Ecologists have long questioned why fluctuating populations tend to persist rather than go extinct. Populations that persist indefinitely are regulated by mechanisms that cause demographic density dependence, which works to bound fluctuation above zero. In a series of studies, I have sought to determine the processes and mechanisms that regulate local populations of coral-reef fish. In the Exuma Keys, Bahamas, fairy basslets (Gramma loreto) live in aggregations on the undersides of coral-reef ledges. These aggregations often constitute local populations because movement between aggregations is rare. The largest individuals occupy prime feeding positions near the front of ledges and force smaller individuals remain near the back where they have lower feeding rates. Based on these initial observations, I designed two experimental studies of the demographic consequences of variation in basslet density. In the first study, I manipulated the density of newly-settled fish to explore the effects of high recruitment on population size. Populations with experimentally elevated recruitment converged in density with unmanipulated populations, primarily due to density-dependent mortality. I found no evidence that density dependence was caused by intraspecific competition; rather it appeared to be due to a short-term behavioral response by predators (aggregative and/or type 3 functional response). In a second study, I manipulated the densities of adults among populations with a standard average density of newly-settled fish. Two measures indicated that the intensity of competition increased at higher densities of adults, which likely made small fish more susceptible to predation, thereby causing density-dependent mortality. Long-term observations indicated that basslet populations were regulated at temporal scales exceeding two generations. At Lizard Island on the Great Barrier Reef, I also examined how patterns of recruitment of coral-reef fishes were modified across a range of natural recruit densities in the presence and absence of resident predators. Predators decreased recruitment and increased mortality for all species, but these effects varied considerably among species. The results of each of these studies stress the importance of both competitive and predatory mechanisms in modifying patterns of abundance established at the time of larval settlement, as well as regulating local population size. / Graduation date: 2002

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Mesophotic reefs represent biodiverse ecosystems that may act as a refuge for depth-generalist coral species threatened in shallow habitats. Despite the importance of coral-algal symbioses, few studies focus on mesophotic zooxanthellae assemblages and their influence on connectivity. This study compared zooxanthellae in Montastraea cavernosa at shallow and mesophotic depths at Flower Garden Banks National Marine Sanctuary and McGrail Bank. Mesophotic corals contained more zooxanthellae and more chlorophyll a and c2 per unit area coral. Increased zooxanthellae within mesophotic corals may represent an adaptive strategy to optimize light capture in low-light environments. Genetic profiles for zooxanthellae assemblages from shallow and mesophotic corals showed similar diversity across banks and between depths. The dominant sequence making up assemblages was identified as Symbiodinium type C1. Similar assemblage diversity suggests that zooxanthellae assemblages will not limit connectivity potential between shallow and mesophotic corals at these reefs. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection

Globally, coral reefs are in severe decline (Jackson et al., 2001) and face potential extinction of 1/3 of reef species by 2050 (Veron, 2011). This decline is the result of the inability of coral communities to recover after disturbance events, often resulting in a shift from coral- to macro-algal dominated regimes. Reef resources managers are in need of tools to assess the condition of these ecosystems prior to, during, and post disturbance, especially in regions of the world where coral cover and diversity are high, yet management resources are scarce. Foraminifera have been widely utilized as bioindicators in both modern and paleoenvironments for more than a century due to their abundance, diverse functional morphology, rapid generation time, global distribution, and rich geologic record (Sen Gupta, 1999; Hallock et al., 2003). The FoRAM Index (FI) was developed as a single metric indicator to assess whether water quality supports coral recruitment and reproduction in Caribbean and Western Atlantic coral reefs (Hallock et al., 2003), yet the FI has not been widely applied to Indo-Pacific coral reefs. This study reports benthic foraminiferal assemblages from Pulau Karangmadjat, Mentawai Islands, Indonesia, and is the first to provide in situ foraminiferal assemblages for the Mentawai region. Results revealed overall low Shannon’s H’ and Fisher’s alpha, and low Buzas and Gibson’s evenness values across 13 sample sites selected from a variety of reef habitat zones. Values for the FI were also calculated and were extremely high across all sites due to the dominance of symbiont-bearing calcarinid taxa, suggesting favorable water quality conditions. Q-mode hierarchical cluster analysis revealed 4 clusters, only one of which corresponded in its entirety to a well defined benthic habitat zone. Overall, a high degree of similarity between foraminiferal assemblages was present for most sites sampled due to the dominance of calcarinids, suggesting prevalence of a macro-algal substrate, and potentially a shift from a coral- to macro-algal dominated regime for this study area. Utilization of indices like the FI, when used in conjunction with non-FI analysis of foraminiferal assemblages, may aid managers in deducing drivers of regime shifts on Indonesian coral reefs, which may ultimately facilitate solutions for reef conservation and recovery following natural and anthropogenic disturbance. Further testing of the applicability of the FI on Indian Ocean and Indo-Pacific reefs is needed to in order to test this hypothesis. