The Red Sea has long been recognized as a global hotspot of marine biodiversity. Ongoing overfishing, however, is threatening this unique ecosystem, recently leading to the identification of the Red Sea as one of three major hotspots of extinction risk for sharks and rays worldwide. Elasmobranch catches in Saudi Arabian Red Sea waters are unregulated, often misidentified and unrecorded, resulting in a lack of species-specific landings information, which would be vital for the formulation of effective management strategies. Here we employed an integrated approach of fisheries dependent and independent survey methods combined with molecular tools to provide biological, ecological and fisheries data to aid in the assessment of the status of elasmobranch populations in the Red Sea. Over the course of two years, we conducted market surveys at the biggest Saudi Arabian fish market in Jeddah. Market landings were dominated by, mostly immature individuals - implying both recruitment and growth overfishing. Additionally, we employed baited remote underwater video (BRUVS) and longline surveys along almost the entire length of the Red Sea coast of Saudi Arabia as well as at selected reef systems in Sudan. The comparison of catch per unit effort (CPUE) data for Saudi Arabian Red Sea BRUVS and longline surveys to published data originating from non-Red Sea ocean systems revealed CPUE values several orders of magnitude lower for both survey methods in the Red Sea compared to other locations around the world. Finally, we infered the regional population structure of four commercially important shark species between the Red Sea and the Western Indian Ocean.We genotyped nearly 2000 individuals at the mitochondrial control region as well as a total of 20 microsatellite loci. Genetic homogeneity could not be rejected for any of the four species across the spatial comparison. Based on high levels of region-wide exploitation, we suggest that, for management purposes, the population structure of all four species should be considered as single stock in the three marginal seas surrounding Arabia. Overall, our combined results indicate a severe depletion of sharks in Saudi Arabian Red Sea waters, likely caused by drastic overfishing of elasmobranch populations.

Observing populations at different spatial scales gives greater insight into the specific processes driving genetic differentiation and population structure. Here we determined population connectivity across multiple spatial scales in the Red Sea to determine the population structures of two reef building corals Stylophora pistillata and Pocillopora verrucosa. The Red sea is a 2,250 km long body of water with extremely variable latitudinal environmental gradients. Mitochondrial and microsatellite markers were used to determine distinct lineages and to look for genetic differentiation among sampling sites. No distinctive population structure across the latitudinal gradient was discovered within this study suggesting a phenotypic plasticity of both these species to various environments. Stylophora pistillata displayed a heterogeneous distribution of three distinct genetic populations on both a fine and large scale. Fst, Gst, and Dest were all significant (p-value<0.05) and showed moderate genetic differentiation between all sampling sites. However this seems to be byproduct of the heterogeneous distribution, as no distinct genetic population breaks were found. Stylophora pistillata showed greater population structure on a fine scale suggesting genetic selection based on fine scale environmental variations. However, further environmental and oceanographic data is needed to make more inferences on this structure at small spatial scales. This study highlights the deficits of knowledge of both the Red Sea and coral plasticity in regards to local environmental conditions.

Phytoplankton is at the basis of the marine food chain and therefore play a fundamental role in the ocean ecosystem. However, the large-scale phytoplankton dynamics of the Red Sea are not well understood yet, mainly due to the lack of historical in situ measurements. As a result, our knowledge in this area relies mostly on remotely-sensed observations and large-scale numerical marine ecosystem models. Models are very useful to identify the mechanisms driving the variations in chlorophyll concentration and have practical applications for fisheries operation and harmful algae blooms monitoring. Modelling approaches can be divided between physics- driven (dynamical) approaches, and data-driven (statistical) approaches. Dynamical models are based on a set of differential equations representing the transfer of energy and matter between different subsets of the biota, whereas statistical models identify relationships between variables based on statistical relations within the available data. The goal of this thesis is to develop, implement and test novel dynamical and statistical modelling approaches for studying and forecasting the variability of chlorophyll concentration in the Red Sea. These new models are evaluated in term of their ability to efficiently forecast and explain the regional chlorophyll variability. We also propose innovative synergistic strategies to combine data- and physics-driven approaches to further enhance chlorophyll forecasting capabilities and efficiency.

Coral reefs are among the most diverse marine ecosystems, but they are threatened by climate change. The foundation of reef ecosystems is the coral holobiont or metaorganism that consists of the coral animal host, photosynthetic microalgae, bacteria, and viruses (among other organisms). While microalgae provide the energy for corals to build the massive three-dimensional skeletons, bacteria support functions related to metabolism, immunity, and environmental adaptation. Conversely, the function of viruses is less well understood. Although viruses were previously associated with coral disease and bleaching, we are missing an overall understanding of the diversity and identity of viruses associated with corals, in particular for understudied areas such as the Red Sea. Here we characterized coral-associated viral community composition using a large metagenomic and metatransciptomic dataset covering > 1 billion sequences across > 100 coral samples collected from 14 different coral species in the central Red Sea. The viral sequence portion shows that coral species significantly differ from each other, but the most abundant viral families were consistently present. Notably, we found a pervasive abundance of Baculoviridae in metagenomes. In contrast, Polydnaviridae were the most abundant viruses in metatranscriptomes, highlighting that the combined approach of metagenomics and metatranscriptomics is informative with regard to deciphering viral diversity and activity. Our study provides a first comprehensive description of viruses associated with Red Sea corals. In line with previous studies, we confirm the presence of Baculoviridae, Polydnaviridae, Phycodnaviridae, Mimiviridae, and Herpesviridae, which may be considered viral families that are globally and commonly associated with corals. The reason for the pervasive abundance of Baculoviridae in Red Sea corals at present remains unknown, but it is tempting to speculate that the association is related to the uniquely warm and salty environment of the Red Sea.

