A Level III fugacity-type model was applied to southern Belize (Stann Creek and Toledo Districts) to predict which of the pesticides most heavily used in banana and citrus farms are most likely to end up in streams and coastal waters via surface runoff. Concentrations of all target pesticides in coastal waters of southern Belize were then measured during two sampling campaigns (dry season and rainy season) in 2008. Several pesticides were measured in significant levels, including some as far out as waters overlying coral reefs. The presence of these pesticides in the coastal waters indicates that agricultural activities in southern Belize may have a potential impact on coral reefs offshore. Results of the predictive model were compared with the empirical data to determine how well the model works in a tropical region such as southern Belize. Overall, there is considerable agreement between the two, indicating that the model employed herein can be applied to other tropical areas. Concentrations of mercury and lead were also measured in the same study area. Mercury levels were uniform and low, suggesting natural sources. Lead levels varied and are most likely explained by the presence of unregulated and illegal waste dumps near streams in the region. An analysis was carried out to examine government policy on pesticide use. Findings indicate a lack of a coherent governmental policy on the sale and use of pesticides, most likely because of too many agencies/ministries being involved and the lack of national standards for these pesticides in the environment.

Understanding how coral reefs respond to natural disturbances is fundamental to assess their resistance and resilience, particularly in a context of climate change. Therefore, and given the escalating frequency and intensity of bleaching events, it is essential to evaluate responses of communities in space and time to disentangle the mechanisms underlying ecological changes. Here, I analyzed a dataset comprising 59 reefs, resulting from 6 years (2014-2016) of a coral reef benthic monitoring program in the Saudi Arabian Red Sea. It encompasses the 2015/2016 mass bleaching event and spans three different geographic regions: north (Duba and Al Wajh), central (Jeddah and Thuwal), and south (Al Lith, Farasan Islands and Farasan Banks). The results indicate significant differences between regions and through time. Coral assemblages from the southern region were the most affected by the 2015 bleaching event, where in some reefs, hard and soft corals cover dropped to <2% in 2017. Important changes in community structure were observed through time in the three regions, with a shift to a macroalgae, turf algae and CCA dominance. Different environmental drivers (salinity, sea surface temperature, fishing index, distance to shore, and photosynthetically active radiation) were analyzed, and highlighted a regionally-based response of the communities to these potential drivers of change. Overall, the examined Red Sea benthic communities presented dynamic patterns in composition. Distance decay plots based on presence/absence showed a general increase in similarity throughout multiple spatial scales in 2019, when compared to previous years. This finding suggests a loss in biodiversity due to thermal anomalies and bleaching events, evidenced by a homogenization (i.e., increase similarity) in the composition of the benthic communities. I document here a patterns of dominance of a few benthic groups with time and a decrease in branching corals. This study provides baseline information about changes in coral reef benthic community structure and identifies environmental factors with a higher impact on a regional scale. This information can be used to guide conservation efforts in these highly biodiverse ecosystems.The resulting datasets can be valuable for anticipating responses of coral communities under future climate scenarios.

Early work on the reproductive seasonality of corals in the Red Sea suggested that corals exhibit temporal reproductive isolation, unlike on the Great Barrier Reef where many species spawn in synchrony. More recent work has however shown high synchrony in the maturity of gametes in Acropora species, suggesting multi-specific spawning is likely to occur in the Red Sea. In this thesis I investigate the patterns of coral reproduction in the central Red Sea. The spawning season in the central Red Sea lasts four months, from April to July and spawning occurs on nights around the full moon. During this period Acropora species show a peak of spawning in April, with some species spawning again in May. The level of synchrony, quantified with a spawning synchrony index, is comparable to other locations where multi-specific spawning has been reported. Observations over two consecutive years show that the synchrony of spawning was lower in spring 2012 than in spring 2011, and thus that spawning patterns are variable from one year to the other. Coral settlement patterns on artificial substrata confirmed a main spawning season in the spring but also supported reproductive data suggesting that some Porites spawn in October-November. Settlement was studied over 2.5 years on a reef, which had suffered recently from high mortality after a local bleaching event. Settlement appeared low but post-bleaching studies from other locations indicated similar abundances and showed that recruits generally did not increase until 5 years after the bleaching event. Abundance of juvenile corals however started to increase significantly three years after the bleaching. Successful recruitment, although low suggests that the coral assemblage on the affected reef will most likely recover as long as it is not affected by another disturbance.

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.

It has been estimated that coral reefs shelter 830 000 species. Well-studied biodiversity patterns provide tools for better representation of species in marine protected areas. A cross-shelf gradient in biodiversity exists for fishes, corals, and macroalgae. Here, an inshore to offshore gradient in biodiversity on the Saudi Arabian coast of the Red Sea was sampled using Autonomous Reef Monitoring Structures (ARMS) with barcoding and metabarcoding techniques. It was hypothesized that differences in community structure would be driven by an increase in habitat area. The difference was attributed to the greater accumulation of sediments close to shore that increases the area habitable for sediment dwelling organisms and favors macroalgal cover. Macroalgae are inhabited by a greater number of species than live coral. Only 10% of the sequences of the barcoded fraction and <1% of the metabarcoded fraction had a BLAST hit on the NCBI database with a previously identified species sequence. In addition, the rarefaction curves for all fractions did not plateau. The ARMS community composition changed from inshore to offshore and was significantly correlated with the percentage of algal and bryozoan plate cover. The differences in community composition were related to changes in habitat but not to sediments retrieved from the ARMS.

