from each other, and evidence of habitat-specialists was found. These results provide essential baseline information about the ecology of understudied cryptobenthic fishes that can be used in future large-scale studies in the Red Sea region.

Patterns of genetic connectivity can help answer key questions about the evolutionary ecology of fishes. This knowledge is particularly useful when considering the management and conservation of species that are impacted by fisheries. Population connectivity in ocean habitats is heavily influenced by environmental and oceanographic factors. These factors can lead to strong genetic differences within populations, causing fragmentation into smaller subpopulations. The Red Sea exhibits pronounced oceanographic gradients in temperature, chlorophyll, and salinity, which have been assessed in various species’ populations and which have been found to have potential impacts on gene flow. The Red Sea also features strong cyclonic and anticyclonic eddies that may facilitate, or possibly inhibit, the transport of larvae throughout the Red Sea, potentially influencing gene flow themselves. The ability of oceanographic factors like eddies to structure wild fisheries populations in this region has yet to be fully determined. To address this, the genetic composition of two of the most highly fished species, (Plectropomus areolatus and Plectropomus pessuliferus marisrubri), in the Red Sea were evaluated utilizing genetic markers (polymorphic microsatellite loci). Samples from three geographically separate regions along the Saudi Arabian Red Sea coastline, as well as from Sudan, were analyzed to address latitudinal and cross-sea connectivity. I was able to determine that little genetic differentiation exists within Plectropomus species across all regions of the Red Sea, indicating high gene flow for these species throughout. These findings highlight the ability of currents and eddies to transport larvae along and across the Red Sea. The results from this study also indicate that a single population of P. areolatus and a single population of P. pessuliferus marisrubri occurs in the Red Sea. The high degree of genetic flow suggests that each species should be managed as individual units. This study presents a plausible avenue for buffering the effects of overfishing currently occurring in Saudi Arabia; Saudi Arabian fish subpopulations may be reseeded by the Sudanese subpopulations.

The stability of marine photosymbiotic holobionts has major implications for the future of coral reef communities. This study aims to describe the stability of the Red Sea giant clam holobiont over the duration of one year and during induced bleaching stress under laboratory thermal manipulations. Tridacnid clams of the species Tridacna maxima were sampled at three reef locations near the central Saudi coast of the Red Sea. Associated Symbiodinium of Red Sea giant clams have previously been described to be part of only Clade A, which suggests a strong specificity in the clam-algal partnership, but specific types and potential shifting of types within this clade have not been examined for giant clams. The results from this study confirm that tridacnid symbiont types shift over time and the change between three A1 types suggests a biological and functional significance of two undescribed A1 Symbiodinium types. Experimental bleaching shows that Red Sea giant clams, although exposed to rather hot temperatures naturally, will bleach at 34°C after two weeks, and severely bleached clams likely will not recover. During bleaching, Symbiodinium types shift as well, and shift more drastically than seasonal shifts during the year. This shifting may be an evolved characteristic of the giant clam to aid in surviving major changes in the environment. However, more research is needed to determine if these holobionts are capable of keeping up with the global forecast of warming in reef environments.

Corals form a symbiotic relationship with photosynthetic zooxanthellae from the genus Symbiodinium; the breakdown of this symbiosis results in the phenomenon known as coral bleaching. This relationship is especially vulnerable to high temperature stress, although corals may survive if they have resistant types of symbionts, or switch their community composition towards them. To assess the variation of the symbiont community in different environmental conditions, I recorded the temperature and collected samples from six scleractinian coral species and one calcifying hydrozoan, in two inshore, two mid-shelf, and two offshore reefs at 1, 15, and 30m depth, analyzing Symbiodinium diversity using Next Generation Sequencing with the SymPortal profile typing approach. The temperature was very similar for all points in winter, when coral samples were collected, but variation between points increased until a maximum at summer, with the shallower parts of the inshore reefs showing higher temperatures and the points at 30m depth showing the lowest. The Symbiodinium composition was more similar between samples of the same host species than among samples of the same reefs or depths. Coral species from the Pocilloporidae family and Millepora dichotoma showed specific association with different profile types, specifically, intragenomic variants of Symbiodinium type A1, which appears to be dominant in the Red Sea although it has not been reported for these species in other regions. The other species showed specific associations with types previously reported in other regions, mostly from clade C and D, although also having different types and intragenomic variants. For most cases, certain profile types, which can reflect different species or populations, appeared to be dominant in particular environmental conditions, following a distribution related with depth, reef type, or both. In conclusion, this study showed that the Symbiodinium composition depends more on the host species than on the environmental conditions, and within each species the adaptation to environmental gradients can rely on tolerant symbiont species or populations characteristic of the Red Sea, or association with different types and clades that are common also in other regions.