A diversity of human-assisted approaches to rehabilitate and boost coral health have been suggested and investigated throughout the past years. Vitamins and trace-metal supplementation is a well-known strategy in human medicine and aquaculture, but vitamin addition is not currently actively tested for coral growth and recovery. These molecules are essential cofactors that have been correlated with coral thermal resistance and upregulated in corals treated with beneficial microorganisms (i.e., probiotics). To assess the effects of B12, B6 and zinc supplementation on coral health, we conducted a 2-month experiment in an open-closed-loop system mesocosm joined to a peristaltic pump continuously dosing the vitamins and/or zinc to individual 250 L tanks. Fragments of five different colonies of Acropora hemprichii were randomly distributed into the respective treatment tanks (B12, B6, zinc, multi-treatment and control). After 21 days, the corals were exposed to a pulse (1 day) of thermal stress, followed by three weeks of recovery. Substantial mortality (55%) in the control treatment was observed during the stress and recovery, with B12, B6, zinc and multi treatments exhibiting significantly less mortality (<20%). Coral health data combined with analysis of microbiome and metabolomic approaches suggest that both vitamins and zinc have a positive effect on coral health recovery. This study is the first to provide evidence that complex B-vitamins accompanied by zinc supplementation, can be a valuable tool for coral reef rehabilitation, and paves the way to further understanding specific mechanisms by which these nutrients promote coral health will be needed.

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This thesis will analyse a sample of maritime terminology used along the Saudi Red Sea coast and attempt to understand why lexica are lacking in such terms; an issue which can be linked to the language change was a consequence of the interaction between Arabs and other ethnic communities since the advent of Islam. This change raised alarm among lexicographers and linguists at the time of documenting the terminology, who set off on long journeys to collect the pure language. In their word collecting they selectively documented the language, ignoring a huge amount of spoken registers because their aim was to collect the classical form of Arabic in order to help Muslims gain a deeper understanding of the Qur>[n and |ad\th. This created gaps in Arabic lexicography, which lacks terminology for material culture. The information about maritime material cultural terminology in the mainstream lexica is disappointing. Although a few terms are listed, lexicographers have failed to provide unambiguous definitions. This study demonstrates why a great number of such terms since the classical time period has not been listed in the available lexica, and what the factors are which led to this situation. Hence, this study is based on maritime terms extracted from informal meetings I had with mariners and fishermen on the Red Sea Saudi coast about their life at sea before the introduction of the engine to vessels. The collected terms are to be investigated against their presence in lexica both synchronically and diachronically. Understanding the meanings of such ignored terms is one of the most important puzzles and this study attempts to solve it by investigating the semantic links between words and the conceptual meanings of their roots following a hypothesis based on Ibn F[ris (d. 395/1004); which assumes that all terms derived from Arabic roots should share a general conceptual meaning. While in the absence of maritime terms in lexica a hypothesis devised from Agius's theoretical framework was applied to search such terms in literary and non-literary works, which assumed to be an alternative source to lexica and examine their occurrence in text and context by reconstructing their origin, function and use.

Connectivity is an important component of coral reef studies for its role in the enhancement of ecosystem resilience. Previous genetic structure and physical circulation studies in the Red Sea reveal a homogeneity within the coral reef complexes in the central and northern parts of the basin. Yet, genetic isolation and relatively low connectivity has been observed in the southern Red Sea. Raitsos et al. (2017) recently hypothesized that coral reefs in the southern Red Sea are more connected with regions outside the basin, rather than with the central and northern Red Sea. Using a physical circulation approach based on a 3-D backward particle tracking simulation, we further investigate this hypothesis. A long-term (> 10 years), very high resolution (1km) MITgcm simulation is used to provide detailed information on velocity in the complex coastal regions of the Red Sea and the adjacent narrow Bab-El-Mandeb Strait. The particle tracking simulation results support the initial hypothesis that the coastal regions in the southern Red Sea exhibit a consistently higher connectivity with the regions outside the Bab-El-Mandeb Strait, than with the central and northern Red Sea. Substantially high levels of connectivity, facilitated by the circulation and eddies, is observed with the coastal regions in the Gulf of Aden. A strong seasonality in connectivity, related to the monsoon-driven circulation, is also evident with the regions outside of the Red Sea. The winter surface intrusion plays a leading role in transporting the particles from the Gulf of Aden and the Indian Ocean into the Red Sea, while the summer subsurface intrusion also supports the transport of particles into the Red Sea in the intermediate layer. In addition, the connectivity with the central and northern Red Sea is more affected by the intensity of the eddies. Evidence also suggests that potential connectivity exists between the coastal southern Red Sea and the coasts of Oman, Socotra, Somalia, Kenya, Tanzania and the north coast of the Madagascar.

Thesis (Ph. D.)--Texas State University-San Marcos, 2006. / Vita. Appendix: leaves 295-329. Includes bibliographical references (leaves 330-348).