Three Aanderaa RCM current meters and a S4 current meter were attached to mooring CM1, located north west of John Brewer Reef and in the free stream. The mooring was deployed in 42m of water and the four current meters were attached to the mooring to study changes in current velocity with depth.Deployment Details:Date Deployed: 31/3/1987Date Recovered: 25/8/1987Instruments Deployed:S4 #s620; Depth: 10mRCM #5239; Depth: 18mRCM #4326; Depth: 26mRCM #5278; Depth: 35m The aim of this project was to collect field data to calibrate a numerical model for the combined tidal and wind-forced circulation at John Brewer Reef, and to apply those circulation patterns to calculate the trajectories, residence times and likelihood of outbreaks of crown-of-thorns starfish on areas of the reef. The model boundary was defined by CM1, CM2, CM3, CM4, CM5 and CM13. However, the current meters attached to moorings CM5 (deployed 2/4/87) and CM13 (deployed 1/4/87) were not recovered. Mooring CM4 (deployed 2/4/87)drifted to the Whitsunday Islands. The current meter was badly fouled and the data were unusable.

This research was undertaken to provide quantitative data on the proportions of Acanthaster planci feeding during the day and night. Coral Reef - Condition, Crown of Thorns Starfish - Activity, Crown of Thorns Starfish - Condition, Crown of Thorns Starfish - Diameter, Crown of Thorns Starfish - Outbreak Status, Food - Preference, Lifeform - Benthic, Percentage Cover, Relative Frequency, Substrate Type, Density - Population, Genus, Species These data were used in Chapter 2 of the PHD Thesis, Keesing JK (1990) Feeding biology of the crown-of-thorns starfish, Acanthaster planci (Linnaeus). Ph.D Thesis, James Cook University of North Queensland, Townsville, 197 pp.

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.

In August/September 1993, surveys of coral community composition and structure were carried out at Scott Reefs (North Scott Reef and South Scott Reef) and two reefs in the Rowley Shoals group (Mermaid Reef and Clerke Reef).Coral communities were surveyed at a total of 94 sites, using a semi-quantitative visual survey method and a subset of these sites were surveyed using a video belt transect technique. Sites were areas of around 100-300 m², arranged along cross-reef profiles on the reef flats in a depth range of 0.5-2 m and on the slopes or adjacent reef floor at 4-6 m and 8-12 m. Aerial photography was used to assist in selection of study areas.During each visual survey a detailed list of coral species was made and the relative abundance of each taxa, as a percentage of total macro-benthos, was estimated. The site descriptors recorded were maximum and minimum depth (measured); and subjective estimates of the following: slope; percentage cover of hard substrate; percentage cover of major benthic groups (hard coral, soft coral, macro algae and sponge); percentage cover of substratum categories (platform; large blocks; small blocks; rubble; gravel; sand). An additional 4 sites were surveyed, without recording detailed species lists.A Sony Hi 8 video camera was used to film five replicate 20 m long belt transects about 40 cm wide, within each of the 3 depth ranges, in a sub-set of the sites used for visual surveys. Estimates of percent cover of hard coral, soft coral, algae and bare substratum were made using point sampling of the video tape. At 25 regularly spaced pauses along each video tape, the identity of each item under five points marked on the screen of the TV monitor (one near each corner and one in the centre) was recorded. Percent cover estimates were used to estimate the heterogeneity of the bottom cover as a basis for designing an appropriate sample protocol for a future monitoring program. The visual surveys were carried out to determine whether recognisable, taxonomically consistent assemblages of coral species occurred at the shallow water study sites and to determine the approximate spatial extent of these corals. The surveys were also used to provide detailed taxonomic descriptions of the coral communities at the sites where the video transects were recorded. These surveys were the first quantitative assessments of coral community structure on northwest Australian offshore reefs, previous coral surveys being largely concerned with taxonomic and biogeographic problems.The information collected during this survey formed the basis of of site selection for the subsequent long-term monitoring project.

Comparisons of leaf turnover by crabs (Sesarma messa) and microbes were carried out at Chunda Bay. Yellowing leaves of Rhizophora stylosa, which were about to fall, were collected. Ten leaves were retained, dried, weighed individually, ashed at 500°C for 24 hours and reweighed to calculate a conversion factor from fresh weight to ash-free dry weight (AFDW). Groups of four leaves were weighed and placed in nylon bags with a 2 mm² mesh size. Single leaves were weighed and 1m lengths of nylon twine were attached to the petiole.Bags (restricting access to leaves by crabs) and individual leaves (allowing access by crabs) were tied to the forest floor within the low intertidal region of a Rhizophora forest at two sites, 100m apart. At intervals of 2 and 6 weeks, three replicates of each treatment were removed from each site. Leaves were cleaned of sediment, dried, weighed and ashed.Measurements of removal of leaves by crabs and leaf litter fall were made on five occasions between April 1985 and January 1986 at Coral Creek in Missionary Bay, Hinchinbrook Island. On each occasion, leaf removal experiments were conducted during both day and night low tide periods. Six 25 m² plots were marked out in the low to mid-intertidal zone of the mixed Rhizophora forest. Sixteen litter catchers were deployed randomly around the experimental plots on each sampling occasion. All litter was removed after 7 days, dried at 100°C for 3 days, sorted into components and weighed.Yellowing leaves of Rhizophora spp. were collected and the area of each leaf measured with a Lambda Area Meter. A 1m length of nylon twine was tied to each petiole. At the beginning of each low tide period, all leaves on the surface of each plot were removed and then a number of the measured leaves were tethered within each plot. All tethered leaves were retrieved after 6 hours and a record was made of whether the leaf had been taken down a crab hole. Additional leaves falling into each plot were also collected. The surface area of each tethered leaf was measured and the loss of leaf area converted to dry weight loss using a pre-established relationship between surface area and dry weight. The area of leaf lost to crabs was visually estimated for the additional leaves falling into each plot.In January 1986, modified leaf removal experiments were carried out in other areas of mixed Rhizophora forest at an additional site at Coral Creek as well as Priest Creek and First Creek in Missionary Bay. This research was conducted to collect quantitative measurements of the rates of mangrove leaf burial and consumption by crabs. This is an additional pathway of leaf litter processing that should be included to mangrove food chain models.

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.

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.