The Australian Institute of Marine Science (AIMS) has been running coral reef monitoring programs since the 1980s, including both the Long-Term Monitoring Program (LTMP) and Marine Monitoring Program (MMP). These monitoring programs are designed to detect changes in coral reef communities at a sub-regional scale. Within this context, a subregion consists of inshore, mid-shelf, and outer shelf reefs across the continental shelf within one band of latitude (considered a sector). Data are modelled for presentation on the AIMS Reef Reporting Dashboard https://apps.aims.gov.au/reef-monitoring/reefs. The Reef Monitoring Reporting (MonRep) platform displays modelled data collected by AIMS' Long-Term Monitoring Program and Marine Monitoring Program at reef level, latitudinal Sector or Natural Resource Management (NRM)-region level in the Reef Monitoring Tool. How the data has been modelled for each graph is explained below for each data type. Benthic community cover Reef-level photo transect data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each major benthic group (live hard coral, algae and soft corals) a model containing the population-level effects of year crossed with major taxonomic groups and the varying effects of transects nested within sites were fit to binomial photo point counts. NRM-region/Sector photo transect data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each NRM region/Sector and major benthic group (live hard coral, macroalgae and soft corals) a model containing the population-level effects of year and the varying effects of depth and transects nested within sites nested within reefs were fit to binomial photo point counts. Manta tow surveys Reef-level manta-tow data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each major benthic group (live hard coral and soft corals) a model containing the population-level effects of year and the varying effects of tows were fit against a beta distribution to percentage cover data. For NRM region//Sector level manta-tow data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each NRM region/Sector major benthic group (live hard coral and soft corals) a model containing the population-level effects of year and the varying effects of tows nested within reef were fit against a beta distribution to percentage cover data. Juvenile hard corals Reef-level data Bayesian hierarchical models (INLA) were used to model the juvenile coral abundances (counts) over time. Specifically, a model containing the population-level effects of year and the varying effects of sites were fit against a zero-inflated negative binomial and also included a (log-transformed) offset for available substrate. NRM region/Sector level data Bayesian hierarchical models (INLA) were used to model the juvenile coral abundances (counts) over time. Specifically, for each NRM region/Sector a model containing the population-level effects of year and the varying effects of sites nested within reefs were fit against a zero-inflated negative binomial and also included a (log-transformed) offset for available substrate. Reef fish Reef-level data Bayesian hierarchical models (INLA) to model the fish abundances (counts) over time. Specifically, for each major fish group (Harvested, Herbivores, Coral Trout, Large fishes and Small fishes) a model containing the population-level effects of year and the varying effects of transects nested within sites were fit against zero-inflated negative binomials. NRM region/Sector level data Bayesian hierarchical models (INLA) to model the fish abundances (counts) over time. Specifically, for each NRM region/Sector and for each major fish group (Harvested, Herbivores, Coral Trout, Large fishes and Small fishes) a model containing the population-level effects of year and the varying effects of transects nested within sites nested

70 selected reefs throughout the Great Barrier Reef (GBR) are sampled in the AIMS Long-term Monitoring Project (LTMP). Underwater visual census is used to survey reef fishes on fixed transects (3 sites per reef, 5 x 50 m transects per site). The abundance and length of all diurnally active, non-cryptic fishes are recorded. A full list of species observed each year can be obtained on request. The overarching goal of LTMP fish surveys are to detect changes in reef fish communities over time at a regional scale, but also to examine the effectiveness of Marine Protected Areas. All fish species counted are largely non-cryptic, easily identified underwater and include both commercial and non-commercial taxa. Because surveys span the annual recruitment season, 0+ individuals are excluded from counts: these are distinguished from adults by their small size and often distinctive colouration. Abundance data for each fish species is subsequently summed over the five transects at each site on each reef to provide reasonable sample sizes for analysis and interpretation. Updated results of surveys can be found at: https://apps.aims.gov.au/reef-monitoring/reefs A subset of the data has been provided to the Ocean Biogeographic Information System (OBIS, http://www.iobis.org/explore/#/dataset/3936). Data have been used for the e-Atlas: http://eatlas.org.au/data/uuid/05bde62a-70ec-407b-b999-30cf369498af

