Dissertations / Theses on the topic 'Great Barrier Reef'

The research undertaken has developed relationships between the concentrations of optically-significant substances (phytoplankton, Colour Dissolved Organic Matter (CDOM), and particulates) found in Great Barrier Reef waters and their respective inherent optical properties. Based on this knowledge, a physics-based spectral deconvolution routine was developed that successfully retrieved the concentrations of these substances from passive ocean colour observations such as those from the MODIS imaging satellite.

A detailed investigation of the internal and external architecture of the shelf-edge reefs (SERs) of the Great Barrier Reef (GBR), Australia is presented here, constituting the most comprehensive seismic stratigraphy study of these drowned reefs. In two sites of the central GBR, seismic reflectors and facies were identified, ground-truthed against core and downhole data from the Integrated Ocean Drilling Program, Expedition 325. Marked depositional differences between the two sites were found and linked to local and regional physiographic and environmental contrasts. A sequential stratigraphy framework was established for these sites, which exhibit a complete depositional sequence dominated by transgressive reefs, bounded by two flooding surfaces. The postglacial flooding of the GBR shelf was also simulated. The measured parameters suggest a strong influence of the local antecedent substrate and of the interplay of regional physiographic variations and sea level change in the development of the SERs. Supported in these new interpretations, local and regional SERs CaCO3 accumulation were estimated. It was found that the Pleistocene SERs of the GBR are equivalent to ca. 20 % of the GBR's Holocene reef mass. Both the magnitude and the timing of the shelf-edge reef accumulation suggest that the drowned reefs in the GBR (and globally) had the potential to influence postglacial climate change. In addition, forward stratigraphic simulations were run on models based on this dataset, which suggest that the ensemble of conditions for reef growth deteriorated as the transgression advanced, resulting in shelf-edge reef demise. The role of the basement substrate was significant, but limited. All together, the multidisciplinary reconstructions in this study represent a useful framework to constrain the development of these under-studied formations, which according to the findings had a significant role in shaping the Quaternary GBR and, possibly, in postglacial climate change.

Scleractinian corals increasingly are studied as geochemical archives of modern- and palaeoclimate, but microsampling for geochemical data is complicated by: 1) the microstructural complexity and spatial variability in skeletal growth in different coral genera; and 2) the rapidity and scale of diagenetic alteration that occurs in living coralla. Geochemical sampling techniques now have spatial resolution into the sub-micrometer to tens of micrometers range, and it is hoped that the spatial resolution can be translated to temporal resolution. This study investigated the effects on geochemical analyses imposed by microstructure and diagenesis in different live-collected coral genera representing somewhat different depositional environments. Suites of samples of four reef-building genera (Acropora, Pocillopora, Goniastrea and Porites) were collected from three adjacent environments in intertidal and subtidal positions near the reef edge at Heron Reef, Great Barrier Reef and studied by means of optical and scanning electron microscopy, combined with vibrational and energy dispersive spectroscopy. The first section of this study compares and documents the microstructure of the four coral genera. Each genus was found to have very different three-dimensional arrangements of microstructural elements, and a new general growth model was proposed for Acropora, to take into account differences in the timing of precipitation of trabeculae and thickening deposits. The results highlight the complexity and spatial variability of skeletal growth in different coral genera. Because microstructural patterns vary in different genera, direct observation of microstructural elements and growth lines are necessary to allow geochemical microsamples to be placed into series that represent temporal sequences with known degrees of time averaging. Coral growth rates (i.e., rates of extension) are discussed to determine the range of temporal relationships that exist between closely spaced skeletal microstructural elements. Such data are necessary in order for coral skeletogenesis to be understood and are critical for constraining microsampling strategies aimed at developing true time series geochemical data at very fine spatial and temporal scales. The second part of the study focused on early diagenetic alteration of the corals, which is an equally important concern for geochemical analysis. Early marine diagenesis was documented in the same live-collected samples of the four common reef-building coral genera. Samples show extensive early marine diagenesis where parts of the coralla less than three years old contain abundant macro- and microborings (sponges, algae, cyanobacteria and fungi) and significant amounts of aragonite, high-Mg calcite, low-Mg calcite and brucite [Mg(OH)2] cements. Many of the cements are associated with microendoliths and endobionts that inhabit recently abandoned parts of the skeleton. The cements are problematic for palaeoclimate reconstruction because geochemical proxies used for paleoclimate studies are meant to reflect ambient seawater chemistry and conditions, but the occurrence of brucite and low-Mg calcite demonstrates how far fluid chemistry in microenvironments within the corals has evolved from ambient seawater. Some Porites lobata specimens have had as much as 60% of the most recently deposited skeletal aragonite (i.e., the part of the skeleton that projects into the layer of living polyps) bored and replaced by low-Mg calcite cement. The low-Mg calcite cement has significantly different trace element ratios (Sr/Ca(mmol/mol) = 6.3 ± 1.4; Mg/Ca(mmol/mol) = 12.0 ± 5.1) than the host coral skeletal aragonite (Sr/Ca(mmol/mol) = 9.9 ± 1.3; Mg/Ca(mmol/mol) = 4.5 ± 2.3), thus providing a serious challenge for Sr/Ca or Mg/Ca based sea surface temperature calculations. This study illustrates that many diagenetic changes that can radically alter important geochemical characteristics of coral skeleton occur very early on the sea floor (i.e., while corals are still alive). Documented cements altered trace element inventories (e.g., Sr and Mg), thus, interfering with the use of those elements in palaeotemperature calculations. Hence, significant diagenetic changes that jeopardise palaeoclimate data do not require long-term diagenesis or meteoric exposure. Some of the diagenetic changes (e.g., calcite filled borings) occur at scales that are very difficult to detect short of visual inspection using SEM. Hence, vetting of coral samples with SEM is required before any sample is subjected to geochemical analysis.

Scleractinian corals increasingly are studied as geochemical archives of modern- and palaeoclimate, but microsampling for geochemical data is complicated by: 1) the microstructural complexity and spatial variability in skeletal growth in different coral genera; and 2) the rapidity and scale of diagenetic alteration that occurs in living coralla. Geochemical sampling techniques now have spatial resolution into the sub-micrometer to tens of micrometers range, and it is hoped that the spatial resolution can be translated to temporal resolution. This study investigated the effects on geochemical analyses imposed by microstructure and diagenesis in different live-collected coral genera representing somewhat different depositional environments. Suites of samples of four reef-building genera (Acropora, Pocillopora, Goniastrea and Porites) were collected from three adjacent environments in intertidal and subtidal positions near the reef edge at Heron Reef, Great Barrier Reef and studied by means of optical and scanning electron microscopy, combined with vibrational and energy dispersive spectroscopy. The first section of this study compares and documents the microstructure of the four coral genera. Each genus was found to have very different three-dimensional arrangements of microstructural elements, and a new general growth model was proposed for Acropora, to take into account differences in the timing of precipitation of trabeculae and thickening deposits. The results highlight the complexity and spatial variability of skeletal growth in different coral genera. Because microstructural patterns vary in different genera, direct observation of microstructural elements and growth lines are necessary to allow geochemical microsamples to be placed into series that represent temporal sequences with known degrees of time averaging. Coral growth rates (i.e., rates of extension) are discussed to determine the range of temporal relationships that exist between closely spaced skeletal microstructural elements. Such data are necessary in order for coral skeletogenesis to be understood and are critical for constraining microsampling strategies aimed at developing true time series geochemical data at very fine spatial and temporal scales. The second part of the study focused on early diagenetic alteration of the corals, which is an equally important concern for geochemical analysis. Early marine diagenesis was documented in the same live-collected samples of the four common reef-building coral genera. Samples show extensive early marine diagenesis where parts of the coralla less than three years old contain abundant macro- and microborings (sponges, algae, cyanobacteria and fungi) and significant amounts of aragonite, high-Mg calcite, low-Mg calcite and brucite [Mg(OH)2] cements. Many of the cements are associated with microendoliths and endobionts that inhabit recently abandoned parts of the skeleton. The cements are problematic for palaeoclimate reconstruction because geochemical proxies used for paleoclimate studies are meant to reflect ambient seawater chemistry and conditions, but the occurrence of brucite and low-Mg calcite demonstrates how far fluid chemistry in microenvironments within the corals has evolved from ambient seawater. Some Porites lobata specimens have had as much as 60% of the most recently deposited skeletal aragonite (i.e., the part of the skeleton that projects into the layer of living polyps) bored and replaced by low-Mg calcite cement. The low-Mg calcite cement has significantly different trace element ratios (Sr/Ca(mmol/mol) = 6.3 ± 1.4; Mg/Ca(mmol/mol) = 12.0 ± 5.1) than the host coral skeletal aragonite (Sr/Ca(mmol/mol) = 9.9 ± 1.3; Mg/Ca(mmol/mol) = 4.5 ± 2.3), thus providing a serious challenge for Sr/Ca or Mg/Ca based sea surface temperature calculations. This study illustrates that many diagenetic changes that can radically alter important geochemical characteristics of coral skeleton occur very early on the sea floor (i.e., while corals are still alive). Documented cements altered trace element inventories (e.g., Sr and Mg), thus, interfering with the use of those elements in palaeotemperature calculations. Hence, significant diagenetic changes that jeopardise palaeoclimate data do not require long-term diagenesis or meteoric exposure. Some of the diagenetic changes (e.g., calcite filled borings) occur at scales that are very difficult to detect short of visual inspection using SEM. Hence, vetting of coral samples with SEM is required before any sample is subjected to geochemical analysis.

This thesis describes the chemical investigations of several ascidian species collected from the Great Barrier Reef, Queensland, Australia. The thesis is divided into two separate components, Part A focuses on the isolation and structure elucidation of 11 previously undescribed ascidian metabolites. All structures were assigned using a combination of spectroscopic and/or chemical methods. Part B relates to the isolation and chemical conversion of a natural product to a combinatorial template. The natural product template was subsequently used in the generation of a solution-phase combinatorial chemistry library. A further two combinatorial libraries were generated from a synthesised model compound that was related to the natural product template. Part A. Investigation of Aplidium longithorax collected from the Swains Reefs resulted in the isolation of two new para-substituted cyclofarnesylated quinone derived compounds, longithorones J (30) and K (31). The former compound had its absolute stereochemistry determined by the advanced Mosher method. From an Aplidium longithorax collected from Heron Island, two new cyclofarnesylated hydroquinone compounds, longithorols C (46) and D (47) and a novel macrocyclic chromenol, longithorol E (48) were isolated. Longithorol C (46) had its absolute stereochemistry determined by the advanced Mosher method. Chemical investigation of the deep-purple colonial ascidian, Didemnum chartaceum collected from Swains Reefs led to the isolation of five new lamellarin alkaloids, which included the 20-sulfated derivatives of lamellarins B (94), C (95) and L (96), the 8-sulfated derivative of lamellarin G (97) and the non-sulfated compound, lamellarin Z (98). The known lamellarins A (63), B (80), C (64), E (65), G (67), and L (71) plus the triacetate derivatives of lamellarin D (82) and N (83) were also isolated. An aberration in the integration of signals in the 1H NMR spectra of the 20-sulfated derivatives (94-96) led to NMR relaxation studies. T1 values were calculated for all protons in the sulfated lamellarins (94-97) and their corresponding non-sulfated derivatives (80, 64, 71, 67). The protons ortho to the sulfate group in compounds (94-97) had T1 values up to five times larger than the corresponding protons in their non-sulfated derivatives (80, 64, 71, 67). A specimen of Eudistoma anaematum collected from Heron Island was shown to contain a new b-carboline alkaloid, eudistomin V (130), in addition to the two known metabolites, eudistomin H (105) and I (106). Part B. The known natural products, 1,3-diphenethylurea (29), 1,3-dimethylxanthine (30), 1,3-dimethylisoguanine (31) and the salts of tambjamine C (16), E (18) and F (19) were isolated from the ascidian, Sigillina signifera collected in Blue Lagoon, Lizard Island. Base hydrolysis on mixtures of the salts of tambjamine C (16), E (18) and F (19) resulted in the production of 4-methoxy-2,2-bipyrrole-5-carbaldehyde (26). This natural product template (26) was used in the generation of an enamine combinatorial chemistry library (98, 103-111) using solution-phase parallel synthesis. The biaryl compound, 4-(2-thienyl)-1H-pyrrole-2-carbaldehyde (59) was successfully synthesised using Suzuki-Miyaura coupling conditions and subsequently used as a template in the generation of an amine (67, 77, 80-87) and imine (78, 92-95) combinatorial library using solution-phase parallel synthesis.

The objective of the research reported in this thesis was to develop a technique to monitor the dynamics of sediments and nutrients entering the coastal ocean with river plumes associated with high intensity low frequency events (e.g. floods), using ocean colour remote sensing. To achieve this objective, an inverse bio-optical model was developed, based on analytical and empirical relationships between concentrations of optically significant substances and remote sensing of water-leaving radiance. The model determines concentrations of water-colouring substances such as chlorophyll, suspended sediments, and coloured dissolved organic matter, as well as the values of optical parameters using water-leaving radiances derived from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS). To solve atmospheric correction in coastal waters, the aerosol type over clear waters is transferred to adjacent turbid water pixels. The vicinity of the Herbert River, central Great Barrier Reef zone, Australia, was used as a case study for the application of the algorithm developed. The satellite ocean colour technique was successfully validated using sea-truth measurements of water-colouring constituents acquired in the area during various seasons throughout 2002-2004. A high correlation between chlorophyll and dissolved organic matter was found in the coastal waters of the region, and when the bio-optical model was constrained to make chlorophyll a function of dissolved organic matter, the relationship between in situ and satellite-derived data was substantially improved. With reliable retrieval of the major water-colouring constituents, the technique was subsequently applied to study fluxes of particulate and dissolved organic and inorganic matter following a flood event in the Herbert River during the austral summer of 1999. Extensive field observations covering a seasonal flood in the Herbert River in February 2004 revealed high sediment and nutrient exports from the river to the adjacent coastal waters during the flood event. Due to rapid settling, the bulk of the sediment-rich influx was deposited close inshore, while the majority of nutrients exported from the river were consumed by phytoplankton in a relatively small area of the coastal ocean. With the help of ocean colour remote sensing, it was demonstrated that river-borne sediments and nutrients discharged by a typical flood in the Herbert River are mostly precipitated or consumed within the first 20 km from the coast and therefore are unlikely to reach and possibly affect the midshelf coral reefs of this section of the Great Barrier Reef lagoon.