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Global climate models project a 21st century strengthening of the Pacific Equatorial Undercurrent (EUC). The consequent increase in topographic upwelling of cool waters onto equatorial coral reef islands would mitigate warming locally and modulate the intensity of coral bleaching. However, EUC water is potentially more acidic and richer in dissolved inorganic nutrients (DIN), both widely considered detrimental to coral reef health. My analysis of the Simple Ocean Data Assimilation product indicates that the EUC has indeed strengthened over the past 130 years. This result provides an historical baseline and dynamical reference for future intensification. Additionally, I reared corals in laboratory experiments, co-manipulating food, light and CO2 (acidity) to test the role of nutrition in coral response to elevate CO2 conditions. Heterotrophy yields larger corals but CO2 sensitivity is independent of feeding. Conversely, factors that enhance zooxanthellate photosynthesis (light and DIN) reduce CO2 sensitivity. Corals under higher light also store more lipid but these reserves are not utilized to maintain calcification under elevated CO2 My results suggest that while mitigation of CO2 effects on calcification is not linked to energetic reserve, EUC fueled increases in DIN and productivity could reduce effects of elevated CO2 on coral calcification. / by Elizabeth Joan Drenkard. / Ph. D.

Throughout the Pacific, many species of echinoderms and molluscs have cultural value and are harvested extensively in subsistence fisheries. Many of these species are sedentary and often associated with distinct reef-top habitats. Despite the significance of reef habitats and their fauna for fisheries and biodiversity etc, little information has been available on the distribution of habitats and their influence on the reef-top fauna in the Cook Islands. This thesis developed a novel approach to assess the status of the shallow-water reef-tops of Rarotonga, Cook Islands, to provide critical information to fisheries and conservation managers. The approach used remote sensing (aerial photography with ground truthing) to map the spatial arrangement and extent of the entire reef-top habitats accurately, and historical wind data and coastline shape to determine the windward and leeward sides of the island. The benthic habitat maps and degree of wind exposure were used to design and undertake a stratified sampling programme to assess the distribution and abundance of the epibenthic macroinvertebrate fauna of the reef-top. I quantified the distribution and abundance of the epibenthic macroinvertebrates and how they varied with habitat, assessed the effectiveness of a traditional ra�ui (marine protected area) for conserving stocks of Trochus niloticus and other invertebrates, and investigated the reproductive biology and impacts of traditional gonad harvesting on Holothuria leucospilota. There were four major habitat types (rubble/rock, sand/coral matrix, algal rim and sand) identified, the most extensive being rubble/rock (45%) and sand/coral matrix (35%). The degree of exposure to winds was found to correlate with the reef development and habitat distribution. The assemblage composition of each major habitat type differed significantly from every other habitat. The rubble/rock habitat had the greatest substratum heterogeneity and structural complexity, and the highest number of species and individuals. The overall abundance of the fauna was dominated by holothurians (68%) and echinoids (30%), while Trochus niloticus and Tridacna maxima accounted for the remaining 2% of the total invertebrate assemblage. Clear habitat partitioning was also found for adult and juvenile Trochus niloticus and Tridacna maxima. In the traditional fishery for Holothuria leucospilota, the mature gonads of males are harvested by making an incision in the body-wall of the animal, removing the gonads and then returning the animal to the reef to allow regeneration. Monthly collections of H. leucospilota were used to describe the reproductive biology of this species. Gametogenesis and spawning were synchronous between the sexes and spawning occurred annually during summer, when water temperature and photoperiod were at their highest. Although the incision in the body-wall and gonad removal had no impact on the survival of H.leucospilota in experimental cages, their body weight, and general sheltering and feeding behaviors were affected. Gonads took at least 41 days to start regenerating, suggesting a considerable delay in the spawning of fished individuals. In 1998, five Rarotongan communities re-introduced the traditional ra�ui system of resource management, prohibiting all fishing and gathering from their reefs. The performance of the Nikao ra�ui, which had been put