The field of marine population connectivity is receiving growing attention from ecologists worldwide. The degree to which metapopulations are connected via larval dispersal has vital ramifications for demographic and evolutionary dynamics and largely determines the way we manage threatened coastal ecosystems. Here we addressed different questions relating to connectivity by integrating direct and indirect genetic approaches over different spatial and ecological scales in a coral reef fish in the Red Sea. We developed 35 novel microsatellite loci for our study organism the two-band anemonefish Amphiprion bicinctus (Rüppel 1830), which served as the basis of the following approaches. First, we collected nearly one thousand samples of A. bicinctus from 19 locations across 1500 km along the Saudi Arabian coast to infer population genetic structure. Genetic variability along the northern and central coast was weak, but showed a significant break at approximately 20°N. Implementing a model of isolation by environment with chlorophyll-a concentrations and geographic distance as predictors we were able to explain over 90% of the genetic variability in the data (R2 = 0.92). For the second approach we sampled 311 (c. 99%) putative parents and 172 juveniles at an isolated reef, Quita al Girsh (QG), to estimate self-recruitment using genetic parentage analysis. Additionally we collected 176 juveniles at surrounding locations to estimate larval dispersal from QG and ran a biophysical dispersal model of the system with real5 time climatological forcing. In concordance with model predictions, we found a complete lack (c. 0.5%) of self-recruitment over two sampling periods within our study system, thus presenting the first empirical evidence for a largely open reef fish population. Lastly, to conceptualize different hypotheses regarding the underlying processes and mechanisms of self-recruitment versus long-distance dispersal in marine organisms with pelagic larval stages, I introduce and discuss the concept of “origin effects”, providing the theoretical background to some of the questions that have arisen during this research. Overall, this thesis has generated significant new insights into the patterns of coral reef fish connectivity, specifically for the Red Sea, where such information has previously been scarce.

Coral bleaching, i.e. the loss of photosynthetic algal symbionts, caused by ocean warming is now the main factor driving reef decline, but not all corals are affected equally. Corals from the Arabian Seas have unusually high temperature tolerances, and recently studies implicated salinity as one of the contributing factors. In particular, a recent heat stress experiment at different salinities using the model system Aiptasia and Red Sea corals, showed that cnidaria at large bleach less at heat stress under high salinities and that this is associated with an increase of the osmolyte, floridoside Here we were interested to assess microbial community changes under heat stress at different salinity levels and whether this could help to explain the increase in thermal tolerance of the metaorganism at high salinities. We determined microbial community composition via HiSeq 16S rRNA gene amplicon sequencing of two anemone strains that differ in their associated symbionts, namely H2-SSB01 (type B1) and CC7-SSA01 (type A4), after six days under ambient (25 °C) and heat stress (34 °C) temperatures at salinities of 36, 39, and 42. Both anemones harbored distinct microbial communities, irrespective of temperature or salinity, that were also different from the bacteria in surrounding seawater. Within both host-endosymbiont pairings, the bacterial community composition at low (36) and intermediate (39) salinities did not differ between ambient and heat stress, but was significantly different at high (42) salinities. Subsequent elucidation of bacterial indicator species revealed several taxa that could be associated with a response to temperature and salinity. Our results underline that microbial community composition adjusts under different environmental settings. Importantly, microbial community dynamics of H2-SSB01 aligned with observed differences in bleaching susceptibility and thermal tolerance, whereas the pattern remains unclear for CC7-SSA01, which harbors an intrinsically higher thermal tolerance. Such responses could argue for a contribution of the microbiome to the observed increase in temperature tolerance of the Aiptasia metaorganism at increased salinities. An alternative interpretation is that the microbiome changes denotes a parallel response to changing salinities.