This thesis describes the chemical investigations of several ascidian species collected from the Great Barrier Reef, Queensland, Australia. The thesis is divided into two separate components, Part A focuses on the isolation and structure elucidation of 11 previously undescribed ascidian metabolites. All structures were assigned using a combination of spectroscopic and/or chemical methods. Part B relates to the isolation and chemical conversion of a natural product to a combinatorial template. The natural product template was subsequently used in the generation of a solution-phase combinatorial chemistry library. A further two combinatorial libraries were generated from a synthesised model compound that was related to the natural product template. Part A. Investigation of Aplidium longithorax collected from the Swains Reefs resulted in the isolation of two new para-substituted cyclofarnesylated quinone derived compounds, longithorones J (30) and K (31). The former compound had its absolute stereochemistry determined by the advanced Mosher method. From an Aplidium longithorax collected from Heron Island, two new cyclofarnesylated hydroquinone compounds, longithorols C (46) and D (47) and a novel macrocyclic chromenol, longithorol E (48) were isolated. Longithorol C (46) had its absolute stereochemistry determined by the advanced Mosher method. Chemical investigation of the deep-purple colonial ascidian, Didemnum chartaceum collected from Swains Reefs led to the isolation of five new lamellarin alkaloids, which included the 20-sulfated derivatives of lamellarins B (94), C (95) and L (96), the 8-sulfated derivative of lamellarin G (97) and the non-sulfated compound, lamellarin Z (98). The known lamellarins A (63), B (80), C (64), E (65), G (67), and L (71) plus the triacetate derivatives of lamellarin D (82) and N (83) were also isolated. An aberration in the integration of signals in the 1H NMR spectra of the 20-sulfated derivatives (94-96) led to NMR relaxation studies. T1 values were calculated for all protons in the sulfated lamellarins (94-97) and their corresponding non-sulfated derivatives (80, 64, 71, 67). The protons ortho to the sulfate group in compounds (94-97) had T1 values up to five times larger than the corresponding protons in their non-sulfated derivatives (80, 64, 71, 67). A specimen of Eudistoma anaematum collected from Heron Island was shown to contain a new b-carboline alkaloid, eudistomin V (130), in addition to the two known metabolites, eudistomin H (105) and I (106). Part B. The known natural products, 1,3-diphenethylurea (29), 1,3-dimethylxanthine (30), 1,3-dimethylisoguanine (31) and the salts of tambjamine C (16), E (18) and F (19) were isolated from the ascidian, Sigillina signifera collected in Blue Lagoon, Lizard Island. Base hydrolysis on mixtures of the salts of tambjamine C (16), E (18) and F (19) resulted in the production of 4-methoxy-2,2-bipyrrole-5-carbaldehyde (26). This natural product template (26) was used in the generation of an enamine combinatorial chemistry library (98, 103-111) using solution-phase parallel synthesis. The biaryl compound, 4-(2-thienyl)-1H-pyrrole-2-carbaldehyde (59) was successfully synthesised using Suzuki-Miyaura coupling conditions and subsequently used as a template in the generation of an amine (67, 77, 80-87) and imine (78, 92-95) combinatorial library using solution-phase parallel synthesis.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Science
Full Text

The Great Barrier Reef (GBR) is facing unprecedented pressures from a range of inputs– one of the most prominent being industrial coastal development. Of these developments, none has more current significance than the Gladstone Port Development (GPD) in Gladstone Harbour at the southern end of the GBR in Queensland, Australia. The Port expansion includes the extension of an existing coal terminal, reclamation and development of new land and three gas processing plants on Curtis Island, plus associated dredging works. These developments are causing controversy globally because they are occurring within the GBR World Heritage Area (WHA). Gladstone Harbour was included within the original World Heritage Listing (WHL) as it met the criteria attributed to the entire GBR – natural environmental assets of Outstanding Universal Value (OUV); including turtles, dugongs, mangroves, seagrasses and coral. These environmental attributes are under serious threat with the GPD, causing a clash between development and conservation in Gladstone Harbour. Moreover, the WH listing for the entire GBR is at risk because of the rapid development of the export industry along the GBR coast. These developments have been allowed because they are occurring in the small percent of the WHA that is not managed by the Federal GBR Marine Park Authority (GBRMPA); rather jurisdiction of these coastal waters falls to the Queensland government. The GBR has long been regarded as epitomising ―best-practice‖ management standards for MPA because of management by the GBRMPA. However, the management ‗best-practice‘ title is now under threat. In this study discrepancies in boundaries and management practices between the GBRWHA and the GBR Marine Protected Area (MPA), come to the fore through the perspectives of high-user stakeholders - the fishers and conservationists/researchers of the region. The stakeholders provide localised insights into the OUV together with views about current management approaches. These perceptions were gathered throughout July 2012 using semi-structured interviews in Gladstone. Using these insights this study explores the way in which multiple interests collide – drawing out and questioning the role of state and federal government in regulating the space. Arguably, the management of the GPD should match the values embedded in the area‘s WH designation, granted in 1981. The extent to which this has happened is explored in this study. This study finds that the WHL of Gladstone Harbour remains significant for local user groups. While there are calls to redraw the GBRWHA it is critical to further understand how locals value the area and the WH listing before maps are re-drawn. The incorporation of stakeholder perceptions into environmental governance for marine habitats is essential to achieve better environmental and social outcomes. In this context, this study embraces a political ecology paradigm which provides a conceptual framework for an explanation of the GPD. Such an approach enables an explanation of the forces at work in the GPD - which allows environmental, political and economic factors to be intertwined into explanations and analysis. This overarching conceptual approach illustrates how multiple interests interact in a way which limits the efficacy of the existing environment governance framework

Declines in coastal water quality are a global problem resulting in enhanced algal biomass, altered community compositions and changes to ecosystem structure and functioning. Poor water quality continues to have a detrimental impact on coral reef health. The abundance of hard corals in the Great Barrier Reef (GBR) region has reduced by 70% over the past century. Key threats such as coral bleaching, skeletal diseases, lack of reef recovery, and the proliferation of crown-of-thorns starfish in the GBR are all exacerbated by eutrophication. The inshore regions of the GBR are at risk of impacts from increased nutrient (as well as sediment and pesticide) loads delivered to the GBR waters. Therefore, the Reef Water Quality Protection Plan 2013 indicates the targets by 2018 should be at least a 50% reduction in anthropogenic dissolved inorganic nitrogen loads, and at least a 20% reduction in sediment and particulate nutrients in priority areas. Fluvial discharge is a primary source of nutrients for algae growth in the GBR lagoon although upwelling, mineral dust deposition, biological nitrogen fixation, and rainfall can also be sources of new nutrients. Fluvial discharges of sediment and nutrients and their impacts on the GBR have been previously studied to describe the presence, nature and extent of land-derived contaminants in GBR waters. Upwelling is also a source of nutrients for the GBR ecosystem, with this study examining a hitherto unidentified seasonal chlorophyll-a (Chl-a) anomaly likely due to upwelling on shelf waters to the southeast of Fraser Island and also off Stradbroke Island
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
Full Text

This thesis describes two new methods, the Toxic Loads and multisubstance Potentially Affected Fraction (msPAF) methods, that have increased ecological relevance when estimating progress made towards improved water quality transported to the Great Barrier Reef (GBR). Pesticides in runoff from agricultural lands in Queensland catchments contributes to the poor water quality impacting the health and resilience of the GBR's ecosystems. Managing the pesticide pollution requires changes to land management practices. The methods presented in this thesis have been implemented in government monitoring and evaluation programs to evaluate the improvement required to protect the GBR from pesticides.

The Great Barrier Reef (GBR), situated off the coast of Queensland, is Australia’s most remarkable natural gift with more than 3000 coral reefs covering an area of 348,000 km2. The GBR contains a huge and marvellous natural habitat for different organisms and plays a critical role in conservation of biological diversity. Besides its environmental aspects, this wonder of nature has a substantial contribution to Australian economy as well. Despite the economic and environmental importance of the GBR, a number of menaces have recently emerged that potentially threaten the future of this beautiful testament. Elevated levels of sediments and nutrients discharged from adjacent coastal river systems have been considered as one of the main threats to the ecosystems of the GBR. While research has been mainly focused on the impact of agricultural activities on dissolved inorganic nitrogen (N) load of rivers in the GBR catchment, the origin and the fate of organic nutrients in both terrestrial and marine environments are not well understood. The overall purpose of this study was to provide insights into the key biogeochemical processes governing the movement and dynamics of soil, sediment and associated particulate organic nutrients in both terrestrial and marine ecosystems, and to improve our understanding of the main origin and fate of sediment and organic nutrients in the GBR catchment.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
Full Text

This thesis defines the response in two time frames, of individual reefs and coral reef ecosystems to sea-level change, through the bio-geological analysis of such reefs, on both active and passive margins. The raised Holocene reefs at Kikai-jima, Japan (Central Ryukyu Islands, ie. active margin) were examined for horizontal and vertical variation in exposed sections, and in drill core to determine the biological response of reefs to sea level fall. Holocene palaeoclimatic signals from a massive fossil coral at Kikai-jima were also investigated and their implications for reef growth and palaeoceanography discussed. Finally, two high-resolution cores from the Northern Great Barrier Reef (ie. passive margin) were examined to determine the biological response of reefs to repeated sea-level rise and fall over the last ~3 50 ky.

Understanding how coral reefs have developed in the past is crucial for placing contemporary ecological and environmental change within appropriate reef-building timescales (i.e. centennial to millennial). On Australia’s Great Barrier Reef (GBR), coral reefs situated within nearshore settings on the inner continental shelf are a particular priority. This is due to their close proximity to river point sources, and therefore susceptibility to reduced water quality as the result of extensive modification of adjacent river catchments following European settlement in the region (ca. 1850 CE). However, the extent of water quality decline and its impact on the coral reefs of the GBR’s inner-shelf remains contentious and is confounded by a paucity of long-term (> decadal) datasets. Central to the on-going debate is uncertainty related to the impact of increased sediment loads, relative to the natural movement and resuspension of terrigenous sediments, which have accumulated on the inner-shelf over the last ~6,000 years. The main aim of this thesis was to characterise and investigate the vertical development of turbid nearshore coral reefs on the central GBR. This aim was achieved through the recovery of 21 reef cores (3 - 5 m in length) from five proximal turbid nearshore reefs, currently distributed across the spectrum of reef ‘geomorphological development’ within the Paluma Shoals reef complex (PSRC). The recovered reef cores were used to establish detailed depositional and palaeoecological records for the investigation of the (1) internal development and vertical accretionary history of the PSRC; and (2) compositional variation in turbid nearshore coral and benthic foraminiferal assemblages during vertical reef accretion towards sea level. Established chronostratigraphic and palaeoecological records were further used to assess the impact of post-European settlement associated water quality change in a turbid nearshore reef setting on the central GBR. Radiocarbon dating (n = 96 dates) revealed reef initiation within the PSRC to have occurred between ~2,000 and 1,000 calibrated years before present, with subsequent reef development occurring under the persistent influence of fine-grained (< 0.063 mm) terrigenous sediments. The internal development of the PSRC was characterised by discrete reef facies comprised of a loose coral framework with an unconsolidated siliciclastic-carbonate sediment matrix. A total of 29 genera of Scleractinian coral and 86 genera of benthic foraminifera were identified from the palaeoecological inventory of the PSRC. Both coral and benthic foraminiferal assemblages were characterised by distinct assemblages of taxa pre-adapted to sediment stress (i.e. low light availability and high sedimentation). At the genus level, no discernable evidence of compositional change in either coral or benthic foraminiferal assemblages was found, relative to European settlement. Instead, variations in assemblage composition were driven by intrinsic changes in prevailing abiotic conditions under vertical reef accretion towards sea level (e.g. hydrodynamic energy, light availability, and sedimentation rate). These findings therefore highlight the importance for considering reef ‘geomorphological development’ when interpreting contemporary reef ecological status. Furthermore, this research emphasises the robust nature of turbid nearshore reefs and suggests that they may be more resilient to changes in water quality than those associated with environmental settings where local background sedimentary conditions are less extreme (e.g. towards the inner/mid-shelf boundary). To this end, this thesis presents new baseline records with which to assess contemporary ecological and environmental change within turbid nearshore settings on the central GBR.