in place to allow trochus stocks to increase, was investigated. Comparisons of macroinvertebrate assemblage composition and species density were made between three fishing treatments, i.e. fished areas adjacent to the ra�ui, within the ra�ui after two years of protection, and in the ra�ui after it had been lifted for three weeks to allow a commercial trochus harvest. Analysis of variance on the count data for the twelve most abundant species, and non-metric multi-dimensional scaling indicated that there were no differences in the microhabitat or the invertebrate assemblage composition between the three fishing treatments. However, there were significant differences between the rubble/rock and sand/coral matrix habitat types. The results on the effectiveness of the Nikao ra�ui are equivocal, due to the small sample size, and the variability between samples which was highlighted by the wide confidence intervals. This study highlights the importance of habitat to the macroinvertebrate fauna of the reef-top and the need for accurate habitat maps to increase the cost-effectiveness of future resource surveys, to provide information to management, and for the design of Marine Protected Areas. The mapping and survey methods must be reliable and repeatable in terms of the limitations of time, and the availability of expertise, funding and resources. The results provide important information for fisheries and conservation managers of Rarotonga and other Pacific Islands to better design rigorous sampling programmes for monitoring the status of reef-top resources, and for evaluating and planning Marine Protected Areas.

Coral reefs are in global decline, with seaweeds increasing as corals decrease. Though seaweeds have been shown to inhibit coral growth, recruitment, and survivorship, the mechanism of these interactions is poorly known. Here we use field experiments to show that contact with four common seaweeds induces bleaching on natural colonies of Porites rus. Controls in contact with inert, plastic mimics of seaweeds did not bleach, suggesting treatment effects resulted from allelopathy rather than shading, abrasion, or physical contact. Bioassay-guided fractionation of the hydrophobic extract from the red alga Phacelocarpus neurymenioides revealed a previously characterized antibacterial metabolite, Neurymenolide A, as the main allelopathic agent. For allelopathy of lipid soluble metabolites to be effective, the metabolites would need to be deployed on algal surfaces where they could transfer to corals on contact. We used desorption electrospray ionization mass spectrometry (DESI-MS) to visualize and quantify Neurymenolide A on the surface of P. neurymenioides and found the metabolite on all surfaces analyzed. The highest concentrations of Neurymenolide A were on basal portions of blades where the plant is most likely to contact other benthic competitors.

Marine protected areas (MPAs) have been established along the East African coast to protect coral communities from human and natural disturbance. Their success is dependent on the degree to which resource populations are self-seeding or otherwise connected. Estimates of contemporary gene flow on or between south-east African reefs are thus required to reveal the interdependence of the South African coral communities and those to the north. Accordingly, the ecologically relevant (1 or 2 generations) connectivity of two broadcast-spawning corals, Acropora austera and Platygyra daedalea, was assessed on reefs in the region, from the Chagos Archipelago to Bazaruto Island in Mozambique and Sodwana Bay in South Africa, using hyper-variable genetic markers. Analysis of genetic diversity and differentiation provided evidence for the existence of four discrete genetic populations of A. austera and five of P. daedalea in the sampled area. Higher genetic diversity was found on northern South African reefs (Nine-mile Reef and Rabbit Rock) and migration patterns inferred from assignment tests suggested that, at ecological time scales, South African reefs are disconnected from those in Mozambique and might originate from a source of gene flow that was not sampled. The analysis of fine-scale genetic connectivity conducted on Two-mile Reef (TMR) demonstrated the existence of significant spatial genetic structure at the reefal scale that might be related to the non-random dispersal of coral larvae, putatively explaining the genetic discontinuity observed in the region. Altogether, the results are consistent with the isolation observed in other studies using less variable markers, and support the hypothesis that there is demographic discontinuity between the coral populations along the south-east African coast. More importantly, Acropora austera and P. daedalea represent different life strategies in the South African reef communities yet manifested similar genetic patterns, suggesting that these corals are responding similarly to forces that are driving genetic connectivity in the region. For management purposes, the genetically distinct populations identified at each of the spatial scales analysed in this study may correspond to management units, or evolutionarily significant units. Furthermore, since some reefs appear to act as “landing-sites” for migrants (Nine-mile Reef) and there is evidence of significant within-reef genetic structure (TMR), an adaptive management framework would be the best option for the MPA in the region. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2014.

