17 to 141 individuals were collected from 8 populations of the fished holothurian species Holothuria scabra (Echinodermata: Holothuroidea), from north-east Australia, the Torres Strait, and the Solomon Islands and investigated by allozyme electrophoresis of 7 polymorphic loci.Two shallow populations of Holothuria scabra were sampled in the area of Hervey Bay (Urangan, Tin Can Bay) in south Queensland during June 1998. Individuals from a deeper population in Hervey Bay (18-20 m) were obtained during 3 trawl shots using commercial prawn-trawling equipment.One intertidal population was sampled ca. 800 km north Upstart Bay in 1998. Data from these samples were used in a previous study investigating the relationship between 2 colour morphs and the gene flow between deep and shallow populations. This population was re-sampled in May 2000 to investigate whether gene frequencies and the small size of individuals (as found in 1998) were stable over time.During August 1999, samples were obtained from 2 reefs in the Torres Strait at the northern end of the GBR (Warrior Reef, Dungeness Reef). Two locations in the Solomon Islands, Kohinggo Island (Solomon Island A) and Kolombangarra Island (Solomon Island B), were sampled in December 1999.Samples from intertidal populations were taken during low tides by walking on the mud flats. During these periods, holothurians in shallow tide pools, usually with at least a sparse seagrass cover, migrate to the surface of the sediment. Since large areas had to be covered to obtain sufficient individuals, no effort was made to obtain subsamples within each of the populations. The length of all individuals was recorded to the nearest centimetre. A subsample of the gut lining (cleaned from sediments) was snap frozen in liquid nitrogen for later analyses.Seven polymorphic enzyme loci were surveyed using allozyme electrophoresis: PGM, HK, GPI, MDH, PEP-1, PEP-2 and PEP-3. Full details of staining and electrophoresis methods are given in:Ballment E, Uthicke S, Peplow L, Benzie JAH (1997) Techniques for enzyme electrophoretic analysis of the holothurians Holothuria atra and Stichopus chloronotus (Holothuroidea: Aspidochirotida). Aust Inst Mar Sci (AIMS) Tech Rep Ser 27:1-47Basic analyses of genetic variability were carried out using programs in the BIOSYS-1. F-statistics, cluster analyses and tests of conformation to Hardy-Weinberg expectations were performed using the TFPGA package. The contribution of asexual reproduction to each population was calculated as described in detail in:Uthicke S, Benzie JAH, Ballment E (1998) Genetic structure of fissiparous populations of Holothuria (Halodeima) atra on the Great Barrier Reef. Mar Biol 132:141-151. Deviations from Hardy-Weinberg equilibrium for each locus at each reef were tested by an exact-test, using the conventional Monte Carlo method with the default settings in TFPGA. To test for evidence of isolation by distance, Mantel¿s tests were performed on transformed (log + 1) geographic distance (km) and Rogers' genetic distances. The significance of Mantel's normalised Z was tested by 10000 random permutations using NTSYS-PC software. The aim of the study was to investigate gene flow between populations separated by different geographic scales (~20-2000 km), along the north-east coast of Australia, Torres Strait and the Solomon Islands, to provide information on connectivity to assist management and add to fundamental knowledge on the biology of this ecologically and economically important species.

The coral, Acropora millepora and the crustose coralline algae, Neogoniolithon fosliei were exposed to 3 photosystem II (PSII) herbicides (diuron, hexazinone and atrazine). Corals were collected at depths between 1 and 3m from Double Cone Island and Hayman Island in the Whitsunday group. The crustose coralline algae was collected from Davies Reef at depths between 5 and 7m.Experiments assessed the effects of the variables temperature (26, 30, 31, 32 °C) in combination with 3 herbicide concentrations, and exposure duration (up to 7 days) on photosynthetic efficiency and bleaching. To examine the effects of the herbicides diuron, atrazine and hexazinone in conjunction with increasing temperatures on coral and crustose coralline algae.

Scleractinian corals were recorded from the fringing reefs offshore from the Daintree National Park during a three day study in November 1985. The field study was supplemented by examination of coral specimens collected by other researchers from these reefs. The checklist produced also includes an assessment of the abundance of each coral species. The aim of this study was to produce an inventory of the scleractinian corals on reefs in the Daintree region of north Queensland.