Coral reefs are important regional sources of natural atmospheric sulfur through stressinduced emissions of dimethylsulfide (DMS). Marine DMS is a source of non-sea salt sulfate, which can influence the microphysical properties of aerosols and low-level clouds. It has been hypothesised that emissions of DMS from coral reefs may influence aerosol nucleation and growth to cloud condensation nuclei, and increase the lifetime and albedo of low-level clouds to shade and cool the coral reef below. However, the source-strength of coral reefs to the atmospheric sulfur budget and the influence on aerosols, clouds and the Earth’s radiative balance is uncertain. This thesis investigates the Great Barrier Reef (GBR), Australia, as a source of DMS and aims to determine whether coral reef-derived DMS can influence regional aerosolcloud processes. A combination of field and remotely sensed observations and climate model simulations are used to address these research objectives. A significant link is identified between remotely sensed proxies of coral physiological stress, atmospheric DMS (DMSa), fine-mode aerosol optical depth (AOD) and particle number concentration (0.5-2.5 μm) in the GBR. However, a ‘tipping-point’ in the observed relationship occurred during mass coral bleaching events, where a decline in DMSa and AOD occurred when the coral thermal bleaching threshold was approached. These relationships may reflect a coral reef-derived source of biogenic aerosol, that can weaken when corals experience high levels of oxidative stress and bleaching. The GBR is an important regional source of DMS, releasing 0.03-0.05 Tg yr-1 of DMS (equivalent to 0.015-0.025 Tg yr-1 S). To derive this estimate, sea surface DMS (DMSw) concentration is parameterised as a function of sea surface temperature and irradiance using observational data in the GBR. The parameterisation is used to calculate the first climatology of DMSw and DMS sea-air flux from the GBR using remotely sensed observations. Current DMS sea-air flux parameterisations do not account for direct coral-air DMS flux, which is an important, albeit intermittent source of DMSa above the background oceanic signal. In this thesis, direct coral-air DMS flux is accounted for by adding a laboratory-based estimate to the calculated sea-air flux, scaled by the percentage of coral reef cover. Assuming that DMS sea-air flux is uniform across coral reef regions, global tropical coral reefs could emit 0.08 Tg yr-1 of DMS (equivalent to 0.04 Tg yr-1 S). While this represents only ~0.2% of global sea-air flux estimates (17.7- 34.6 Tg yr-1 S as DMS), it is a disproportionate volume released from 0.1% of the ocean surface. The influence of coral reef-derived DMS on the atmosphere over north-eastern Australia is investigated by incorporating the GBR DMSw climatology and coral-air DMS flux estimate into the Australian Community Climate and Earth-System Simulator Coupled Model (ACCESS-CM2). Inclusion of coral reef-derived DMS increased the concentration of atmospheric DMS by approximately 150% and gas-phase sulfur dioxide and sulfuric acid by up to 18% over the GBR. The findings demonstrate that DMS emissions from the GBR are an important source of sulfate aerosol precursors, with potentially important implications for local-scale aerosol-cloud interactions. However, no significant influence on modelled aerosol sulfate mass or number concentration was detected, even with a reduction in anthropogenic sulfur dioxide emissions, indicating that coral reef-derived DMS may not significantly influence the regional atmosphere at temporal and spatial scales that are resolved by global climate models. The research presented in this thesis demonstrates that the GBR is an important regional source of DMS and contributor to the atmospheric sulfur budget. While DMS emissions from the GBR may not play an important role in the regional radiative balance, it is expected that a stronger response may occur at local, sub-daily time scales, as observational studies have suggested. Understanding the influence of natural aerosols is key to reducing uncertainty in our estimates of radiative forcing, particularly in coral reefs which are threatened by ongoing climate change. Given the global initiatives to shift towards renewable energy, aerosol and cloud processes may become more sensitive to changes in natural aerosol sources in future. However, further research is required to understand the complex aerosol-cloud system and how it responds to changes in anthropogenic and natural emissions.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
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Macroalgae, or seaweeds, are photosynthetic primary producers found in marine, freshwater, and estuarine environments; however, most diversity is found in marine environments. Macroalgae consist of a diverse range of functional groups including filamentous, fleshy and encrusting, and calcareous crustose or non-crustose algae. The diversity and complexity of macroalgae serve different ecological roles and their physiological response under various environments will have implications on community assemblages and overall reef community structure. On coral reefs, changing environments continue to result in highly variable responses in non-calcified macroalgae compared to their calcified counterparts. Yet the roles of physiological mechanisms in fleshy macroalgae are comparatively understudied. Macroalgae with varying inorganic carbon (Ci) affinities can have trait variability within physiological processes, making general predictions of responses to environmental stress difficult. Simultaneously, physical gradients such as depth or stressors like warming are interacting with various changing abiotic factors, e.g. elevated pCO2, and affecting resource availability. The underlying drivers involved in macroalgal responses will be indicative of their capability to tolerate a rapidly changing environment. Thus, I aimed to examine the physiological plasticity of non-calcifying macroalgae across various environmental gradients in the context of global change and to elucidate the physiological mechanisms influencing any changes in macroalgal responses. Three separate experiments were conducted on the Great Barrier Reef, Australia, to investigate various changes in growth rates, inorganic carbon uptake, photosynthetic and respiration rates (using O2 evolution), and photophysiology (using the PAM) of tropical reef macroalgae. In chapter 2, I examined the responses of four species of fleshy macroalgae with varying affinities for inorganic carbon to three temperatures under ocean acidification (OA). I conducted a tank experiment to assess changes in growth, oxygen evolution (i.e. metabolism), and carbon physiological responses to individual and interacting warming and OA conditions. I found that HCO3- -using species benefitted from OA while CO2 - using species were unaffected, which was reflected from carbon isotope values. Both respiration and photosynthesis resulted in varying responses and there was a decoupling between photosynthesis and growth rates. Additionally, I found that if only two temperature levels were examined, 24 ºC and 30 ºC, physiological responses would have been unaffected. In chapter 3, I selected an ecologically important brown algal genus, Lobophora, as the model organism to determine functional relationships in their physiological responses to a temperature gradient. I conducted a tank experiment at five temperature levels to assess growth, photosynthetic, and respiration rates. I found that growth had a non-linear response curve while photosynthesis and respiration had negative linear responses curves as a function of temperature. Importantly, responses across four temperature levels from 24.5 ºC to 30 ºC elicited negligible responses (as seen in Chapter 2). However at 32 ºC, there were detrimental effects. Finally, in chapter 4, I examined the ability of macroalgae to modulate their physiology to changes in light in situ with a reciprocal transplant experiment. To examine the underlying physiological drivers affecting macroalgal performance further, I complemented the field experiment with a tank experiment using four light levels to mimick changes in light along the reef slope with OA. I selected two species with different Ci affinities, a HCO3- -user and a predominantly CO2 -user, to assess how carbon physiology is affected by light and whether it drives changes in growth, metabolism, and photophysiological responses. Results indicated the effect of depth in situ affected the HCO3- -user more than the predominantly CO2 -user. Conversely, when light interacted with OA, the predominantly CO2 -user was more affected physiologically than the HCO3- -user, highlighting the energy constraints on species that rely more on CO2 for physiological processes. Overall, this thesis highlights underlying drivers of physiological responses and the ability of macroalgae to modulate their responses in order to buffer a changing environment. Environmental gradients will be an important addition to evaluating ecophysiological studies for a more comprehensive understanding of physiological performance, tolerance, and adaptive capacity in various organisms. As ecosystems continue to face global-scale changes and macroalgae become more abundant in tropical reefs due to increased substrate availability because of coral mortality, physiological information on ecologically relevant species and the underlying mechanistic drivers will be critical for understanding pattern responses and providing a scale to which species may respond across different taxa.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
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Coral reefs are one of the most diverse and complex ecosystems on the planet and provide incomes, food, and important ecosystem services for hundreds of millions of people. However, reefs are in global decline and are changing from highly diverse and topographically complex ecosystems dominated by coral species to species-poor and structurally simple ecosystems dominated by macroalgae. The reason of this decline is complex but can be attributed to multiple local stressors such as overfishing, marine pollution and declining water quality, and global stressors such as global warming and ocean acidification product of anthropogenic activities. Corals and algae compete intensely for space, light and nutrients in coral reefs, and this competition is a structuring and shaping process which determines the abundance of both groups of species. Therefore, the general aim of this thesis is to explore experimentally and descriptively the dynamics between corals and macroalgae in coral reefs from three approaches. The first approach focuses on the temporal variability of coral-algal interaction and its implications for coral mortality in different reef habitats. The second study explores the spatial variability of coral-algal interactions and coral health at the local and regional scales within a terrestrial gradient of influence. The third study addresses the potential effects of ocean acidification on competitive mechanisms utilised by algae during coral-algal competition and explores coral-algal competitive outcomes under different levels of ocean acidification. This study was carried out in Heron Island and Keppel Islands, in the southern Great Barrier Reef, Australia.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
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The causes of increasing outbreaks of Acanthaster planci on the Great Barrier Reef have been a point of hot debate in recent years. It is unknown whether the increased success is due to nutrient runoff, salinity levels, or a decrease in predation, among other possibilities. In this paper I argue that the primary influence on outbreak status is sea surface temperature. From existing literature, I demonstrate that sea surface temperature in the Great Barrier Reef has increased by 0.4°C per year over the past three decades. I attempt to tie this increase with an increase in frequency of A. planci outbreaks on a selection of reefs throughout the Great Barrier Reef region. Due to the development of A. planci, specifically the fact that it takes them between 2 and 3 years to reach full maturity, I examined the potential relationship between an outbreak and the sea surface temperature 1 and 2 years before the event. Through my exploration of the data and my subsequent data analysis, it is clear that there are no statistically significant results when comparing the three classifications of outbreak (active, incipient, and recovering) and not outbreaking populations with temperature at each of the three time relationships. However, when I considered the three stages of outbreak to be “affected” and those not outbreaking to be “unaffected”, I found a statistically significant relationship. This finding has important implications when looking at the temperature changes that have been predicted for the Great Barrier Reef region due to global climate change. If the water temperature continues to increase, A. planci will more often be living within their optimal temperature range and will be more successful, continue to have major outbreaks that devastate the reef ecosystem, and eventually destroy it all together.

73-deoxychondropsin A (73-DOC), a natural product of the polyketide family sourced from the marine sponge Ircinia ramosa, has previously shown inhibition of vacuolar-type H+-ATPases. This enzyme is crucial for osteoclastic bone resorption and is important in the pathogenesis of metabolic bone diseases, which affect both osteoclasts and the bone-forming osteoblasts. Following extraction of 73-DOC from I. ramosa tissues, in vitro experiments were performed to establish the differential effects of 73-DOC on primary osteoclast and osteoblast differentiation and function. Dose-response and time course analyses, as well as confocal microscopy assessments of cellular acidification, showed that 73-DOC inhibited mouse and human osteoclast resorption at concentrations 5-10-fold lower than those causing inhibition of osteoblast activity. The inhibition of bone resorption whilst maintaining bone formation demonstrates a novel application for 73-DOC and potential as a therapeutic for osteolytic diseases such as osteoporosis. Symbiotic microorganisms have frequently been proposed as the true producers of sponge-sourced secondary metabolites. Whilst symbionts are typically resistant to culturing, metagenomic approaches allow for microbial biosynthetic genes from the sponge holobiome to be cloned and ultimately expressed in a heterologous host, leading to a sustainable supply of the compound. To clone and sequence the biosynthetic gene cluster responsible for 73-DOC, a metagenomic fosmid library was screened for conserved features of polyketide synthase biosynthesis. Metagenomic DNA was also directly sequenced and screened using in silico analysis tools, which led to the annotation of genes with putative partial involvement in 73-DOC biosynthesis. Further work required to identify the remaining biosynthetic components was suggested.

This research investigates the initiation and growth of Holocene Halimeda algal limestone build-ups in the Great Barrier Reef. Legacy sediment samples and newly acquired analytical data were combined to explain inter-reef Halimeda bioherm origins, temporal growth and development, spatial distribution, geomorphology, carbonate volume, nutrient source, and habitat significance. Halimeda bioherms are much more complex than previously thought. The project contributes a significant new understanding of the Halimeda bioherm geological and ecological system in space and time, elevating the importance of Halimeda bioherms as Holocene sedimentary archives and modern inter-reef benthic habitats.

This thesis is an experimentally based study of the processes of biological destruction on dead coral substrates on the Great Barrier Reef. By placing recently killed coral samples in reef environments it has been possible to compare the impact of bioerosion processes on hard coral skeletons between different environments and reefs. The experiments have shown that once a dead coral substrate becomes available it is subjected to recruitment by a diverse assemblage of endolithic borers that excavate the interior of the substrate, while its surface is eroded by the grazers that are adapted to scraping carbonate substrates to remove epilithic and endolithic algal growth. Experiments on Lizard Island reef have identified grazing as the major destruction agent on coral substrates over the initial 4 years of exposure. Major differences between environments in the amount of grazing are controlled by the distribution of the highly mobile herbivorous fish community that is dominated by scarids and acanthurids. Subtidal reef slopes and lagoon environments of water depths less than 20 m are subjected to higher rates of grazing erosion than shallow reef flat environments. These differences in grazing are a result of tidal cycles limiting the access of grazing fish to reef flats to high tides only. The variability of grazing activity by bioeroding fish is highly complex due to ecological and behavioral factors. However, over time periods important to the geological development of reef environments, these factors would be less important than the major physical features of the reef that determine scarids and acanthurids populations between environments. The Lizard Island experiments indicate that extensive borer populations require at least 4 years to develop and that consecutive 2-year sampling periods show significant differences in the successful recruitment of borers. Early cryptofauna to colonise dead coral substrates are small fabriciniid polychaetes. These small polychaetes are followed by larger cirratulids, spionids, eunicids and sabellines. Sipunculans, bivalve molluscs and sponges only become important in the experiments after 4 years. This importance of time to the extent of borer excavation in experimental substrates suggests that reef surfaces will be extensively bored if they survive the destructive effects of grazing. Recruitment differences within and between environments and season will influence the structure of the borer community. However, the long-term erosional impact of endolithic borers on reef framework will be closely linked to the rate of surface destruction by grazers. The geological impact of the relationship between grazing and boring is further revealed in experiments in the southern Great Barrier Reef. These experiments were designed to assess the differences in grazer and borer communities for 2 years on reefs that represent adolescent, mature and senile stages of evolution at sea level. These reefs were Llewellyn, One Tree, and Wreck. Experimental samples placed in reef slope, flat, and lagoon environments show that destruction caused by grazing fish is reduced as lagoon environments are restricted by sedimentary infill that expands reef flat conditions. In addition, grazing by gastropods becomes increasingly important in these reef flat conditions. However, the rates of erosion by these grazing molluscs in senile environments on the protected surfaces of substrates are considerably less than the rates of destruction caused by fish in subtidal adolescent reef environments. With reduced destruction, accretion by encrusters is important on substrates. This accretion further protects surfaces, preserving the volume of the substrate and allowing the establishment of borer communities. Through the turnover of these borers and the addition of encrustation, substrates may be preserved, but they are likely to be converted from original coral to substrates composed of bored encrustation. Extrapolating the patterns of the accretion - erosion balance on experiments to the long term impact on reef surfaces predicts that framework in senile reef environments will be subjected to many cycles of boring and encrustation, producing a highly altered reef rock. Dead coral framework in adolescent environments is subjected to rapid destruction by grazers such that borer communities may remain in early successional stages. The conversion of framework to sediment through this destruction is an important contribution to the infilling of the lagoons and to the way that growth frameworks are ultimately incorporated into the foundation of the reef. In addition to these experiments in subtidal environments, an experiment was designed to measure rates of surface destruction on windward intertidal reef crest surfaces at One Tree Reef. Using an instrument that measures differences in the elevation of reef surfaces through time it was possible to establish that rates of destruction increase toward the reef margin and that the highest rates recorded approach the rates of construction that have been estimated by others for the environment. Biological processes, including grazing, are interpreted to be responsible for this destruction since longer exposure to subtidal conditions increases erosion and the activity of grazers and borers. The intertidal pavement that is submerged for longer periods during tidal cycles recorded rates of erosion more than twice those recorded on the supertidal cemented rubble platform. The rates indicate the magnitude of accretion that has been necessary to maintain this environment in intertidal conditions. Overall, the study provides a different view of short-term biological processes that effect the long-term geological development of reefs. The changing relationship of grazing, boring and accretion on frameworks as a reef evolves provides a geological record that is a potential measure of the physical and ecological change that has occurred in the past, and is occurring on reefs today.