Ecosystems comprise large groups of highly interdependent organisms. Cnidarians, such as sea anemones and corals, are keystone species in many marine ecosystems, especially coral reefs. Each individual cnidarian also constitutes an ecosystem unto itself, a "holo- biont", consisting of the host animal and accompanying microbial symbionts. To interro- gate cnidarian holobionts, I used computational approaches to analyze the transcriptomes of three cnidarians and build mechanistic models of their microbial symbionts. In par- ticular, I analyzed and annotated the transcriptomes of the cauliflower coral Pocillopora damicornis, the lined sea anemone Edwardsiella lineata, and the starlet sea anemone Ne- matostella vectensis, providing information about the molecular functions expressed by these organisms, and allowing development of a corresponding set of public databases: PocilloporaBase, EdBase, and an updated version of StellaBase, that facilitate access to the corresponding datasets. Additionally, I developed a method to infer the phylogenetic antiquity of transcripts. This method also allowed me to identify transcripts from other organisms (e.g., microbes) belonging to the anemone or coral holobiont. In parallel – in order better to understand the microbial symbionts that share envi- ronments with cnidarian hosts, I also developed new computer-simulation approaches for modeling metabolic interactions between different microbial species. These approaches are based on genome-scale stoichiometric reconstructions of metabolic networks and on Flux Balance Analysis (FBA). In addition to contributing to the development and testing of a new FBA-based platform for modeling communities in structured environments (Compu- tation Of Microbial Ecosystems in Time and Space, or COMETS), I used this platform for specific in silico experiments on microbial symbiosis. In particular, I computed all pairwise interactions between 582 different prokaryotic models, and identified global patterns of pu- tative positive (cross-feeding) vs. negative (food competition) interactions in this matrix of species pairs. I found that about 7% of the pairs yielded a greater biomass when grown together than when grown separately as monocultures. Despite existing challenges, such as the limitations of gap-filling steps in model construction and the need for a better knowl- edge of nutrient composition in natural environments, this approach could in the future help forecast shifts in the coral holobiont under likely scenarios of marine environmen- tal changes. In general, this work demonstrates how the integration of high-throughput sequencing technology and mechanistic systems-biology simulations, can provide unique tools to analyze interactions between microbes, and to mitigate or reverse adverse changes in marine ecosystems.

In 2010, Thailand’s Andaman Sea experienced unprecedented mass coral bleaching. Between 50% to 90% of corals suffered bleaching along the Andaman coast both inside and outside Marine Protected Areas (MPAs). This dissertation examines the implications of climate change for these coral reef ecosystems in MPAs. The study explores the potential and effectiveness of conservation management strategies using MPAs and resilience building to address this global challenge in the context of Thailand. This dissertation examines how resilience-based management can be enhanced in Thailand’s MPAs on the Andaman coast in the face of climate change. In particular, the research: 1) Identifies resilient reefs in the Andaman bioregion, 2) Assesses coral reef resilience in a specific MPA to identify management interventions, 3) Examines current MPA coverage and suggests strategies to improve coverage, and 4) Illustrates the potential of social media to enhance coral reef resilience in Thailand. The study employs a mixed methods approach consisting of literature review, a review of available secondary data, workshops, field surveys and social media data tracking. Twenty-two resilience indicators were selected and used to assess reefs at 62 survey stations across the eastern Andaman bioregion. A review of existing Andaman MPA coverage, spacing and design was conducted to determine the gaps and opportunities for expanding the MPA network. A science communication campaign focused on the importance of parrotfish in saving coral reefs using online social media was launched and monitored. The study sites were classified into high (28), moderate (23) and low (11) resilience based on resilience scores. The results provide the first comprehensive resilience assessment of coral reefs in the Andaman sea. The identified resilient reef areas serve as cornerstones in developing a more resilient MPA network and provide a conservation-based platform for long-term marine spatial planning in the eastern Andaman region. Resilience scores for Mu Ko Surin National Park were analyzed in more detail to provide an example of the process for undertaking a finer scaled analysis with a localized weighting system. Management interventions were developed accordingly including strict protection areas and recovery zone designations aiming to improve coral resilience. Expanding MPA coverage and developing MPA networks is an urgent priority for Thailand to reach the CBD target of at least 10% of marine and coastal habitat protected by 2020. This study suggests three important areas for consideration: 1) Expanding MPAs by prioritizing resilient areas and incorporating other types of conservation areas; 2) A ‘bottom-up’ approach that incorporates adaptive and flexible governance; and 3) Implement biological corridors to address key shortcomings of current MPAs. The findings from the parrotfish campaign highlighted the importance of science communication and the usefulness of social networks for conservation. The campaign demonstrated that social media, when used properly and effectively, is powerful for public engagement and helps create an enabling environment for change in public policy and practice for marine conservation. This dissertation offers insights into opportunities to improve the management of large tropical marine ecosystem and how coral reef resilience can be enhanced by developing MPA networks in the face of climate change. / Graduate

