Thesis (Ph.D.) - University of St Andrews, May 2008.

Thesis (Ph.D. (Zoology & Entomology)) - Rhodes University, 2009.

Theses (M.S.)- -University of Hawai'i at Hilo, 2009. / Advisor : Misaki Takabayashi. Bibliography : p.70-76.

Summary of author's thesis, University of Stockholm. / Includes bibliographical references (p. 25-29).

Thesis (M.S.)--University of Delaware, 2008. / Principal faculty advisor: George W. Luther, III., College of Marine & Earth Studies. Includes bibliographical references.

Deep-sea systems are understudied compared to any other ecological system on Earth, but they are important for ecosystem functioning and services. The deep sea is important in the climatic regulation of Earth, and it is a new frontier for resource provisioning for humanity. Impacts, such as increased carbon emissions and deep-sea fishing and mining will likely influence the system, but these effects are not well understood. To recognise these impacts, common patterns in community structure need to be understood. This study aims to assess community structure in the deep sea by looking at patterns in body size and biodiversity. It uses polychaetes (bristle worms) as a study group as they are the most abundant group in the benthic macrofauna in terms of density and play key roles in the food web. Body size is an important component of the community structure, as body size is correlated with many other traits of the organism, from physiological rates (e.g. heart or breathing rates) to population dynamics (e.g. production rates or population abundances) and species richness. It is thought that body size of deep-sea (endo)benthic organisms declines with increasing depth, which is often related to food availability which itself declines with increasing depth. Many contradictory results on body-size change with increasing depth, however, have been reported, including no change, increasing, or a parabolic relationship. It is demonstrated here (Chapter 2) that there is much variety in body-size estimates between different geographic regions and taxonomic groups. These differences can ultimately influence the predictions of other traits, and might hint at what might happen in changing climatic conditions. It sets the basis to argue that there should be a focus on explaining why there are differences, instead of focusing on finding a general trend for organisms in all geographical regions. Furthermore, it is unlikely that food availability alone can explain a change in body size. An alternative explanation is offered (Chapter 3), where habitat complexity is shown to influence body size. Sponge density, in the form of habitat complexity, can have a structuring effect on the community potentially through the loss of spicules that add complexity to soft-sediments, and this in turn can influence body size of organisms. Deep-sea community structure in terms of family richness has been studied at local spatial scale. Fewer studies have been performed on regional spatial scale and these studies lack extensive sampling coverage of environmental gradients. Here (Chapter 4), the first study is presented on the maintenance of deep-sea family composition on regional scale with high sampling coverage along a variety of environmental gradients. It is shown that energy (food) availability, habitat complexity, and long-term temperature are important in influencing the polychaete distribution in this region. It is shown that there is an unusual high proportion of an opportunistic group, the Capitellidae, present in the study area. Biodiversity is important for the maintenance of ecosystem functioning, but human impacts result in the restructuring of biodiversity. The first deep-sea biodiversity - ecosystem functioning relationship for macrofauna is presented (Chapter 5). It is shown that there is a positive and saturating relationship between biodiversity and ecosystem functioning. However, fishing intensity seems to influence this relationship by potentially affecting secondary biomass production, abundance and taxonomic and functional diversity measures. It is suggested that as the disturbance of fishing negatively impacts taxonomic and functional evenness, a system is created where opportunistic species are dominant, like communities found in disturbed areas such as under fish farms. This will have consequences for the state of the system and energy transfer to trophic levels higher up.

An increase in worldwide industrialized shark fisheries resulting from the growing demand for shark products, especially shark fins in Asian markets, as well as high levels of bycatch mortality associated with multi-species fisheries have raised suspicions of substantial declines in global shark populations. Due to varying responses by individual species to fishing pressure, it has become necessary to manage sharks on a species-specific basis, which requires the collection of more accurate catch and trade data. The accumulation of such data is hindered, however, by difficulties in identifying species from only landed carcasses, body parts, or fins. This is especially true for many of the commercially important carcharhinid (Family Carcharhinidae) sharks, which are easily confused with one another due to strong morphological similarities and overlapping distributions. The forensic assays described in this thesis expand on a molecular approach developed in the M. Shivji laboratory (Guy Harvey Research Institute, Nova Southeastern University) to resolve these shark species identification issues and allow for rapid and accurate identification of shark body parts. The method involves the development of species-specific primers based on interspecific DNA nucleotide polymorphisms within the nuclear ribosomal internal transcribed spacer 2 (ITS2) locus, and inclusion of these primers in highly streamlined multiplex polymerase chain reaction (PCR) assays. Chapter One describes two separate multiplex PCR assays, each addressing different forensic objectives for U.S. Atlantic and global populations of seven carcharhinid shark species, known as the ridgeback sharks: night (Carcharhinus signatus), dusky (Carcharhinus obscurus), Caribbean reef (Carcharhinus perezi), sandbar (Carcharhinus plumbeus), bignose (Carcharhinus altimus), silky (Carcharhinus falciformis), and tiger (Galeocerdo cuvier). An assay is described in Chapter Two for distinguishing the bull (Carcharhinus leucas) and Java (Carcharhinus amboinensis) shark, carcharhinid species that display high levels of morphological similarity as well as similar habitat preference and distributions. The development of species-specific primers for identification of two additional carcharhinid shark species found in international fin markets, gray reef (Carcharhinus amblyrhynchos) and spottail (Carcharhinus sorrah), is detailed in Chapter Three. All of the assays and primers presented here have proven effective for various applications in domestic and international fisheries law enforcement, shark species management, and conservation. The efficient, economical, and simple basis of the assay lends itself to widespread routine application in practical contexts, such as collection of species-specific shark catch and trade data and clarification of the extent of species distributions. Further confirmation of the utility of this assay on a global scale is found in the success of this approach and individual primers for identifying dried shark fins from the Hong Kong fin market, confiscated fins from the U.S., South Africa, Guam, and Palau, and unknown identity samples from a Madagascar fishery.