Stacy Bierwagen studied how reef sharks utilise and influence coral reef ecosystems. She found that reef shark populations are stable and have distinct food web links and prey compared to other predatory fishes on the Great Barrier Reef. This information benefits the understanding of reef shark roles on coral reefs.

The role of turbidity and sedimentation is a key problem for nearshore coral reefs worldwide. However, little is known about how sedimentation interacts with other environmental factors such as hydrodynamics, temperature and light and how coral species vary in their sediment responses. Here, I investigate the response of corals to sediment under varying flow, temperature and light regimes in two controlled mesocosm experiments, and then preliminarily examine the role of sedimentation in structuring coral assemblages using a new method for manipulating sedimentation rates in field settings. The first experiment was designed to test the specific hypothesis that coral stress (using the foliaceous Turbinaria mesenterina as a study species) associated with sedimentation is reduced under turbulent flow conditions that prevent long-term sediment deposition on coral tissues. To provide a rigorous assessment of the physiological response, three key physiological parameters were used: tissue lipid concentration, skeletal growth rate and photosynthetic performance (maximum quantum yield). The second experiment investigated interactions between sediment stress and stresses associated with high temperature and light – a problem highly topical in the context of climate change. Lastly, the field experiment consisted of an array of six erosive sediment blocks (plaster of paris and silicate-based sediment) suspended above the fringing reef at Pelorus Island (Queensland, Australia) to simulate replicate sediment gradients. The sediment responses of three coral species (Acropora formosa, Montipora tuberculosa, and Porites cylindrica) were followed and compared over a fifteen-day sedimentation even, using the relative surface area of tissue lesions/necrosis as the response variable. Experiment 1 demonstrated that sediment concentrations (or sedimentation rates) of up to 110.7 ± 27.4 mg cm-2 d-1 had no effect on colony growth rate, lipid concentration or photosynthetic yield in T. mesenterina under high flow (23.7 ± 6.7 cm s-1) or stagnant conditions. Also, interactions between flow and sediment treatments were non-significant. This is a surprising result that indicates that T. mesenterina is highly resistant to sediment deposition under low flow as well as sediment abrasion under wave action. Horizontal colonies subjected to sediment loads of up to 100 mg cm-2 under stagnant conditions were able to clear their surface within two hours, suggesting that rapid and energy efficient clearing of sediment is a key mechanism of alleviating sediment stress. These results may explain the success of T. mesenterina on reef crests as well as deep reef slopes on highly turbid, inshore coral reefs in the Great Barrier Reef lagoon. Results of experiment 2 showed that sediment treatments of up to 246 ± 47 mg cm-2 d-1 had no effect on colony growth rates, lipid concentrations or chlorophyll concentrations in either of the study species under the low (Control) light conditions (190 ± 60 μmol photons m-2 s-1). In high light (270 ± 110 μmol photons m 2 s-1), however, lipid and chlorophyll concentrations declined significantly indicating a bleaching response. Interestingly, temperature treatments (25.5 ± 0.1 and 28.4 ± 0.1°C) had no effect on the lipid or chlorophyll responses of T. mesenterina. Also, sediment, temperature, and light treatments did not interact significantly, further demonstrating that the physiology of this species is highly robust to these environmental stressors. Of the three physiological responses measured, chlorophyll concentration proved to be the most sensitive. The field experiment (experiment 3) showed contrasting sediment responses among the three study species, consistent with predictions based on growth forms. Specifically, the prevalence of tissue lesions in M. tuberculosa (flat, foliaceous) increased significantly with sedimentation rate, whereas Acropora formosa and Porites cylindrica showed minimal tissue lesions, which were not correlated with sedimentation rates. This result suggests that sediment can act as a selective pressure on coral reefs, potentially related to the functional morphology of the species in the assemblage.

The role of turbidity and sedimentation is a key problem for nearshore coral reefs worldwide. However, little is known about how sedimentation interacts with other environmental factors such as hydrodynamics, temperature and light and how coral species vary in their sediment responses. Here, I investigate the response of corals to sediment under varying flow, temperature and light regimes in two controlled mesocosm experiments, and then preliminarily examine the role of sedimentation in structuring coral assemblages using a new method for manipulating sedimentation rates in field settings. The first experiment was designed to test the specific hypothesis that coral stress (using the foliaceous Turbinaria mesenterina as a study species) associated with sedimentation is reduced under turbulent flow conditions that prevent long-term sediment deposition on coral tissues. To provide a rigorous assessment of the physiological response, three key physiological parameters were used: tissue lipid concentration, skeletal growth rate and photosynthetic performance (maximum quantum yield). The second experiment investigated interactions between sediment stress and stresses associated with high temperature and light – a problem highly topical in the context of climate change. Lastly, the field experiment consisted of an array of six erosive sediment blocks (plaster of paris and silicate-based sediment) suspended above the fringing reef at Pelorus Island (Queensland, Australia) to simulate replicate sediment gradients. The sediment responses of three coral species (Acropora formosa, Montipora tuberculosa, and Porites cylindrica) were followed and compared over a fifteen-day sedimentation even, using the relative surface area of tissue lesions/necrosis as the response variable. Experiment 1 demonstrated that sediment concentrations (or sedimentation rates) of up to 110.7 ± 27.4 mg cm-2 d-1 had no effect on colony growth rate, lipid concentration or photosynthetic yield in T. mesenterina under high flow (23.7 ± 6.7 cm s-1) or stagnant conditions. Also, interactions between flow and sediment treatments were non-significant. This is a surprising result that indicates that T. mesenterina is highly resistant to sediment deposition under low flow as well as sediment abrasion under wave action. Horizontal colonies subjected to sediment loads of up to 100 mg cm-2 under stagnant conditions were able to clear their surface within two hours, suggesting that rapid and energy efficient clearing of sediment is a key mechanism of alleviating sediment stress. These results may explain the success of T. mesenterina on reef crests as well as deep reef slopes on highly turbid, inshore coral reefs in the Great Barrier Reef lagoon. Results of experiment 2 showed that sediment treatments of up to 246 ± 47 mg cm-2 d-1 had no effect on colony growth rates, lipid concentrations or chlorophyll concentrations in either of the study species under the low (Control) light conditions (190 ± 60 μmol photons m-2 s-1). In high light (270 ± 110 μmol photons m 2 s-1), however, lipid and chlorophyll concentrations declined significantly indicating a bleaching response. Interestingly, temperature treatments (25.5 ± 0.1 and 28.4 ± 0.1°C) had no effect on the lipid or chlorophyll responses of T. mesenterina. Also, sediment, temperature, and light treatments did not interact significantly, further demonstrating that the physiology of this species is highly robust to these environmental stressors. Of the three physiological responses measured, chlorophyll concentration proved to be the most sensitive. The field experiment (experiment 3) showed contrasting sediment responses among the three study species, consistent with predictions based on growth forms. Specifically, the prevalence of tissue lesions in M. tuberculosa (flat, foliaceous) increased significantly with sedimentation rate, whereas Acropora formosa and Porites cylindrica showed minimal tissue lesions, which were not correlated with sedimentation rates. This result suggests that sediment can act as a selective pressure on coral reefs, potentially related to the functional morphology of the species in the assemblage.

Marine organisms are a source of a diverse range of secondary metabolites. This thesis describes the isolation and structure elucidation of novel alkaloid and terpenoid metabolites from marine invertebrates which were collected from the Mackay - Capricorn Section of the Great Barrier Reef Marine Park (Keppel Bay and the Capricorn Bunker Group).

B-Carboline, its N,N symmetrical dimer and a series of novel asymmetrical dimers of B-carboline, were isolated from a didemnid ascidian (genus Didemnum). The asymmetrical dimers, however, were isolated in such low yield from the ascidian that their structures could not be conclusively determined. Derivatization of B-carboline allowed the preparation of these compounds in sufficient quantities to allow the elucidation of their structures by NMR spectroscopy. Two other new asymmetrical dimers of B-carboline, not observed in the ascidian, were also prepared and their structures elucidated.

Tetronic acids are commonly isolated from sponges of the genus Ircinia. A novel sesterterpene tetronic acid was isolated from the sponge Ircinia (= Psammocinia) wistarii. This novel compound (a sulfate ester) was highly unstable; rapid decomposition of the sulfate ester resulted in the formation of the known compounds ircinianin and wistarin. The isolation and structure elucidation of the novel sulfate ester is described in Chapter 3 of this thesis.

Alcyonolide 5, a novel diterpene triacetate, was isolated from two soft corals of the order Alcyonacea. This compound, is one of a series isolated from corals of the genera Alcyonium and Efflatounaria.

The bastadins are a series of (typically macrocyclic) tyrosine derivatives, commonly isolated from the sponge lanthella basta. During these investigations a new bastadin was isolated from lanthella quadrangulata.

The norcembrenolides, a series of norditerpenes, are commonly isolated from the soft corals of the genus Sinularia. The soft coral Sinularia numerosa was found to contain two of these compounds. One was the known compound norcembrenolide (the first representative of this class), the second was a stereoisomer of norcembrenolide. The chemical literature reports several compounds of this type, however, there appears to be a degree of confusion surrounding the structures of these stereoisomers. This thesis resolves the confusion surrounding the stereochemistry of these isomers, and assigns a structure to the minor metabolite of S. numerosa.

Approximately 200 marine invertebrates were collected during the course of these investigations. Many known compounds were isolated from the marine invertebrates that were collected from the Mackay - Capricorn Section of the Great Barrier Reef Marine Park. This afforded an opportunity to survey the natural products which may be found in this region, and highlights some of the difficulties associated with finding novel compounds within this region.

There are a number of studies that have examined solar irradiance in the environment above and below the ocean surface. Unlike other previous studies, this thesis maps both surface and underwater irradiances using a combination of geostationary and Sea WiFS satellite data and surface measurements. Detailed estimates of broadband, PAR and UVB solar radiation, both above and below water, is obtained for the Great Barrier Reef region in northeast Australia. The study area covers the Coral Sea including the Great Barrier Reef (GBR), northeast of Queensland (10° S - 26° S, 142° E - 155° E). Geostationary meteorological satellite (GMS) data collected for periods between 1995 and 2005 are combined with the models to obtain broadband solar radiation at the surface. PAR and UVB underwater irradiance are estimated from the attenuation coefficients K\(_d\) derived from the Sea WiFS instrument for the period of 1998-2005. In developing algorithms, a look-up table (LUT), which contains senes of broadband surface solar radiation and the Earth-atmosphere reflectivity, is created from the Streamer radiative transfer model. The broadband Earth-atmosphere reflectivity α\(_{EA}\) derived from the GMS data is used to estimate the surface solar radiation from the LUT algorithms. The attenuation coefficients K\(_d\) for PAR, UVB and Sea WiFS wavebands are obtained from Monte Carlo models, and relationships between these Kd values are derived as a result. Using Sea WiFS-derived K\(_d\) data, PAR and UVB underwater irradiance are estimated across the regions from the K\(_d\) relationships. Comparisons between the satellite-derived surface solar radiation and the measurements at Rockhampton and Cairns give good agreement with root-mean-square difference (RMSD) of 2.26 MJ-m\(^{-2}\)-day\(^{-1}\) and 2.85 MJ-m\(^{-2}\)-day\(^{-1}\) , respectively. The Sea WiFS-derived K\(_d\) at six different wavebands obtained from Monte Carlo models are compared to the measurements at Heron Island, with a smallest RMSD value of 0.075m\(^{-1}\). Maps of solar radiation both above and below the water surface are provided for the study area. On average, strong solar radiation is exhibited in summer and autumn periods at latitude bands between 18° S and 26° S. The temporal information suggests there is a small increase in solar radiation of about 1 percent per decade. The underwater PAR and UVB irradiances along the GBR coastline at 2.5 m depth were in magnitude of ~300 W-m\(^{-2}\) and ~120 mW-m\(^{-2}\), respectively. Monthly distribution at 2.5 m depth underwater for PAR shows an outstanding feature throughout between September and February. There are patterns of high PAR irradiance throughout the summer months of 2001/2002 and 2002/2003. Results of the satellite-derived solar radiation are used to examine the 2002 coral bleaching events. A correlation between maximum solar radiation and the bleaching data are seen in summer months of 2001/2002.