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

Utah prairie dogs were transplanted onto the site of a former colony located on Jones Bench in the northwestern corner of Capitol Reef National Park. Shrubs on Jones Bench were significantly taller than those found on active colonies of Ut ah prairie dogs located nearby on the Awapa Plateau. Therefore, the Jones Bench site offered an opportunity to test the hypothesis that shrub height is a major inhibitory factor on occupation of sites by prairie dogs. Four sites of 5 ha each were delimited on Jones Bench prior to the transplanting o~ animals. Vegetation treatments were carried out on three of the sites and the fourth was used as a nonmanipulated control . Mechanical treatments by rotobeating and railing were accomplished in late August, 1978. A herbicidal treatment (2,4-D) was done on the third site in the spring of 1979. Shrub height and percent cover were significantly reduced on all three treatment sites. Post-treatment effects on the vegetation during the first year showed that the greatest percent moisture in herbage was found on the railed site, followed by the herbicide, rotobeaten, and control sites. Herbage production was approximately three times greater on the rotobeaten and railed sites than on the control and herbicide sites. Measurements of the visual obstructions of prairie dogs showed that the rotobeaten site had the greatest visibility followed by the railed, herbicide, and control sites. Prior to release of prairie dogs on the study area, 200 artificial burrows arranged in a matrix, were dug with an enginepowered post-hole auger on each site. In late June and early July, 1979, 200 Utah prairie dogs were live-trapped near Loa, Utah. A total of 50 immature males, immature females, mature males, and mature females were released on each site. The animal's fur was dyed with a specific mark representing their respective transplant site before their release. The transplanted animals were monitored daily for 23 consecutive days following the release of the first animals and biweekly thereafter throughout the summer and early fall. Significant differences were found in the number of animals reestablished on each site except between the herbicide treatment and control site. The majority of all animals transplanted moved onto the rotobeaten site; the railed, herbicide, and control sites were selected in decreasing order. Results indicated that when transplanting animals onto sites of former colonies, particularly sites that are overgrown with shrubs, the chances of a successful transplant could be increased by first reducing shrub height and density. Proof of reestablishment at the Jones Bench site will be evident if reproduction is observed in the spring of 1980.

Holocene carbonate sediments from Mexican reefs in the Caribbean and Gulf of Mexico display variations in constituent composition, texture and mineralogy which are related to their locations on the reefs. Samples were collected at barrier reef environments at Akumal and Chemuyil, on the northeast coast of the Yucatan Peninsula; at the oceanic atoll of Chinchorro, off the southeast coast of the peninsula; and at the shelf atoll of Alacranes, in the Gulf of Mexico. Samples were collected through a depth range of 0-40 m, which encompasses back reef, shallow fore reef, and deeper fore reef environments. Constituent-particle analysis of reef sediments indicates that lagoon facies are dominated by Halimeda with lesser amounts of coral and coralline algae. In contrast, fore reef facies are dominated by coral, with lesser amounts of Halimeda and coralline algae. Greater than 90% of the sediments (dry weight) occur in the interval 0.125-2.00 mm, with mean grain sizes (Mz) approaching 0.5 mm at most sites. Mz generally decreases with increasing depth at three of the four sites. Reef sediments are moderately to poorly sorted and typically become more poorly sorted with increasing depth. Sediments collected from reef channels (grooves) are consistently better sorted than those from the reef interstices (spurs). Mineralogically, the sediment is predominantly aragonite (63-93%) and high-Mg calcite (3-33%), with minor amounts of low-Mg calcite (3-9%). The sediment is chiefly composed of these three polymorphs of CaC03 (96.32- 99.83%) with only a small percentage of insoluble (non-carbonate) material. The non-carbonate fraction of the sediment is dominated by organics (0.14-3.16%) with lesser amounts of clay minerals and amorphous silica (0.00-0.66%). Quantitative analysis of Mexican reef sediments in the Caribbean and Gulf of Mexico allows the delineation of reef zonations based on constituent-particle composition. Q-mode cluster analysis of constituent-particle data from epireefal sediments enables the separation of lagoon, shallow fore reef (10-15 m) lithofacies. These groupings were maintained even when constituent-particle data from the barrier reefs were combined, and also when data from the atoll reefs were combined. Similar cluster groupings were obtained when constituent-particle data from a Jamaican fringing reef were combined with data from the Mexican barrier reefs. This indicates that coastal reef sediments from Jamaica and Mexico are surprisingly similar in constituent-particle composition and facies zonations. However, cluster analysis failed to produce clear associations when constituent-particle data from barrier reefs and atoll reefs were combined. The sedimentological zonations observed in the study reflect the community composition of the living reefs, and indicate that community composition, at least for calcifying organisms, is potentially preservable.

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.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / Hard benthic reefs are increasingly known as highly diverse biodiversity ecosystems where sponges constitute a significant proportion of inhabitants. Nearly 60% of the seabed over the inner and outer shelf on the Agulhas Bank comprises hard substrata, and in combination with the convergence of the cold Benguela and the warm Agulhas Currents serves to create a nutrient rich zone supporting multiple fish nurseries. Here we provide the first information on hard benthic reef habitats on the subphotic zone of the Agulhas Bank complex marine protected area, which include Alphard Banks, 72 Mile Reef and 45 Mile Reef, as well as the shallow reefs which include 12 Mile Reef, 6 Mile Reef, 7 Mile Reef, Marthas Reef and inshore reefs within the Tsitsikamma marine protected area. The aim is to provide baseline data on the sponge fauna by identifying species and describing the biodiversity of these hard reefs between the depths 10–200 m on the south coast of South Africa. / 2024