The pelagic stingray, Pteroplatytrygon violacea, is a bycatch species in the global pelagic longline fishery. However, little research has been conducted on its basic biology, including prey composition, trophic positioning, and habitat utilization. Descriptions of the habitat utilization have largely been through indirect analyses of catch rates in commercial fisheries, which also provided no information on actual behaviors. The first chapter of this thesis will describe the habitat utilization and behavior of four individual pelagic stingrays using electronic tagging technology. Prior diet descriptions were hampered, in part, by low sample sizes and accordingly provided little information on the ecological interactions of these animals. Similarly, the second chapter of this thesis will therefore provide a new diet description for the pelagic stingray using a combined analysis of traditional stomach contents with stable isotope values, thereby addressing both ingestion and assimilation. A more robust study of the trophic dynamics of the pelagic stingray, in conjunction with the description of its habitat utilization, will provide a better understanding of its role within the pelagic ecosystem. Ultimately, the goal is to obtain knowledge of the less economic species with good science so when management approaches shift from species-specific to ecosystem based, the transition will already have known information to change efficiently.

The queen conch (Strombus gigas) is a large marine gastropod found throughout the tropical western Atlantic including Florida. Overfishing and habitat loss have led to Caribbean-wide population declines requiring regional protections. On Florida’s east coast, aggregations of conch were previously reported just south of a major shipping port near Ft. Lauderdale, unusually high latitude for the species. This study was designed to investigate the spatial extent and population demographics of the Ft. Lauderdale conch. In summer 2012, broad-scale population surveys were conducted to document benthic cover and conch distribution and size data along 72 random transects stratified across four habitats within 2 km north and south of the inlet. Younger conchs were found throughout the study area, but mostly in the colonized pavement west (CPW) habitat while old conchs were found exclusively at one CPW site south of the inlet. Significantly more conch were found on the CPW south habitat than any other. Benthic cover data suggests that CPW south may have a unique community composition dominated by macroalgae and sand. In summer 2013, the CPW south habitat was surveyed using cross-shelf transects measuring aggregation extent and demographics. Five hundred and twenty five conch were found, at a density of 495 conch per hectare. Confirmed mating sightings, females with eggs, and solitary egg masses were found indicating mating in this nearshore habitat is successful. Future research should include expanded broad-scale surveys to determine if other aggregations exist and monitoring to examine the effects of environmental change on this vulnerable species.

Batch cultures of the cyanobacteria Synechococcus spp. (strains 48 Syn and 2346) and Porphyridium cruentum (Rhodophyta) were grown in nitrogen-limited (N:P=4:l) and phosphorus-limited (N:P=50:l) seawater media. Optical properties, including particle size (forward angle light scatter), particle granularity (right angle light scatter) and relative mean channel red (> 600 nm) and green (510-550 nm) fluorescence were measured for 10 days using a flow cytometer. Dissolved nitrogen (nitrate), phosphorus (phosphate), cell abundance and chlorophyll concentrations were also measured. Results indicated that phosphorus-limited cultures yield higher chlorophyll concentration, fluorescence and granularity (right angle scatter) values than did nitrogen-limited cultures. Comparison of these samples with a preliminary investigation shows nutrient-rich cultures (N:P=4:l, N:P=50:l) have larger particle size and higher fluorescence values than relatively nutrient-poor cells cultured in f/20 media. Secondary (R2) populations have been determined for all samples, either by light scatter or fluorescence anomalies. Particularly notable was Synechococcus 2346 (phosphorus-limited) which exhibited a secondary population characteristic for more than half of the experiment. Highly fluorescent particles are suggested as either formative daughter cells, cellular “clumping" or a cellular optical response to batch culture turbidity; these particles have a profound influence on the relative refractive index of the culture with time. Flow cytometric analysis can be an effective tool in the determination of not only differences in the optical properties and fluorescent signatures of various cyanobacterial strains, but also of population variation within a single strain.