The population genetic structure of species may be determined by complex interactions among many ecological, evolutionary and genetic processes. I investigated the population genetic structure of coral reef fishes on the Great Barrier Reef (GBR), Australia to better understand how these various processes may interact in a natural system. I firstly examined the spatial genetic structure of a low dispersal species to determine if its genetic structure varied among spatial scales and among regions located in the centre and on the periphery of its distributional range. I then examined the population genetic structure of species with different dispersal potentials and among species sampled at central and peripheral locations in their species range. Using mtDNA control region sequences and three microsatellite loci, I examined the spatial genetic structure of a direct developing coral reef fish, Acanthochromis polyacanthus, with comparatively low dispersal rates. The spatial genetic structure of this species was scale-dependent with evidence of isolation-by-distance among regions, but not within regions. Very strong genetic structure was detected among reefs within regions consistent with a metapopulation model. Pairwise genetic distances increased from offshore and older populations, to inshore and younger ones, supporting a metapopulation propagule-pool model of colonisation. Genetic diversities, mismatch, and coalescence analyses all identified large variation in the demographic history of this species among populations and regions. Evidence of genetic bottlenecks was detected by mismatch analysis in the majority of populations sampled, but in most populations these bottlenecks appeared to be older since genetic diversities and coalescence based population growth estimates did not indicate recent genetic bottlenecks. In contrast, three populations displayed low genetic diversities and large population growth rates indicating a more recent genetic bottleneck. Reductions in genetic diversities of local populations resulted in overall lower genetic diversity and a higher regional expansion rate in the southern region located towards the distributional margin of this species. In all, these results suggest that A. polyacanthus exists as a metapopulation within regions on the GBR and that metapopulation dynamics may differ among regions located in the centre and on the periphery of this species. The pelagic larval duration (PLD) can both affect and record the ecology and evolution of coral reef fishes and emerging evidence suggests that this trait displays considerable intraspecific variation. Here I present new estimates of PLD for ten species of Pomacentridae and two species of Gobiidae, and coupled with previously published estimates, examine spatial and temporal variation of PLDs within and among these species. In eight of the twelve species examined here, within-population mean PLDs differed between sampling times, locations within regions, and among regions. In contrast, the range of these same PLD estimates overlapped at all spatial and temporal scales examined in eleven of the twelve species, but not between regions in one species (Amphiprion melanopus). Therefore, despite tight error estimates typically associated with estimates of PLD taken from a particular population at a particular time in some taxa, the overlapping ranges in PLD reported here indicate that the length of the pelagic larval phase is a much more plastic trait than previously appreciated. Pelagic larval duration (PLD) is a commonly used proxy for dispersal potential in coral reef fishes. Here I examine the relationship between PLD, genetic structure and genetic variability in coral reef fishes from one family (Pomacentridae) that differ in mean larval duration by more than a month. Genetic structure was estimated in eight species using a mitochondrial molecular marker (control region) and in a sub-set of five species using nuclear molecular markers (ISSRs). Estimates of genetic differentiation were similar among species with pelagic larvae, but differed between molecular markers. The mtDNA indicated no structure while the ISSR indicated some structure between the sampling locations. I detected a relationship between PLD and genetic structure using both markers. These relationships, however, were caused by a single species, Acanthochromis polyacanthus, which differs from all the other species examined here in lacking a larval phase. With this species excluded, there was no relationship between PLD and genetic structure using either marker. Genetic diversities were generally high in all species and did not differ significantly among species and locations. Nucleotide diversity and total heterozygosity were negatively related to maximum PLD, but again, these relationships were caused by A. polyacanthus and disappeared when this species was excluded from these analyses. These genetic patterns are consistent with moderate gene flow among well-connected locations and indicate that at this phylogenetic level (i.e., within family) the duration of the pelagic larval phase is not the primary factor affecting patterns of genetic differentiation. Using mtDNA (control region) and nuclear (ISSR) markers, I investigated the population genetic structure of three congeneric species pairs of pomacentrid coral reef fishes (Pomacentridae) in the context of species’ borders theory. This theory predicts that population located on the periphery of the species’ range should be smaller and more fragmented and hence, display stronger genetic structure and lower genetic diversities compared to more centrally located populations. Each species pair consisted of one species sampled at two central locations within its geographic range, and another species sampled at the same locations but which constituted one location toward the centre of its range and another close to its edge. Contrary to expectations from theory, I did not find the predicted border effects in the population genetic structure of the species examined. Gene flow estimates did not differ among central and peripheral species. Genetic diversities were not lower in peripheral populations compared to central populations or in species sampled towards the periphery compared to those sampled in the centre of their ranges. Indeed, genetic diversities were much greater in the peripheral species compared to their central counterparts. The distribution of genetic variation indicated that secondary contact among differentiated lineages may, in part, be responsible for the high genetic diversity in these peripheral species. Elevated mutation rates mediated by environmental stress on the species’ margin may have contributed further genetic variability in these species.

Minimization of observer-related error is important for coral reef monitoring programs because highly variable data will decrease the resolution by which environmental change can be detected. Thirty-eight Reef Check volunteers were tested on their benthic identification skills on the Great Barrier Reef and their performance improved after practice and feedback sessions. Participants who had prior experience with environmental volunteer programs initially scored consistently higher than those without this experience. A similar but less consistent trend was found for more experienced divers. This information can be used to assess how much training volunteers require to remove the effects of different experience attributes. All participants' scores moderated towards the end of the study. The misidentifications still made involved similar benthos for all participants. This may reflect a lack of previous familiarity with these benthos types. The Reef Check categories that participants found most difficult to identify included hard coral, soft coral, recently killed coral, sponge and other benthic organisms. The effectiveness of future training sessions could be increased if focus is placed on these problem areas of identification within these categories.

This thesis presents the results of research into the environmental history of the Great Barrier Reef since European settlement, with particular emphasis on the period from 1860 to 1970 for which comparatively little scientific information about this ecosystem has been collected. Few environmental histories of the Great Barrier Reef have been written; those that exist have made limited use of archival and oral history sources. My research used archival and oral history sources more extensively in order to write three narratives of changes in the coral reefs, islands and marine wildlife of the Great Barrier Reef. Recent scholarship within the sub-discipline of environmental history has acknowledged that the production of such narratives – that focus on the changing relationship between human societies and the environment – is an essential task of environmental historians. My narratives are based on detailed descriptions of environmental changes, collected using qualitative methods including textual analysis and semi-structured interviewing; those narratives constitute an interpretive account of numerous ways in which humans have used and modified the Great Barrier Reef between 1860 and 1970. Changes in coral reefs are described in the context of the geomorphological evolution of the east Australian continental shelf during the Holocene epoch, which resulted in deteriorating water quality and the progression of some reefs – especially nearshore reefs – from juvenile to senile geomorphological states. Subsequent natural and anthropogenic impacts have brought several of these vulnerable reefs close to critical ecological thresholds, beyond which their recovery from degradation is unlikely. My research has found evidence that early European reef fisheries, coral mining, coral collecting, shell collecting, the creation of access channels and tracks, and military impacts have degraded some coral reefs; I present evidence to indicate the extent of these various impacts. In particular, no accounts of historical coral mining and coral collecting in the Great Barrier Reef have previously been written, yet those activities resulted in the removal of considerable quantities of coral from many reefs over long periods of time. As a result, some coral reefs were probably far from pristine at the time of the formation of the Great Barrier Reef Marine Park (GBRMP) in 1975. Changes in many islands of the Great Barrier Reef have also been substantial: for example, the construction of the navigation beacon at Raine Island, the removal of guano from many islands, the destruction of native vegetation and fauna, the introduction of exotic species such as coconut palms and goats, and the development of infrastructure. Some islands have been significantly transformed as a result of these activities, including Raine Island, several islands of the Capricorn-Bunker Group, and the most accessible tourist resort islands in the Cairns, Townsville and Whitsunday areas. Considerable impacts have also occurred on some marine wildlife species, including the commercial fishing of dugongs and turtles in the Great Barrier Reef and in adjacent coastal waters. I provide reconstructions of the extent and impacts of those fisheries, based on analysis of the reports and records of various Queensland Government Departments together with oral history evidence. I also describe other changes in marine wildlife, including the effects of the commercial humpback whale fishery and the effects of Indigenous hunting of dugongs and turtles. Together, the three environmental history narratives contained in this thesis represent an account of almost continuous human exploitation of the Great Barrier Reef between 1860 and 1970 which probably amounts to considerable degradation of the ecosystem, at least in localised areas and for particular species. Consequently, my research has several implications for the contemporary environmental management of the Great Barrier Reef World Heritage Area (GBRWHA). I argue that the re-evaluation of some ecological baselines is necessary, as documentary and oral history evidence indicates that the Great Barrier Reef has been exploited earlier, for a longer period, in more locations and more intensively than has previously been documented. In particular, some coral reefs, islands and marine wildlife species require additional scientific research and monitoring – linked with agreed performance indicators – in order to ensure their effective conservation. In addition, I have evaluated the use of qualitative methods in environmental history research. While the coverage of documentary sources describing the Great Barrier Reef is uneven for the period before 1970, those sources contain rich information about environmental changes. In comparison, oral histories provided sparse data, although some evidence about coral mining was obtained only from oral history sources. My research indicates that the use of multiple methods can best inform accounts of environmental changes in the Great Barrier Reef.

Corals are frequently injured by natural processes and human activities. The response of scleractinian corals to damage is dependent on the nature and extent of damage, the characteristics of the injury, the life-histories of the coral, and the prevailing abiotic and biotic conditions. In this thesis I have examined several aspects of injury including (1) the nature and extent of natural injury, (2) the response of corals to injuries with different characteristics and (3) the influence of morphology and life-history in response to damage. The spatial and temporal patterns of coral injury were recorded to determine the nature and extent of damage in common reef-crest corals at Lizard Island. The total amount of partial mortality on reef-crest corals was low (<2%) although there was a three-fold difference among sites. Sites with low partial mortality had reef-crest assemblages dominated (both numerically and in cover) by tabular and bushy corals. These corals have low levels of partial mortality, and on average, fewer small colonies with injuries. Conversely, the site where the partial mortality was three times higher had a lower abundance and cover of tabular corals, and an increase in the number and cover of massive and digitate corals. Massive and digitate corals, on average, have a higher amount of partial mortality and more small colonies with injuries. The amount of injury present on a colony at a particular time is a balance between vulnerability (i.e. frequency of injury and resilience to damage) and recovery rate. An investigation into the patterns of injury over time showed that vulnerability to damage and recovery of injuries was species specific. In general Goniastrea retiformis had a high number of old injuries, a slow regeneration rate, and was injured infrequently, suggesting that injuries tended to accumulate on colonies over time. The addition of new injuries was also low for Acropora gemmifera, however colonies had few pre-existing injuries and faster recovery rates, reducing the accumulation of injuries on colonies. The injury dynamics for A. hyacinthus differed between censuses because of a change in injury regimes from routine to catastrophic, the latter regime caused by an outbreak of Acanthaster planci. Under routine conditions, there were few pre-existing injuries on colonies, a moderate addition of new injuries, and rapid regeneration, suggesting a fast turn-over of injuries. Under catastrophic conditions, there were many more pre-existing injuries, a high number of new injuries, and more injuries increasing in size than recovering, resulting in an accumulation of injuries. The regeneration of injuries was influenced by the characteristics of the injury including initial size, type, and position within the colony The complete regeneration of an injury was more probable for small injuries (0 - 4 cm2) than larger injuries. However, recovery rates were also dependent on the type of injury as scraping injuries had a much faster regeneration rate than tissue mortality or breakage. Additionally, recovery was influenced by the position of injuries within colonies for one species Porites mayeri where the rate of regeneration of central injuries was greater than edge injuries. Conversely, the recovery of central and edge injuries was similar for A. robusta, A. hyacinthus, A. palifera, Pocillopora damicornis, and Porites lichen. Variations in levels of partial mortality, zones of tissue from which regeneration can take place, degrees of settlement by other organisms, intensities of damage, and amounts of resources available for regeneration all contributed to the differences in recovery rates found between injuries with varying characteristics. The regeneration of injuries requires resources that are in limited supply. In this study, there was a marked effect of injury on reproduction for A. hyacinthus, A. gemmifera and G. retiformis, inferring a trade-off between reproduction and regeneration. Presumably the resources usually available for gamete production are being reallocated towards polyp regrowth and defence against fouling organisms. In contrast, injury had no effect on the survival or growth of colonies over nine months for the three species. This result suggests that future reproduction is being preserved through the iteration of new polyps but at the expense of current reproduction. It also suggests that these species are resistant to damage since their survival was unaltered by damage in the short-term. Species resistant to damage have evolved two alternative, but not mutually exclusive, strategies in response to injury. Corals can invest resources in defensive mechanisms to avoid damage (avoidance strategies) or regrow lost parts after injury has occurred (tolerance strategies). Both strategies were utilised by corals in this study, although the amount of investment in either strategy varied. Generally, the longer-lived species, G. retiformis and A. gemmifera, seemed to invest more resources towards defence than the shorter-lived A. hyacinthus since the number of new injuries present on colonies was higher for the latter species. Conversely, the shorter-lived coral invested more in tolerance strategies by responding to infrequent damage events or minimal tissue losses with rapid regrowth. The cost of such a strategy is that shorter-lived species are more vulnerable to repetitive injury. Experimental studies showed that branching species had more regrowth potential than massive and semi-massive species supporting the hypothesis by Jackson (1979) that morphology plays a role in the pattern of investment in regeneration and defence. The morphology of a coral influences its longevity, reproductive output, growth rate, and other life-history processes including regeneration. Consequently, the morphological strategy of an organism has evolved over time in response to a large number of biotic and abiotic processes including partial mortality. In conclusion, this study on injury and regeneration of scleractinian corals has increased our knowledge of the underlying mechanisms that affect the recovery of corals from damage, and has provided a basis for understanding the consequences of different injury regimes on coral reefs. This is important because injury can adversely affect corals at the individual, population and community level and thus impact on the general ecology of coral reefs.