Stratification and flushing of a small lagoon in the windward reef flat of Davies Reef in the central Great Barrier Reef was examined in 1980/1981 using three complementary experiments.In the first experiment, salinity-temperature-depth (STD) profiles were taken each 0.5 hr for 2 days (25-27th April, 1980). On the 27th April at low tide (1400hrs), the resident bottom water of the lagoon was marked with fluorescein dye. The dye was sampled with Niskin bottles, at 2m intervals from and including the bottom every 4 hours until the dye could not be detected. STD profiles were taken concurrently. Dye sampling commenced at 1630hrs, to avoid photodegradation, and fluorescence was measured on an Amico-Bowman spectrophotofluorometer. STD and dye experiments were repeated from the 2-5th November, 1980. Rhodomine dye was used on this occasion to allow daylight sampling and dye profiles were taken at 30 minute intervals. In the second experiment, 7 Aanderaa RCM4 current meters were deployed from the 15th June to 15th July 1980, in a vertical string, with a spacing of 2.7m in a position where the water depth was 20m below the reef flat. Temperature, pressure and vector-current profiles were recorded every 10 minutes. This array functioned as a thermistor string, as currents in the lagoon were near the determination limit of the current meters. An additional Aanderaa RCM4 current meter, measuring currents and water temperature was deployed midway between two lagoons, south west of the study site. Wind vectors were accessed from twice daily recordings at the weather station at the Cape Cleveland lighthouse. In the third experiment temperatures at the top and bottom waters of the lagoon were recorded every 10 minutes between the 24th April 1980 and 21st March 1981. Wind measurements were taken from the weather station at the Cape Cleveland lighthouse. Experiments were undertaken to gain an understanding of thermal stratification and the trapping of bottom water in reef lagoons on three time scales by: 1. using temperature and dyes to mark diurnal events2. studying currents on the reef flat and stratification in the lagoon for 1 month3. using temperature to infer events from a time series of approximately 1 year

A round 1.4m yellow buoy has been deployed in the Davies Reef lagoon as part of the sensor network infrastructure at Davies Reef in the central Great Barrier Reef off Townsville, Australia. The buoy is configured as a sensor-float with a Campbell Scientific logger, a spread-spectrum radio for communicating with the on-reef wireless network, a SeaBird Inductive modem and initially a surface mounted (30cm under the water surface) thermistor and bottom mounted SeaBird SBE39 (temperature and pressure). The project looks to deploy sensor networks at seven sites along the Great Barrier Reef to measure a range of physical parameters at a range of scales. The project will install communications, data and platform infrastructure that will support future sensor work looking at biological and chemical parameters. Wireless Sensor Networks Facility (formerly known as Facility for The Automated Intelligent Monitoring of Marine Systems (FAIMMS)), part of the Great Barrier Reef Ocean Observing System project (GBROOS) (IMOS)

Six instruments were deployed on the Scott Cay West Transect (J). Instruments were deployed along a transect down the reef slope.Code: SCW5; Depth: -2.0m; Instrument: Odyssey; Serial #: 6568; Code: SCW4; Depth: -1.0m; Instrument: Odyssey; Serial #: 6538;Code: SCW3; Depth: 1.8m; Instrument: Odyssey; Serial #: 6332;Code: SCW2; Depth: 4.8m; Instrument: Tidbit; Serial #: SL3-31060;Code: SCW1; Depth: 19.8m; Instrument: S4; Serial #: 615; File Name: SCWuvCode: SCW1; Depth: 19.8m; Instrument: SBE16; Serial #: 2123; File Name: SCWct This deployment was a component of the "Physical Environment" sub-project of the project "Biological and Physical Environment at Scott Reef 2003" Two of the temperature loggers were exposed at low tide.

Time series data are often observed in ecological monitoring. Frequently such data exhibit nonlinear trends over time potentially due to complex relationships between observed and auxiliary variables, and there may also be sudden declines over time due to major disturbances. This poses substantial challenges for modelling such data and also for model-based adaptive monitoring. We propose novel methods for finding adaptive designs for monitoring when historical data show such nonlinear patterns and sudden declines over time. This work is motivated by a coral reef monitoring program that has been established at Scott Reef; a coral reef off the Western coast of Australia. Data collected for monitoring the health of Scott Reef are considered, and semiparametric and interrupted time series modelling approaches are adopted to describe how these data vary over time. New methods are then proposed that enable adaptive monitoring designs to be found based on such modelling approaches. These methods are then applied to find future monitoring designs at Scott Reef and form a set of recommendations for future monitoring. Through applying the proposed methods, it was found that future in formation gain is expected to be similar across a variety of different sites, suggesting that no particular location needed to be prioritised at Scott Reef for the next monitoring phase. In addition, it was found that omitting some sampling sites/reef locations was possible without substantial loss in expected information gain, depending upon the disturbances that were observed. The resulting adaptive designs are used to provide recommendations for future monitoring in this region, and for reefs where changes to the current monitoring practices are being sought. Furthermore, as the methods used and developed throughout this study are generic in nature, this research has the potential to improve ecological monitoring more broadly where complex 28 data are being collected over time.