The coral reefs of Kane'ohe Bay, on the windward coast of O'ahu, Hawai'i, have changed markedly over the last half century. Some of the most spectacular coral reefs in Hawai'i were reported from Kane'ohe Bay in the late 1800's and early 1900's, but with the beginning of extensive military dredge and fill operations during the World War IT era, conditions in the bay began to change dramatically. After the War, rapid urbanization of the area began and conditions in the bay continued to decline until pressure from the public and scientific community led to the diversion of the large sewage discharges in the southeast lagoon to a newly built deep ocean outfall outside the bay in 1977-1978. Although conditions temporally improved, recent surveys indicate that current conditions in the bay are not as favorable as expected. This study provides a time series analysis of changes in coral and algae cover in Kane'ohe Bay based upon a series of coral reef surveys conducted throughout the bay in 1970171, 1983, and 1990. Beginning in 1970171, conditions in the bay were highly degraded and scientists speculated that eutrophication and sedimentation, as a result of urbanization and construction, were the primary cause of an observed decline in lagoon corals communities in the southeast lagoon and an explosive growth of the green "bubble algae", Dictyosphaeria cavemosa, which was smothering corals in the middle lagoon. In . 1983, six years after major sewage discharges were diverted from the bay, surveys indicated dramatic improvements in water quality and the reefs showed signs of recovery. D. cavemosa algae levels, associated with earlier nutrient pollution, plummeted to less than twenty percent of their former abundance levels and coral cover increased by over two hundred percent. Although it was predicted that the coral reefs of Kane'ohe Bay would continue to recover, surveys in 1990 indicate that coral recovery slowed or ceased and the growth of the green "bubble algae", D. cavemosa, more than doubled compared to 1983 levels. In addition to the failure of the t~o dominant coral species Porites compressa and Montipora capitata to continue to recover, almost all of the less common coral species including Pocillopora damicomis, Fungia scutaria, Cyphastrea ocellina, and some others, showed significant declines in reef cover. Although this study was not able to detennine the exact causes of the observed changes in Kane'ohe Bay, it is suggested that high nutrient inputs provided favorable conditions for the changes in coral and algae cover. High nutrient levels are thought to have been derived from a number of sources including chronic sewage pollution, increased sedimentation from runoff, and reef kills associated with acute but large episodes of freshwater runoff. Some of these nutrient inputs may have been the result of non-point source and point source sewage pollution derived from leaky sewer lines, cesspool and septic tank discharges, commercial tour and recreational boat waste discharges, and periodic sewage bypasses from municipal wastewater treatment plants and sewage pump stations. Other nutrients may have been derived from increased sedimentation following extensive land clearance, land development, and highway construction. Additional factors may include a decrease in herbivorous fish species owing to over fishing and the ability of D. cavemosa algae to concentrate nutrients from underlying substrates and excretion from infaunal organisms. Other factors such as increased nutrient recycling from the sediments, possible increased nitrogen fixation from reefs, and natural fluctuations in relative species abundances may also be responsible for some of the observed changes in coral reef community structure. Although rare, the largest nutrient fluxes followed the catastrophic freshwater reef-kill events caused by severe rainstorms in conjunction with low tides and low wind conditions in 1965 and 1987-1988. Although the cause and effect relationship is still uncertain, the highest levels of Dictyosphaeria cavemosa algae ever recorded in Kane'ohe Bay occurred in the years following these storm events. Results of this study indicate that further research is needed to monitor ongoing conditions in the bay and determine what is preventing the reef ecosystem from returning to its former more pristine condition. Because water quality parameters generally remained the same or improved compared to previous polluted conditions, it is suggested that current measures of water quality are not reliable in forewarning against coral reef degradation in Kane'ohe Bay. Although a reduction in all future development in and around the bay would probably help maintain environmental conditions at the status quo, additional regulations and enforcement may be needed to help reduce disturbances caused by existing land and water use. It is suggested that a reduction in nutrient inputs to the bay would be beneficial to reef corals. Recommendations made by the Kane'ohe Bay Task Force outlined in the Kane'ohe Bay Master Plan should serve as a model and be implemented as soon as possible. Continuing assessment of the Kane'ohe Bay coral reef ecosystem and surrounding watershed will then need to be made on a regular basis to ensure that further degradation of the reefs is not occurring. / Thesis (M. A.)--University of Hawaii at Manoa, 1995. Includes bibliographical references (leaves 166-175).