The Great Barrier Reef is regarded as one of the natural wonders of the world and is recognised as having World Heritage significance. The wealth and complexity of its natural attributes form the basis of a rich and complementary human history. However, management of the region is focused on the conservation of natural attributes, sometimes at the cost of human interests and cultural values. This is symptomatic of the way in which many heritage properties are managed and is a source of problems in the identification and interpretation of heritage. There is a need to better understand the human dimensions of such ‘natural wonders’ to ensure effective management. In order to address some of these issues, this thesis explores visitor experiences and knowledge of the Great Barrier Reef with a particular focus on the non-local experiences and knowledge that underpin the region’s global recognition. One of the major issues for management is the mutable nature of heritage values. This research therefore seeks to develop an understanding of how such heritage values are formed, transformed and sustained over time. It takes an historical approach to understand the ways in which visitor knowledge of the Reef has been constructed and transmitted both temporally and spatially. Methods novel to heritage assessments are developed and implemented to identify and contrast visitor experiences in the past and those of the present. The study focuses on visitor sensory experiences of the Reef as a means to understand knowledge of place. A concept of sensuousness is defined and used to understand how knowledge of place is constructed through the human senses, and communicated within and between generations. The research identifies a number of significant changes in the way in which visitors have constructed and understood the Great Barrier Reef. These include the creation of idealised Pacific islands at the expense of an Australian location and character; the transformation of the dangerous underwater world into a controlled and benign coral garden; and the synecdoche of the coral garden as representative of the Reef as a whole. Central to these constructions is the way in which simulacra are used to create experiences that are increasingly both dislocated and disembodied. As a consequence visitor knowledge of the Reef has shifted from sensuous perception of the Reef as a place or series of places, to the construction of imaginative and photographic simulacra that manifest as experiences of space and non-place. Through the exploration of this case study, the thesis makes a contribution to both theoretical and methodological issues in heritage studies.

Thesis (Ph.D.) - James Cook University, 2003.
Computer disc "contains samples of footage from a selection of home movies, documentaries and advertisements for the Great Barrier Reef". Typescript (photocopy). Appendices: leaves 314-353. Bibliography: leaves 275-313.

The patterns of movement of three species of coral reef fish were investigated in two tagging studies on the Great Barrier Reef. In the first study, done within the lagoon at Lizard Island on the northern GBR, the frequency of movement of Lutjanus carponotatus, Plectropomus leopardus and Siganus doliatus within and among sites and three habitat categories were examined in a multiple capture-recapture fish trapping study spanning a period of 22 months. Rates of growth, mortality and tag loss were estimated from the capture-recapture data also. The second study was a large-scale tag-recovery program designed to estimate the extent of movement of Plectropomus leopardus within and among five individual coral reefs in the Cairns Section of the Great Barrier Reef Marine Park. The rates of loss of t-bar anchor tags and dart tags were compared as was the frequency of loss of different coloured t-bar anchor tags. A total of 4,736 fish from 21 families and 109 species were trapped over the duration of the small-scale movement study in the Lizard Island lagoon. The catch was dominated by the Siganidae, Lutjanidae, Lethrinidae, Serranidae, Haemulidae and Acanthuridae, which collectively comprised over 88% of the catch at each site. Siganus doliatus and Lutjanus carponotatus were the two most common species and together accounted for 36 % of the total catch. P.leopardus was less common accounting for less than 5% of the catch at each site. Catch per unit effort (CPUE) of P.leopardus, L.carponotatus and S.doliatus varied among the three sites. However, the CPUE of each species was highest in the reef habitat and lowest in the sand habitat at all sites. Fish trappping proved to be an effective, but selective, technique to simultaneously sample these species of coral reef fish at many locations and across a variety of habitats with limited logistical support. The patterns of movement of the three species within the Lizard Island lagoon were found to differ considerably. P. leopardus regularly moved among trapping positions and across habitat types while the movements of L.carponotatus and S. doliatus were considerably more restricted. The majority of individuals of L.carponotatus (68%) and S.doliatus (69%) were recaptured at the position of release while the majority (66%) of P. leopardus recaptures had moved among trapping positions. L. carponotatus exhibited a strong fidelity for the habitat of release. The frequency of movement among habitat categories for fish released in the reef habitat was considerably (although marginally significant) lower than for fish released in the patch or sand habitat categories. S. doliatus was found to show a strong fidelity for the habitat of release also. However, the frequency of movement among the reef and patch reef habitats was higher than observed for L.carponotatus. This may be related to foraging patterns of siganids which feed over the reef flat at high tide. The results indicate that the movements of L.carponotatus and S. doliatus are generally restricted to less than a few hundred meters with the majority of fish not moving from their position of release. The frequency of movement of L.carponotatus and S.doliatus across reef-sand habitat boundaries was considerably lower than the frequency of movement across reef-patch reef or patch reef-sand habitat boundaries. This suggests that reef-sand habitat boundaries may represent less permeable management boundaries than arbitrary boundaries located within continuous sections of reef mosaic. Estimates of survivorship for each species were made from the multiple capture-recapture data using program RELEASE version 2.6. The estimates of survivorship for L. carponotatus and S. doliatus for the reef and patch reef habitats suggested that survivorship was higher (but not significantly at α = 0.05) in the reef habitat than in the patch reef habitat. There were insufficient data to examine the effect of habitat on survivorship for P. leopardus. Estimated survivorship also appeared to vary among sampling periods. The estimates of survivorship were adjusted for tag loss and converted to estimates of annual rate of natural mortality. These were very high for each species, in comparison to estimates available in the literature, which suggest that there may have been a significant effect of capture and tagging. The results suggest that survivorship may vary among habitats and over time. Consequently, the common assumption of constant mortality within and among populations and over time requires greater scrutiny. Rates of growth for P. leopardus, L. carponotatus and S. doliatus were estimated using growth increment data from the small-scale tagging study. Estimated von Bertalanffy growth equation parameters, L(∞) and K, were 576 mm and 0.21 for P. leopardus, 357 mm and 0.12 for L. carponotatus and 201 mm and 0.71 for S. doliatus. There was evidence of high individual growth variability for each species. This, combined with the lack of data for individuals in the lower end of the size range of each species, suggests that the estimates of L(∞) are likely to be positively biased, and hence the estimated K negatively biased. The age-based parameter estimates for L. carponotatus obtained from the same location suggested this was the case, with L(∞) and K estimated to be 312 mm and 0.31, respectively. There was considerable variation in size at age for L. calponotatus, again suggesting that there may be significant variation in growth among individuals: This highlights the need for age-based estimates of population parameters for coral reef fish as length is likely to be a poor proxy for age. The relationship between estimates of age from readings of sectioned and whole otoliths and otolith weight were examined for L. carponotatus. Readings of whole and sectioned otoliths were the same up until age 5-6 after which readings of whole otoliths tended to underestimate age relative to readings of sectioned otoliths. There was a high correlation (r² = 0.94) between otolith weight and age from sectioned otoliths of L. carponotatus, indicating otolith weight may be an objective and cost-effective alternative for obtaining age-based estimates of population parameters for some coral reef fish. All P. leopardus and L. carponotatus were double tagged in both studies. The Bayliff and Morbrand model was used to estimate rates of tag loss. Type I tag loss was not significant for L. carponotatus. However, the instantaneous rate of loss of t-bar anchor tags was high (0.0034, ±95% CI = ±0.0021). Type I tag loss was significant for t-bar anchor tags for P. leopardus. The estimate of the proportion of tags remaining following type I tag loss for P. leopardus was 0.8927 (95% CI = 0.8140-0.9791), while L, the instantaneous rate of tag loss was 0.0010 (±95% CI = ±0.0005). The estimated proportion of t-bar anchor tags lost annually were 72% and 60% for L. carponotatus and P. leopardus, respectively. This clearly demonstrates that tag loss rates can be substantial and assuming they are negligible will result in seriously biased parameter estimates. Dart tags were found to be shed at a significantly greater frequency than t-bar anchor tags (Likelihood X²(0.05,1.) = 10.678; p < 0.005) suggesting that t-bar anchor tags are the less effective of the two tag types used. The colour of the t-bar anchor tags used didn't significantly effect their frequency of loss (Likelihood X²(0.05,5,243) = 1.902; p < 0.8625). This demonstrates that different colours of tag may be used to batch code releases of reef fish without incurring differential frequencies of tag loss due to the colour of the tags. A total of 8,043 fish were caught from the five reefs over five trips of the large-scale tagging study. Catch was dominated by Serranidae, Lutjanidae and Lethrinidae which comprised greater than 97% of the total catch. The species composition was dominated by six species, Plectropomus leopardus (57%), Cephalopholis cyanostigma (12%), Lutjanus carponotatus (6%), L.bohar (3%), Lethrinus miniatus (3%) and L. atkinsoni (4%). The contribution of these six dominant species to the catch varied significantly among trips and reefs. Plectropomus leopardus comprised a greater proportion of the catch on the trips done during the spawning season (September 1992 and October 1993). This may indicate an increase in the catchability of P. leopardus during the spawning season. The difference among reefs was mainly due to the higher proportion of Cephalopholis cyanostigma and Lutjanus bohar and the lower proportion of Lethrinus miniatus and Lutjanus carponotatus at two reefs compared to the other three reefs studied. Catch Per Unit Effort of P. leopardus varied significantly among trips and within reefs. However, there was no significant difference in CPUE among reefs. The pattern of CPUE among trips and within reefs indicated that the observed increase in CPUE that occurs during the spawning season is likely to be the result of an increase in the catchability of P. leopardus when the fish are aggregated to spawn. The average size (mean length to caudal fork) of P. leopardus decreased significantly over the five trips, with a monotonic reduction in average size from April 1992 to February 1994. Mean size of P. leopardus varied significantly among reefs and blocks (1.5-2.5 km strip of reef perimeter) also, with Taylor Reef having a significantly greater average size than the other reefs and Beaver Reef having a significantly smaller average size than all other reefs. Although the overall reduction in mean size of P. leopardus across all reefs is indicative of fishing and cause for concern, in the absence of size-at-age information it is not possible to accurately interpret these effects in terms of differences in the population dynamics of P. leopardus among reef or over time. The significant effect of block on mean length of P. leopardus suggests that there may be significant differences in either age-structure or growth rates within reefs also. These results highlight the need for rigorous and powerful sampling programmes, which include within reef strata, for monitoring changes in relative abundance and size and age-structure- of exploited populations of coral reef fishes. A total of 4,627 P. leopardus were tagged and released on the five reefs with a total of 443 recaptured; 300 from the public and 143 from the four tag-recovery exercises. Ninety-nine percent of the research returns of P. leopardus were returned from the reef of release. One inter-reef movement was recorded from Taylor to Beaver Reef. These results indicate that the extent of inter-reef movement was negligible. In contrast, 36% of the public returns were returned from reefs other than the one on which they were released. The majority of inter-reef movement from the public returns was from Beaver (Closed) to Taylor reefs and from Potter Reef to other reefs in the cluster. The disparity in the extent of inter-reef movement of P. leopardus from Beaver Reef (Closed to fishing) between the public and research returns appears to be the result of infringement and misreporting of location of capture by the public. It is suggested that the level of fishing effort on Beaver Reef (Closed to fishing) indicated by the tag returns may be sufficient to negate the potential effects of protection from fishing. This was supported circumstantially by the CPUE and length frequency data for P. leopardus. In contrast to the negligible level of inter-reef movement by P. leopardus, there was considerable movement within reefs. On average 35% of the P. leopardus returned had moved out of the 1.5-2.5 km block in which they were released. The extent of movement varied among reefs and appeared to be related to movement to, or from, spawning aggregations. The results of the large-scale movement study suggest that partial reef closures may not effectively protect the populations of more mobile reef fish such as P. leopardus, due to their relatively high frequency of movement within reefs, and that it would be more effective to use individual reefs as the minimum spatial unit for reserve design.