The study consisted of laboratory and field components. Under laboratory conditions, the temperature of standardized individual color chart fields submerged in seawater was determined at contrasting levels of flow and irradiance using a calibrated micro-thermistor with a 1 mm measurement tip. The same method was then used to measure the microtemperature environment around 3 corals (2 massive and 1 branching species) that varied in colony pigmentation from light to dark brown. Coral surface warming at high irradiance (noon) and low irradiance (early morning or late afternoon) in outdoor flow chambers: colonies of the hemispherical species Favia matthai at flow speeds of 1, 2, and 5 cm s-1, and colonies of the digitate species Acropora millepora at flow speeds of 2 and 5 cm s-1. Pigmentation was measured as background fluorescence (F0), determined with pulse-amplitude-modulated fluorometry. The ambient water temperature was 29.38C. In the field, the natural distributions of coral darkness were quantified on 4 reefs across the continental shelf of the Great Barrier Reef, spanning from turbid coastal conditions to clear-water offshore. Reefs were: High Island (a turbid inshore reef with high water nutrient concentrations); Fitzroy Island (an inshore reef with greater water clarity and less exposure to terrestrial runoff from river flood plumes than High Island); Hastings Reef (a mid-to outer-shelf reef, 71% relative distance across the continental shelf); Flynn Reef (on the outermost edge of the continental shelf). Tissue darkness was measured in the first 40 scleractinian coral colonies that were encountered along 6 line intercept transects that ran slope parallel at the windward and leeward side at 4, 8, and 12 m depths (a total of 240 colonies on each reef), including all hard coral species. Measurements of the temperature microenvironment around cnidarians with contrasting darkness on inshore reefs were conducted for 4 consecutive days in January 2005, when sea surface temperatures were 28-29°C, and no signs of coral blanching or bleaching were observed. To assess the effects and interactions of 3 of the factors involved in controlling the temperature microenvironment of coral colony surfaces, namely irradiance, flow, and colony darkness. True measures of short-wave radiation, absorptivity, and convection were not attempted: photosynthetically active irradiance was measured as a proxy for short-wave radiation; colony darkness (pigmentation) was used as a proxy for absorptivity; and water flow was manipulated to vary heat convection from the colony surfaces. The use of these variables helped relate the experimental results to underwater measurements that are readily available in the field.Mean visibility across the continental shelf was estimated by spatial models as 5 m at High Island, 8 m at Fitzroy Island, 18 m at Hastings Reef, and 25 m at Flynn Reef. Concentrations of suspended solids and chlorophyll decreased across these reefs.Cnidarians measured on the reef: the flat-encrusting stony coral Montipora tuberculosa, 4 other species of stony corals (including hemispherical, foliose and branching growth forms), two species of octocorals, and the zoanthid Palythoa. Additionally, surface warming was determined in the dark, thick, sediment trapping turf algal mats on these reefs. The experimental tanks measured Favia matthai, Acropora millepora ,and Porites.A standardized coral color chart printed on a thin, lightly textured plastic sheet was used - 'Coral Health Chart', University of Queensland, Australia: www.CoralWatch.org - the 6 color fields on the chart increase on a log scale from score 1=near-white, to score 6=dark brown.

Fresh leaves of seven species of tropical seagrasses, collected from Magnetic Island, north Queensland, were analysed for sterol and fatty acid composition. The species examined were Cymodocea serrulata, Enhalus acoroides, Halodule uninervis, Halophila ovalis, Halophila ovata, Halophila spinulosa and Thalassia hemprichii.Samples were extracted with CHC13-MeOH (1:1). Sterols and fatty acid methyl esters were prepared from the extracts. Sterols (as the methyl ethers) and fatty acid methyl esters were analysed by GLC.Fatty acids and sterols were identified by their mass spectra and by co-chromatography with standards where available. This research was undertaken to determine if chemical markers were present in seagrass leaves, which would allow seagrass derived material to be traced through coastal ecosystems. Variations in sterol and fatty acid composition were examined for potential chemotaxonomic significance.

Specimens of the decapod shrimp, Acetes sibogae australis, were collected along the jetty of the Australian Institute of Marine Science (AIMS) and specimens of the copepod, Acartia australis, were collected from Davies Reef lagoon. The copepods were transported in a 20 litre bucket to the AIMS laboratory within six hours. In the laboratory each species was transferred to gently aerated aquaria containing unfiltered sea water collected from the same site as the animals and placed in a constant temperature room (24-25°C).Physiological activities and biochemical components were measured for subsamples of Acetes sibogae australis at 2, 14, 26 and 50 hours after capture. Measurements for subsamples of Acartia australis were made at 6, 14, 26 and 49 hours after capture. Respiration and excretion of ammonia and phosphate were measured using a water bottle method. Twelve replicate bottles containing Acetes sibogae australis were incubated for 2.5-3.5 hours, while 8 replicates bottles containing Acartia australis were incubated for 3.5-4.5 hours. At the end of incubation, separate water samples were siphoned off dissolved oxygen analysis and for ammonia and phosphate analyses.Animals from the incubation bottles were filtered onto GF/C filters and frozen in liquid nitrogen and stored in a freezer until analysed within 24 hours. Half of the filters from each experiment were homogenized in trichloroacetic acid for extraction of adenine nucleotides. ATP was determined by the luciferase-luminescence method, and ADP and AMP by the same method after enzymatic conversion to ATP. The remaining GF/C filters were homogenized in ETS-B solution, and these extracts were used to determine electron transport system (ETS) activity and the concentrations of protein and RNA. Laboratory studies were undertaken to investigate the decline in physiological activities, including respiration and excretion rates, of two species of marine zooplankton after capture. The results were used to assess whether capture stress or shortage of food contributed to declines. These experiments were a component of the project "The effect of laboratory conditions on the extrapolation of experimental measurements to the ecology of marine zooplankton".