Ocean warming and increased sedimentation from coastal activities are major threats to coral persistence. This study assessed the effects of increased temperature and sedimentation on the survival and growth of Acropora cervicornisrecruits. The potential for adults from different regions and genotypes to confer their offspring with higher or lower tolerance to heat and/or sediment was also determined. Gametes were collected and brought to the laboratory for cross fertilization of different genotypes within the regions collected. Larval rearing and settlement were then performed in the laboratory. Newly settled recruits were reared at 29 and 31°C (current summer temperature for August 2017 and +2°C as predicted for 2050) and 4 deposited sediment levels and turbidity (0, 30, 60, and 120mg cm-2, corresponding to 0, 4.52-5.35, 8.16-9.7, and 18.53-19.4 NTU). Recruit survival and growth were measured weekly for 3 months. Increased temperature reduced survival, suggesting faster usage of energy reserves. Regardless of temperature, survival was maximized under 30mg cm-2sediment; the highest sediment level drastically reduced survival. Increasing temperature by 2°C was as deleterious as doubling the natural level of deposited anthropogenic sediment, suggesting that eliminating local stressors may allow recruits to better sustain ocean warming. Growth was not affected by temperature nor sedimentation. Recruits produced by parents from the Florida Keys had a lower initial size but higher growth rate than those from Broward County. None of the parental genotypes conferred their offspring with higher or lower tolerance to warming and/or sedimentation. Reducing turbidity to 4.52-5.35 NTU or less during coastal construction may facilitate the persistence of this species by reducing recruit mortality the first 3 months post-settlement.

Acropora cervicornis, commonly known as the staghorn coral has historically been a major contributor to reef structural complexity, providing habitat for many functionally important fish species throughout Florida and the Caribbean. Unfortunately, due to disease, bleaching, and local anthropogenic stressors, A. cervicornis populations have suffered drastic declines that have negatively impacted associated reef fish populations. In order to promote recovery, A. cervicornis fragments can be cultivated in nurseries and outplanted back onto reefs. This practice can effectively increase A. cervicornis abundance, but the long-term effects on local fish assemblages, and specifically functionally important grazing fishes, has not been assessed. Fish assemblages at natural (control) sites were compared to outplanted A. cervicornis sites in Southeast Florida. Fish surveys were conducted each summer at four locations from 2012 to 2017. Each location contained three outplanted A. cervicornis and one or two control sites. Outplant sites were defined by 50 A. cervicornis colonies in a 36 m2 area. Control sites occupied the same area but did not contain outplanted colonies. The fish assemblage structure was assessed in terms of composition, demography, and functional temporal trends as well as with the increasing structural complexity of the outplanted corals, defined as total linear extension (TLE). Significant temporal trends were recorded for total fish abundance, grazer abundance, and diversity. Structural complexity (outplanted A. cervicornis measured in TLE m-2) was found to be a significant predictor of total fish abundance, grazer abundance and diversity. Fishes 2-5 cm total length were most numerous indicating that the outplant sites may be providing habitat for juvenile reef fishes, particularly algae consumers. These findings suggest that A. cervicornis restoration may be creating a positive feedback loop in which outplanted corals create habitat for grazing fishes that in turn reduce algae competition, potentially providing new habitat for coral settlement.

Coral reefs are "constructional physiographic features of tropical seas consisting fundamentally of a rigid calcareous framework made up mainly of the interlocked and encrusting skeletons of reef-building (hermatypic) corals (Wells,1957). The principal organisms responsible for the construction of modern day coral reefs, the stony corals, comprise the cnidarian order Scleractinia, which is closely allied to the sea anemones (Actinaria). Individual polyps secrete a calcium carbonate skeletal cup (calyx) beneath the basal epidermis. In most coral species the polyps remain connected by living tissue forming a colony and calcium carbonate is deposited beneath the basal epidermis of the entire colony, thereby constructing a three-dimensional mass of calcium carbonate which increases in size with the passage of time. The living tissues of reef building corals are packed with unicellular symbiotic dinoflagellates termed zooxanthellae which have been shown to be of Importance in both the calcification of the skeleton and in production of organic material on the reef.

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