In situ rates of photosynthesis and calcification were determined for four species of reef-building crustose coralline algae on the windward crest and slope of a coral reef at Lizard Island, in the northern region of the Great Barrier Reef (GBR). The species studied were Porolithon onkodes (Heydrich) Foslie, Neogoniolithon fosliei (Heydrich) Setchell & Mason, Hydrolithon reinboldii (Weber-van Bosse & Foslie) Foslie, and Paragoniolithon conicum (Dawson) Adey, Townsend & Boykins. Rates were measured with an underwater respirometer incorporating oxygen, pH, light and temperature probes located within an ultra-violet transparent incubation chamber. Measurements of photosynthesis were also made in the laboratory using a 'Clark' type oxygen electrode and a specially constructed acrylic cell. The photosynthetic quotients (PQ) of the four species were determined from in situ measurements of oxygen, pH, and total alkalinity, with corrections for changes in seawater temperature over the period of incubation. Light-saturation curves for photosynthesis (P-I curves) and calcification (C-I curves) were constructed from each set of in situ and laboratory measurements using non-linear, least squares regression analysis. The curves were examined for evidence of photoadaptation and for estimation of the rates of maximal gross photosynthesis, absolute dark respiration, maximal light-enhanced calcification, and dark calcification. Individuals from selected habitats at depths of between 0 and 18 m were studied both in situ and in the laboratory. The specimens received from 85 to 2% of surface irradiance as measured in units of photosynthetic photon flux density (PPFD) between 400 and 700 nm. Light-saturation curves. In situ data were modelled by the hyperbolic tangent function. The less variable laboratory data revealed subtle differences in the shapes of the light-saturation curves of different species and were modelled by one of four related mathematical functions. The functions tested for accuracy of fit were the hyperbolic tangent, a simple exponential, a general exponential, and the right rectangular hyperbola. Specimens collected from 0 m exhibited slow rates of transition from light-limited to light-saturated photosynthesis. Many of these individuals were not entirely saturated at irradiance levels above those naturally occurring in the field. Rates of photosynthesis were generally lower in the laboratory than in situ. Specimens measured in situ at depths representing the lower limits of the species distributions were found to exhibit light-response curves which did not indicate saturated levels of photosynthesis or calcification. Photoadaptation. Adaptive changes were observed in the photokinetic parameters describing the shapes of the light-saturation curves of all species under both laboratory and in situ conditions as the quantity of irradiance diminished. Compensation points ((Ic), 95% saturation levels (I₀₉₅), and intercepts between the initial slopes of the curves and the horizontal asymptotes ((Ik) decreased. Rates of respiration (R), maximal gross photosynthesis (Pgm), and light-enhanced calcification (C light) based on real surface area also tended to fall. The initial slopes of the curves (α) for photosynthesis (based on projected or real surface area) and calcification (based on total protein content) increased with decreasing irradiance. The ratios of gross photosynthesis to respiration (Pᵍml-R) increased marginally with decreasing irradiance. The rates of dark calcification (C dark) and light-enhanced calcification expressed on the basis of total protein content were variable and did not vary predictably with diminishing irradiance. The natural logarithms (In) of Ic, Ik, and I₀₉₅ were directly proportional to the natural logarithms of the percentages of surface irradiance (In %SI) transmitted to the depths at which the algae were growing. Similar double logarithmic relationships were observed between Pᵍm, R,(C light)(based on real surface area) and In %SI for some species. The natural logarithms of for photosynthesis normalised on the basis of real surface area, and for calcification normalised on the basis of total protein content, were inversely proportional to In %SI for all species. Similar double logarithmic relationships were observed between Pᵍm l-R and In %SI for some species. Primary production. Photosynthetic quotients (PQ) were determined for each species. Mean PQ values for P. onkodes, N. fosliel, and H. reinboldii ranged from 1.21 to 1.33. The mean PQ for P. COM. CUM was 1.07. Mean rates of maximal net organic carbon production per hour ranged from 0.083 to 0.168 g C m⁻² (real surface area) in situ, and from 0.068 to 0.148g C m⁻² in the laboratory. Mean rates of net carbon production integrated over the course of a 24 hour day ranged from 0.180 to 1.352 g C m⁻²(real surface area) in situ, and from 0.123 to 1.206 g C m⁻² in the laboratory. Rates of gross primary production or consumption per day were directly proportional to peak noon irradiance. The rate of carbon production per day could thus be estimated for any amount of irradiance on a cloudless day. Calcification. Using an adaptation of the alkalinity anomaly technique, the precipitation or solution of calcium carbonate was estimated by subtracting the calculated change in pH resulting from photosynthesis and respiration from the measured change in pH. Mean maximal rates of in situ calcification per hour ranged from 0.156 to 0.923 g CaCO₃ m⁻² (real surface area). Mean rates of calcification integrated over a 24 hour day ranged from 0.87 to 9.86 g CaCO₃ m⁻² (real surface area). Rates of calcification per day were directly proportional to peak noon irradiance for all species except H. reinboldii. The rate of calcification per unit of surface area decreased with increasing depth and decreasing irradiance. Calcification rates were always considerably higher in the light than in the dark. Dark rates of calcification were highly variable. In several cases solution of CaCO₃ was observed in the dark. Relationships between calcification and irradiance, and photosynthesis and irradiance, were similar but not identical. In shallow water, greater irradiance was required for the saturation of calcification than for saturation of photosynthesis. These data suggest that calcification is largely controlled by photosynthesis but is probably influenced by other factors, among them tissue biomass. Conclusions. Crustose coralline algae are highly significant producers of organic and inorganic carbon on coral reefs. Their rates of photosynthesis may have been underestimated by the use of semi-artificial procedures. Their rates of calcification are comparable with corals and in certain reef zones their great abundance may result in overall calcification rates which exceed that of 98-99% of the rest of the reef. As expected crustose coralline algae photoadapt and their ability to do so influences but does not necessarily control their distributions on the reef.

Rodrigo Gurdek explored larval dispersal patterns of the stripey snapper on the Great Barrier Reef. He found that highly dynamic currents apparently link regional and local reefs over time, consistent with genomic analyses. Findings denote the importance of incorporating temporal fluctuations in dispersal when assessing connectivity and recovery of populations.

Inshore turbid zone coral reefs on the central Great Barrier Reef (GBR) are situated within 20 km of the coast where terrigenous sediments influence coral communities, carbonate production and reef growth. They exist within a range of geomorphic settings from open coastal settings to muddy coastal embayments, and include fringing and nearshore reefs and shoals. Inshore regions on the central GBR are characterised by high sediment yields and suspended sediment loads, elevated nutrients and fluctuating salinities. These marginal environmental conditions are widely viewed as unfavourable for sustained and vigorous coral reef growth, and thus it is commonly claimed that inshore turbid reefs are stressed and/or degraded. However, recent research has challenged this and demonstrates that many have high coral cover and robust coral communities, and that reefs have rapidly accreted to sea level despite exposure to elevated terrigenous sediments. The importance of terrigenous sediments for coral community composition and turbid zone reef growth has yet to be quantitatively evaluated due to a lack of detailed data and limited knowledge on sedimentary interactions and processes in these highly dynamic sedimentary settings. The overall aim of this research was to provide a comprehensive assessment of carbonate and terrigenous sediment regimes for inshore turbid reefs on the central GBR by quantifying carbonate production and destruction together with sediment deposition, resuspension and transport across the reef. Specifically, the objectives of this research were to: 1) examine benthic community composition and distribution; 2) examine spatial variations in sediment texture and composition; 3) investigate the influence of spatial and temporal variations in turbidity on benthic cover; 4) quantify the sedimentary regime and examine its role in reef growth; 5) investigate spatial and temporal variations in coral growth and carbonate production; and 6) quantify carbonate production and destruction together with sediment import, storage and export to assess reef growth. This research focused on two inshore turbid zone reefs on the central GBR; Middle Reef, a nearshore reef situated between Magnetic Island and Townsville, a large urban area with a major port; and Paluma Shoals, approximately 30 km north of Townsville on a more exposed coastline and distal to direct anthropogenic pressures that may influence Middle Reef. These two sites were chosen to examine the influence of variable hydrodynamic and sedimentary regimes on coral community composition and distribution, and on net carbonate production and reef growth. At both reefs coral cover was high (>30%) and diversity was moderate to high (>50 species). The coral community distribution was independent of depth and was instead driven by spatial variations in sedimentation rates and turbidity, largely controlled by reef morphological interactions with waves, currents and tides. Coral communities were dominated by either fast-growing species such as Acropora and Montipora, most abundant on the exposed windward reef edges, sediment tolerant species such as Turbinaria, Galaxea and Goniopora which dominated the leeward reef edges and were also abundant at the base of windward reef slopes, and Goniastrea which dominated the reef flats. Investigations into temporal community dynamics at Middle Reef show that coral cover on the windward reef edge (73%) has increased over the last 15 years despite a history of episodic mortality events. These data demonstrate that these coral communities are robust and resilient, and challenge perceptions that inshore turbid reefs are degraded. Reef morphology influenced sediment composition, distribution and resuspension over both reefs. Sediments consisted of varying proportions of silt, sand and gravel, and the carbonate component was dominated by coral and mollusc fragments. The mean grain size decreased from the eastern windward reef slopes to the western sheltered leeward edge reflecting wave energy dissipation across both reefs. The mean grain size was greater at Paluma Shoals, where higher wave energy resuspended and redistributed sediments over the reef and finer sediments were winnowed away. As such, sediment composition and distribution was not significantly correlated to reef benthos. In contrast, lower wave energy and limited redistribution of sediments at Middle Reef resulted in a strong correlation between sediment composition and reef benthos. Given spatial distributions in both wave energy and sediment composition, sediment resuspension rates and turbidity also varied across both reefs. These turbidity gradients were reflected in coral community distributions with a greater abundance of heterotrophic corals in reef habitats characterised by rapid and large fluctuations in turbidity. Local wind speed data accounted for <73% and <56% in the variance in turbidity at Paluma Shoals and Middle Reef respectively, and was used to generate a site-specific turbidity model. The model will enable future researchers to direct real time management for turbidity risk assessments, identify increases in turbidity above the natural turbidity regime and assess the implications for coral communities and reef health. A detailed quantitative assessment of the sediment regime (deposition, resuspension and removal) developed using both established and new techniques, reveals that despite high sediment flux rates (<20, 000 tonnes annually), net sedimentation rates are low (<50 g/m²/day) due to sediment resuspension and removal. Established techniques included the use of data loggers to measure spatial and temporal variations in turbidity with waves and currents, whereas sedimentation and resuspension rates were measured using 'sediment trays'. The use of sediment trays overcame the limitations of commonly used 'sediment traps' which over-estimate sedimentation rates and preferentially collect larger particles. The sediment regime was quantified across two depth zones (0.5 to -1.5 m, <-1.5 to -3.5 m at LAT), and within five geomorphic habitats (eastern, central and western windward reef edge, inner basins or reef flat and leeward reef edge) to provide data for a model that illustrated the direction and rate of sediment delivery, deposition and removal across both reefs. The model illustrated that >81% of sediments imported annually onto turbid reefs are exported as suspended sediments due to high wave energies, which corresponded to elevated turbidity (>50 mg/L). These results suggest that despite a high sediment flux rate through these reef systems, sediment deposition is limited and therefore does not impede inshore reef growth and survival within terrigenous settings. Coral growth is influenced by environmental conditions such as sea surface temperatures (SST) and water quality, and can be used to assess coral condition as well as the rate of carbonate production. In this study the coral growth rates (linear extension, density, calcification rates) of three fast-growing corals (Acropora, Montipora, Turbinaria), common to both inshore turbid reef and offshore clear-water reefs, were studied in situ on Middle Reef to provide some of the first data used to quantify carbonate production for inshore turbid reefs. Our investigations found that Acropora growth rates (average rate of 6.3 cm/year) were comparable to those measured at similar depths on mid to offshore reefs on the GBR. Montipora linear extension (2.9 cm/year) was greater than current estimates available for both turbid and clear-water reefs, and Turbinaria, although characterised by low linear extension (1 cm/year), had a dense skeleton (1.3 g/cm³) and may be more resilient to physical damage. Spatial variations in coral growth and carbonate production rates were driven by water motion and sediment dynamics, and temporal variations indicated that coral growth was lower during the summer when SSTs (mean 29 °C) and rainfall (monthly 500 mm) were high. In summary, high contemporary growth rates on inshore turbid reefs is in accord with rapid accretion rates established from the fossil record for numerous turbid reefs on the GBR and indicate that corals on Middle Reef are resilient to their marginal environmental conditions. This research provides the first quantitative assessment of carbonate production and destruction together with sediment import, storage and export, to evaluate the rate and mode of reef growth for inshore turbid reefs. The mean net carbonate production rate was 12 kg/m²/year at Middle Reef and 7 kg/m²/year at Paluma Shoals, although varied between habitats with lowest rates measured on shallow reef flats (>1 kg/m²/year) and highest rates at the base of reef slopes (<19 kg/m²/year). The mean net carbonate production rate was converted to a reef accretion rate, which was greater at Middle Reef (5.2 mm/year) reflecting the higher coral and Acropora cover than at Paluma Shoals (3 mm/year). The mode of reef growth for each reef habitat was determined by comparing the rate of sediment deposition to carbonate accumulation; if carbonate production was high and sediment deposition limited, it was production-dominated; if sediment accumulation was greater than carbonate production, it was import dominated; and if the rate of sediment resuspension was greater than the rate of sediment deposition, it was export dominated. The mode and rate of reef growth were used to construct a reef growth model, with accretion in deep reef habitats taken as a proxy for early reef growth. The model provides an assessment of reef growth in a terrigenous setting with depth and time, quantitatively links sedimentary processes to ecological processes over time and space, and can be used to assess how reef growth may respond to future environmental changes such as increased sediment delivery, rising sea-level and increased SSTs.

This study examines the implications of disease for the structure and resilience of Great Barrier Reef (GBR) coral assemblages. Annual disease surveys in the northern and central sections of the GBR between 2004 and 2006 indicate that disease is ubiquitous and persistent throughout much of the GBR. Seven diseases commonly affect a wide range of anthozoan taxa, albeit at relatively low levels of prevalence (~ 3% of scleractinian corals). Nonetheless, values recorded for disease prevalence and for rates of tissue loss and mortality indicate that the acute impacts of diseases such as black band disease (BBD) and skeletal eroding band (SEB) can be similar to those of diseases that have caused significant declines in Caribbean coral populations, highlighting the significant role disease is likely to play in structuring at least some GBR coral assemblages. Two families, the Pocilloporidae and Acroporidae, consistently ranked highest in a disease susceptibility hierarchy determined for GBR corals. Consistency in spatial patterns in the prevalence of BBD coupled with consistency in disease susceptibility hierarchies over cross- and long-shelf gradients in turbidity, wave action, and water quality, indicate that these environmental factors are not the primary drivers of disease occurrence on the GBR. Instead, concordance in family rankings for susceptibility to disease and susceptibility to other factors that compromise coral health (thermal bleaching, injury from predators, and interactions with macro-algae) suggests that fast growing, branching morphologies of acroporid and pocilloporid corals, and their resultant high abundance in many Indo-Pacific coral assemblages, enhance the vulnerability of these families to a diversity of pathogens, in addition to a range of other biological and physical stressors. Experimental studies demonstrated the important role that injury is likely to play in the development of SEB. Halofolliculina corallasia, the putative pathogen of SEB, rapidly colonised artificial wounds, however, despite initial increases in ciliate densities on wounds, ciliates failed to become pathogenic and cause additional tissue mortality on any of the three coral species tested experimentally. In addition to injury, environmental factors that compromise coral health or the presence of other microbial agents may be required before ciliates become pathogenic. In combination with correlations between family rankings for susceptibility to disease and susceptibility to other factors that compromise coral health, these results highlight the need for management strategies that limit activities and factors that compromise coral health, in order to minimise the spread and transmission of coral diseases. Partial mortality over three months caused by the three diseases examined in this study ranged from 85.7 ± 1.6% for BBD to 12.9 ± 1.7% for SEB, while rates of whole colony mortality over two years ranged from 84% for BBD to 39% for SEB. Tissue loss was not associated with growth anomalies (GAs) in this study. The combined partial and whole colony mortality caused by BBD was at least two-fold higher than mortality caused by SEB in northern GBR coral populations, however the seven-fold higher prevalence of SEB, combined with further reductions in the growth rates and reproductive output of surviving portions of A. muricata colonies, indicate that SEB could have greater fitness consequences for GBR Acropora populations than BBD. The potential for failure of gametogenesis in a large proportion of Acropora colonies with GAs, indicates that the impact of a chronic outbreak of GAs on the fitness of Indo-Pacific coral populations could rival those of both SEB and BBD. Sub-lethal impacts of these diseases on growth and reproduction of Acropora muricata also varied, suggesting that this species can vary its resource allocation strategy to maximise contributions to future generations in response to differing levels of disease virulence. Continued investment of resources in colony growth and reproduction in colonies with BBD may represent an attempt to maximise short-term fitness, given rapid rates of tissue loss and the high probability of dying. In contrast, colonies with GAs or slower progressing diseases such as SEB may divert resources from physiological processes not directly linked to colony survival in response to the greater likelihood that some portion of the colony will survive and recover. Predicted increases in disease with ocean warming and anthropogenic impacts pose the greatest threat to the persistence of the highly susceptible acroporid and pocilloporid corals in this region, taking into consideration both the lethal and sub-lethal impacts of diseases highlighted in this study and the double jeopardy represented by their high vulnerability to other disturbances including cyclones, bleaching and crown-of thorns outbreaks on the GBR.