Throughout the Pacific, many species of echinoderms and molluscs have cultural value and are harvested extensively in subsistence fisheries. Many of these species are sedentary and often associated with distinct reef-top habitats. Despite the significance of reef habitats and their fauna for fisheries and biodiversity etc, little information has been available on the distribution of habitats and their influence on the reef-top fauna in the Cook Islands. This thesis developed a novel approach to assess the status of the shallow-water reef-tops of Rarotonga, Cook Islands, to provide critical information to fisheries and conservation managers. The approach used remote sensing (aerial photography with ground truthing) to map the spatial arrangement and extent of the entire reef-top habitats accurately, and historical wind data and coastline shape to determine the windward and leeward sides of the island. The benthic habitat maps and degree of wind exposure were used to design and undertake a stratified sampling programme to assess the distribution and abundance of the epibenthic macroinvertebrate fauna of the reef-top. I quantified the distribution and abundance of the epibenthic macroinvertebrates and how they varied with habitat, assessed the effectiveness of a traditional ra�ui (marine protected area) for conserving stocks of Trochus niloticus and other invertebrates, and investigated the reproductive biology and impacts of traditional gonad harvesting on Holothuria leucospilota. There were four major habitat types (rubble/rock, sand/coral matrix, algal rim and sand) identified, the most extensive being rubble/rock (45%) and sand/coral matrix (35%). The degree of exposure to winds was found to correlate with the reef development and habitat distribution. The assemblage composition of each major habitat type differed significantly from every other habitat. The rubble/rock habitat had the greatest substratum heterogeneity and structural complexity, and the highest number of species and individuals. The overall abundance of the fauna was dominated by holothurians (68%) and echinoids (30%), while Trochus niloticus and Tridacna maxima accounted for the remaining 2% of the total invertebrate assemblage. Clear habitat partitioning was also found for adult and juvenile Trochus niloticus and Tridacna maxima. In the traditional fishery for Holothuria leucospilota, the mature gonads of males are harvested by making an incision in the body-wall of the animal, removing the gonads and then returning the animal to the reef to allow regeneration. Monthly collections of H. leucospilota were used to describe the reproductive biology of this species. Gametogenesis and spawning were synchronous between the sexes and spawning occurred annually during summer, when water temperature and photoperiod were at their highest. Although the incision in the body-wall and gonad removal had no impact on the survival of H.leucospilota in experimental cages, their body weight, and general sheltering and feeding behaviors were affected. Gonads took at least 41 days to start regenerating, suggesting a considerable delay in the spawning of fished individuals. In 1998, five Rarotongan communities re-introduced the traditional ra�ui system of resource management, prohibiting all fishing and gathering from their reefs. The performance of the Nikao ra�ui, which had been put in place to allow trochus stocks to increase, was investigated. Comparisons of macroinvertebrate assemblage composition and species density were made between three fishing treatments, i.e. fished areas adjacent to the ra�ui, within the ra�ui after two years of protection, and in the ra�ui after it had been lifted for three weeks to allow a commercial trochus harvest. Analysis of variance on the count data for the twelve most abundant species, and non-metric multi-dimensional scaling indicated that there were no differences in the microhabitat or the invertebrate assemblage composition between the three fishing treatments. However, there were significant differences between the rubble/rock and sand/coral matrix habitat types. The results on the effectiveness of the Nikao ra�ui are equivocal, due to the small sample size, and the variability between samples which was highlighted by the wide confidence intervals. This study highlights the importance of habitat to the macroinvertebrate fauna of the reef-top and the need for accurate habitat maps to increase the cost-effectiveness of future resource surveys, to provide information to management, and for the design of Marine Protected Areas. The mapping and survey methods must be reliable and repeatable in terms of the limitations of time, and the availability of expertise, funding and resources. The results provide important information for fisheries and conservation managers of Rarotonga and other Pacific Islands to better design rigorous sampling programmes for monitoring the status of reef-top resources, and for evaluating and planning Marine Protected Areas.