Herbivorous coral reef fishes play an important role in helping to structure their environment directly by consuming algae and indirectly by promoting coral health and growth. These fishes are generally separated into three broad groups: browsers, grazers, and excavators/scrapers, with these groupings often thought to have a fixed general function and all fishes within a group thought to have similar ecological roles. This categorization assumes a high level of functional redundancy within herbivorous fishes. However, recent evidence questions the use of this broad classification scheme, and posits that there may actually be more resource partitioning within these functional groupings. Here, I use a compound-specific stable isotope approach (CSIA) to show there appears to be a greater diversity of functional roles than previously assumed within broad functional groups. The δ13C signatures from essential amino acids of reef end-members (coral, macroalgae, detritus, and phytoplankton) and fish muscle were analyzed to investigate differences in resource use between fishes. Most end-members displayed clear isotopic differences, and most fishes within functional groups were dissimilar in their isotopic signature, implying differences in the resources they target. No grazers closely resembled each other isotopically, implying a much lower level of functional redundancy within this group; scraping parrotfish were also distinct from excavating parrotfish and to a lesser degree distinct between scrapers. This study highlights the potential of CSIA to help distinguish fine-scale ecological differences within other groups of reef organisms as well. These results question the utility of lumping nominally herbivorous fishes into broad groups with assumed similar roles. Given the apparent functional differences between nominally herbivorous reef fishes, it is important for managers to incorporate the diversity of functional roles these fish play.

Although the Red Sea presents a unique environment with high temperature and salinity, it remains an area that is understudied. This lack of information is reflected in many areas, one which is biodiversity. Despite increasing work on biodiversity throughout the Red Sea and an increase in Cephalopoda studies, Cephalopoda in the Red Sea remain underrepresented, which is especially pronounced in molecular analyses. Members of the class Cephalopoda are considered to be major contributors to coral reef ecosystems, serving as part of the food chain and exhibiting population increases due to targeted teleost fisheries and global climate change. In order to assess the biodiversity of Cephalopoda in the Saudi Arabian Red Sea, 87 specimens were collected from 25 reef locations between 17°N and 28°N latitude, as well as from the largest fish market in the Kingdom of Saudi Arabia. Taxonomic identification of specimens was determined using morphological comparisons with previously reported species in the Red Sea and the molecular barcoding region Cytochrome Oxidase I. 84 Red Sea sequences were compared with sequences from GenBank and analyzed using a complement of Neighbor-Joining, Maximum-Likelihood, and Bayesian inference trees. Species complexes were also investigated for Sepia pharaonis and Sepioteuthis lessoniana, which had been previously reported. From 17 cuttlefish, our study yielded three species, two of which matched previously reported species in GenBank. In addition, two distinct clades of Sepia pharaonis were identified. Of 35 squid collected, four species were identified, one of which did not match any other accepted species in literature, while Sepioteuthis lessoniana in the Red Sea formed a distinct clade. From 30 different specimens a total of five genera of Octopoda were present, forming six distinct species. Five Octopoda species collected did not match previously reported species, although many specimens were paralarvae or juveniles, so morphologically we could not compare to previously described species in the Red Sea. Cephalopoda fisheries in the Red Sea is low, and as their populations increase worldwide, this could be a viable fishery for Saudi Arabia. As such, further investigation into the role which cephalopods play in supporting biodiversity in the Red Sea is essential.

Between 33 and 91 percent of marine species are currently undescribed, with the majority occurring in tropical and offshore environments. Sponges act as important microhabitats and promote biodiversity by harboring a wide variety of macrofauna and microbiota, but little is known about the relationships between the sponges and their symbionts. This study uses DNA barcoding to examine the macrofaunal communities associated with sponges of the central Saudi Arabian Red Sea, a drastically understudied ecosystem with high biodiversity and endemism. In total, 185 epifaunal and infaunal operational taxonomic units (OTUs) were distinguished from the 1399 successfully-sequenced macrofauna individuals from 129 sponges representing seven sponge species, one of which (Stylissa carteri) was intensively studied. A significant difference was found in the macrofaunal community composition of Stylissa carteri along a cross-shelf gradient using relative OTU abundance (Bray-Curtis diversity index). The abundance of S. carteri also follows a cross-shelf gradient, increasing with proximity to shore. The difference in macrofaunal communities of several species of sponges at one location was found to be significant as well, using OTU presence (binary Jaccard diversity index). Four of the seven sponge species collected were dominated by a single annelid OTU, each unique to one sponge species. A fifth was dominated by four arthropod OTUs, all species-specific as well. Region-based diversity differences may be attributed to environmental factors such as reef morphology, water flow, and sedimentation, whereas species-based differences may be caused by sponge morphology, microbial abundances, and chemical defenses. As climate change and ocean acidification continue to modify coral reef ecosystems, understanding the ecology of sponges and their role as microhabitats may become more important. This thesis also includes a supplemental document in the form of a spreadsheet showing the number of macrofauna individuals of each OTU found within each sponge sample.