The Coral Sea, located to the Northeast of Australia (8ºS to 30ºS and 142ºE and 170º E) covers an area of a million square kilometres and harbours the largest Coral Reef system in the world. The Coral Sea has a very complex bathymetry, great temporal variability and very strong and narrow currents which renders it difficult for the implementation of an adequate observing system. A better understanding of this region’s circulation patterns is important because of its location at a major ocean pathway from the equator to the subtropics that may potentially influence the ENSO cycle (Gu and Philander 1997; Kleeman et al. 1999; Schneider et al. 2002; Schneider 2004). Existence of jet like structures in the southwest Pacific was first identified by Webb (2000). Since Webb’s discovery, a number of studies have been carried out to observe these jets and understand their influence on the circulation of the Coral Sea (Stanton et al. 2001; Hughes 2002; Ridgway et al. 2002; Kessler and Gourdeau 2006; Kessler and Gourdeau 2007; Ganachaud et al. 2008; Gourdeau et al. 2008; Schiller et al. 2008). Numerical models have so far provided most of our knowledge of the Coral Sea circulation but have been calibrated and validated against very few in situ measurements. Moreover, model results have been incapable to realistically represent the seasonal variability of the jets (Qu and Lindstrom 2002; Kessler and Gourdeau 2007) nor the SEC bifurcation along the Great Barrier Reef (Ganachaud 2007). This thesis aims to investigate: • The mean and seasonal variation of the surface circulation of the Coral Sea in terms of Eulerian and Lagrangian statistics derived from surface drifters. • The interaction of the Coral Sea jets with the complex bathymetry of the Coral Sea and their contribution to the Western Boundary Currents (WBCs). • The Coral Sea inflow and residence times in the Great Barrier Reef from in situ measurements, • And finally, the East Australian Current (EAC) flow interaction with the complex southern Great Barrier Reef (GBR) bathymetry. The spatial structure of the surface currents in the Coral Sea were described, at mesoscale, in terms of Eulerian and Lagrangian statistics computed from the low passed drifter velocities (36 hour cut-off period) obtained between September 1981 and December 2009. Pseudo-Eulerian maps of the surface mean flow, mean kinetic energy and eddy kinetic energy were produced to study the circulation at meso-scale in the region. The surface mean flow depicts well the presence of the North Vanuatu Jet as a large (over 2 degrees of latitude) and strong jet (velocities greater than 20 cm s-1) and the North Caledonia Jet which is much narrower (0.5 degrees of latitude) and relatively strong (velocities greater than 15 cm s-1). The jets enter the Coral Sea between the Solomon Archipelago and New Caledonia, and flow westward toward the Australian Shelf where they contribute to the formation of the southward flowing East Australian Current and the northward flowing North Queensland Current. Interestingly, part of the NCJ appears to be deflected to the north by the presence of the Queensland Plateau at ~152°E, where it joins the NVJ at ~ 150°E. A novel surface current structure was also observed in the Solomon Sea, flowing to the southeast along the western side of the Solomon Islands. The seasonal variability of the surface circulation of the Coral Sea show that most of the variability is contained in the northern Coral Sea, north of 15ºS. This is defined by a strengthening of the North Coral Sea gyre, during the winter, which can clearly be depicted in our mean flow map. The NQC surface transport doubled and the NGCC strengthens. Highest MKE values were observed during the winter, and are concentrated along the NVJ path and the western boundary currents. Surface circulation and residence time of the Great Barrier Reef were derived from drifters that had entered the GBR. The Coral Sea inflow in the GBR is a key parameter to understand the connectivity of coral reef fauna. Knowledge of connectivity patterns is important to enable the formulation of realistic management strategies to ensure successful conservation of reef biodiversity, especially under the looming spectre of climate change. Secondly the data were used to resolve the flushing time of waters in the GBR which has important implications for flushing time of pollutants of terrestrial origin. These results, including diffusion and kinetic energy quantification, are also invaluable for hydrodynamic model calibrations, providing for the first time, an evaluation of the parameters measured in situ Finally, data from a long term mooring array deployed along the Capricorn Bunker shelf and slope, combined with satellite imagery and outputs from a global ocean model, is used to quantify the influence of the EAC to the circulation in the Capricorn Channel. A North westward flow can be observed along the shelf which was observed to strengthen and to reach a maximum of 10 cm s-1during the summer months and a minimum of ~0 cm s-1during the winter months. High energy was observed in the velocity; temperature and sea level between 20-40 days and 70-140 days periodicities were observed. The results suggest the formation of a cyclonic eddy, over the Marion Plateau, periodically every 20-40 days, modulated by a 70-140 days periodicity. This eddy may drive the northwest ward flow along the shelf and therefore allowing intrusions of oceanic water over the shelf. This has very important implications for the ecosystem health as it provides inflow of cooler and rich in nutrient to the shelf, especially during the summer months. The processes controlling the eddy formation remain unclear but appear to be related to the presence of an anti cyclonic anomaly at 25S. This anomaly appears to affect the flow of the EAC forcing it to bifurcate along the CB shelf.

The reproductive output of exploited tropical reef fishes is intimately linked to factors such as mating patterns, sexual selection, sex ratios and reproductive success, because they affect an individual's fecundity and hence long term productivity. This information is critical to fisheries management, yet few studies have estimated annual fecundities and time schedules of egg production in exploited reef fishes. This study examines temporal and spatial patterns in egg production and spawning behaviour of an exploited serranid on the northern Great Barrier Reef. Spatial patterns in the spawning behaviour of Plectropomus leopardus (coral trout) were examined by direct observations underwater at Scott and Elford Reefs for 3-4 years. A major (termed primary) spawning aggregation was located at each reef. These aggregations formed at the same sites each year, lasted for 5 days and formed around three consecutive new moons. Spawning occurred during a 33 min period spanning sunset. Maximum numbers of coral trout at these sites were 128 at Scott Reef, and 59 at Elford Reef. Smaller aggregations (termed secondary) were also located. Although their formation was inconsistent, their occurrence was also linked to the new moon phase. The distribution and density of coral trout in a 6.5 km² area surrounding the primary site at Elford Reef was mapped using visual census surveys. Individuals were tagged within this area to estimate the catchment area of the aggregation site, and to track the movements of individuals to the site. The primary site was estimated to draw fish from a population of around 3,000 adults in an area of only 1.5 km², and it was estimated that around 14% of the population used the aggregation site to spawn. However, certain individuals showed high site fidelity, returning to the site on subsequent evenings within a new moon phase, on subsequent new moons within the season, and the following year. Temporal patterns in egg production were determined from histological sections of gonads. Annual fecundity was estimated from counts of hydrated oocytes (batch fecundity) and from the proportion of females with post-ovulatory follicles (spawning frequency). The time schedule of hydrated oocytes was closely linked to lunar phase and time of day. Spawning occurred predominantly during the new moon and first quarter lunar phases at dusk. The average number of spawnings per female per year was estimated at 30, and annual fecundities of between 2.6 and 4.7 million eggs were obtained. The results indicate that Plectropomus leopardus employs both aggregative and non-aggregative spawning. The high spawning frequency and range of mating mechanisms may maximise egg output. I suggest this flexibility in P. leopardus spawning strategies improves their resilience to exploitation.

Understanding spatio-temporal patterns in habitat use is critical for assessing the ecological role of a species, its vulnerability to human impacts and environmental change, and the efficacy of conservation and management strategies. Investigating these patterns for young sharks (neonates, young-of-the-year [YOY], and juveniles) can also improve understanding of the functioning of shark nurseries, and the potential benefits of marine protected areas (MPAs). The overall objectives of this thesis were to (1) characterise spatio-temporal patterns in coastal shark distributions, (2) explore the ecological drivers of these patterns, and (3) evaluate the potential implications of heterogeneous space use for population sustainability and the efficacy of coastal MPAs. Portfolio theory predicts that contributions from a diverse range of young shark habitats may reduce variability in the overall production of adults, and maintain population resilience. This thesis examined case studies of portfolio effects in teleost fish and evaluated the relevance and potential implications of these processes for shark populations. Environmental heterogeneity in young shark habitats can result in locally adapted habitat-use patterns and life-history traits. Therefore, young shark habitats may be differentially impacted by anthropogenic disturbance or environmental change, with different habitats being productive at different times. In addition, increased stability in productivity may occur when the effects of localised disturbance in one area are buffered by production in others. Understanding intra-population variations in abundance and habitat use, and the extrinsic drivers of these, is fundamental to understanding the potential for portfolio effects in shark populations. In the context of portfolio effects, multi-year fishery-independent surveys of shark communities were used to investigate diversity in shark nursery area function along a 400 km stretch of coastline in north Queensland, Australia. Multivariate analyses were used to explore spatio-temporal variations in immature shark community structure. Generalised linear models were used to identify spatial, seasonal and inter-annual variations in the occurrence or abundance of young sharks, and the ecological drivers of these variations. Potential benefits of MPAs for tropical coastal sharks were explored on the basis of variations in shark abundance, length-frequency distributions and species composition. In addition, tag-recapture data from fishery-dependent and fishery-independent sources were used to investigate the movements of individuals across MPA boundaries. A total of 1987 sharks from six families and 22 species were captured in fishery-independent surveys, with 19 species of Carcharhiniformes dominating (99.2%) the total catch. Australian sharpnose Rhizoprionodon taylori (52%) and blacktip Carcharhinus tilstoni/Carcharhinus limbatus (12%) sharks were numerically dominant. Spot-tail Carcharhinus sorrah (8%), pigeye Carcharhinus amboinensis (6%), scalloped hammerhead Sphyrna lewini (5%), milk Rhizoprionodon acutus (5%) and whitecheek Carcharhinus coatesi (5%) sharks were moderately abundant. In total, 642 sharks were classified as immature, including 383 YOY individuals. Immature sharks from 18 species were present; however, interspecific variation in life-history-stage composition was apparent. Catch data also indicated community-wide spatial structuring of sharks on the basis of body size rather than life-history stage. Multivariate analyses identified significant spatial heterogeneity in immature shark communities among bays. In addition to building on traditional shark nursery paradigms, these results demonstrated that data on nursery function from restricted areas may not accurately portray patterns occurring over broader geographic scales. General and species-specific patterns in shark abundance were characterised by a range of biotic and abiotic variables. Relationships with turbidity and salinity were similar across multiple species, highlighting the importance of these variables in the functioning of communal shark nurseries (i.e. those used by multiple species). In particular, turbid environments were important for all species at typical oceanic salinities. Mangrove proximity, depth and water temperature were also important, however their influence varied between species. These extrinsic factors, along with intrinsic life-history-associated factors, were identified as potential drivers of interspecific variations in the occurrence of young sharks. Seasonal variations characterised the occurrence of YOY pigeye, YOY spot-tail and neonate blacktip sharks, whereby relative occurrences peaked during all or part of the summer wet season. In contrast, spatial variations were more pronounced for YOY blacktip and scalloped hammerhead sharks, with higher respective occurrences in Repulse and Rockingham Bays compared to other locations. Such varied utilisation of coastal ecosystems has important implications for the management of coastal habitats and the conservation of shark populations. Species composition varied significantly between management zones, and overall shark abundance was higher inside MPAs. In addition, length-frequency distributions of blacktip and pigeye sharks inside MPAs comprised a greater proportion of larger-bodied individuals compared to those in open zones. Tag-recapture locations indicated repeated or prolonged occupancy of MPAs by some species. These results suggested that sub-bay-sized coastal MPAs may increase the survival of young sharks to maturity or shelter parts of breeding stocks. Therefore, MPAs do not necessarily need to be large to benefit multiple sympatric species comprising diverse life histories and habitat use patterns. Spatial heterogeneity in shark occurrence and abundance suggested that proximate bays are likely to vary in terms of the services they provide to young sharks, and thus their level of contribution to adult populations. Further, the occurrence of young sharks appeared to be more complex than would be predicted by the timing of parturition alone. The ecological drivers of habitat use identified in this thesis may promote spatial diversity in habitat use along environmentally heterogeneous coastlines, and may therefore have important implications for population resilience. By being among the first studies to investigate the implications of heterogeneous space use by young sharks, this thesis may serve as a model to facilitate future research on portfolio effects and the associated benefits for shark populations.