Data on the general appearance and condition of coral reefs which have been manta towed in the Long Term Monitoring Project (LTMP). The data from 4 reef zones - front (seaward) and back (leeward), and north and south (flanks 1 and 2) - are used to create a web page on each zone for each reef (http://apps.aims.gov.au/reef-monitoring/). The general condition of the reef is recorded, along with its structural complexity (1 and 2), the percentage of live and bleached coral, the dominant benthic lifeform, and dominant hard coral cover and genus. The general abundance of reef fish and giant clams (Tridacna gigas) is also recorded. To provide a broad overview of the reef environment. Coral Reef - Zone, Lifeform - Benthic, Relative Frequency, Genus. May include some information on coral disease.

Benthic organisms were surveyed annually on fixed sites in one habitat on each of 47 selected core survey reefs from 1993 to 2005 in 6 regions throughout the Great Barrier Reef (GBR). Surveys were undertaken at 3 sites per reef, with 5x50m transects surveyed per site.In 2004 a new zoning plan was implemented in the Great Barrier reef Marine Park and in 2006 the pattern of surveys was changed. The original set of reefs (47) are surveyed in odd years (e.g. 2007) and a different set (56 reefs) are surveyed in even years. The new set consists of paired reefs (one no-take, and one open to fishing) surveyed to assess the effects of rezoning. The paired reefs are near Cairns and Innisfail, Townsville, Mackay, the Swain Reefs and the Capricorn-Brunker group.From 1993 to 2006 video transects were recorded and sub-sampled at 200 points per sample. The program was modified in 2007 to allow collection of data from single frames shot at 1m intervals along each transect using a digital still camera.Benthic groups recorded are: Abiotic; Hard coral; Soft coral; Coralline algae; Macro algae; Turf algae; Sponge; Other; Indeterminate. To annually monitor the cover of benthic organisms, reef fish abundance and crown-of-thorns starfish populations on various reefs of the Great Barrier Reef.The program has been designed to track changes in reef communities over time across sub-regions of the GBR. Parameters: Percentage cover of different substrate types and benthic organisms (particularly corals), identified to benthic group or lifeform level. Data on reef fish abundance and diversity are collected at the same sites and times.

The coral and communities at the AIMS Long Term Monitoring (LTM) sites at Scott Reef, Seringapatam and Rowley Shoals were re-surveyed, following periodic surveys since 1994. In addition to the Proposed Field Program, the following work was completed: Benthic LTM surveys at three additional sites at Scott Reef. Coral species diversity surveys at four additional sites at Scott Reef. Benthic LTM surveys of coral communities at 13 sites in the deep lagoon (20-60m) at South Reef using ROV. Colony size-frequency surveys at six sites at Scott Reef. Genetic samples of surviving Seriatopora hystrix from 7 sites at Scott Reef. Additional temperature loggers and current metres deployed at Rowley Shoals. Video and photographic documentation of the Rowley Shoals, in water and from air using drones This project is a co-investment between Woodside Energy Ltd (WEL) and AIMS, in order to build scientific knowledge at Scott Reef, Seringapatam and Rowley Shoals and was undertaken between 4th – 25th November 2017.

In 6 sectors of the Great Barrier Reef (Cooktown/Lizard island, Cairns, Townsville, Whitsunday, Swain and Capricorn Bunker) 49 of the key manta tow reefs are designated 'core' survey reefs and are also surveyed using the scuba search technique. Where possible, three or more reefs in each sector have been selected in each of three positions across the continental shelf: inshore, mid-shelf and outer shelf. Results of scuba searches for juvenile Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, and the mollusc Drupella. Observations have been obtained since October 1989 and are ongoing. Data includes counts of COTS and Drupella, coral feeding scars caused by COTS and Drupella, and the outbreaking status of COTS and Drupella. Also recorded are the percentage of bleached coral and the number of corals affected by disease. Diseases identified are: white syndrome, black band, skeletal eroding band and brown band. Any scar of unknown origin is also recorded. Information is also recorded about the reef environment of each survey (e.g. reef slope, substratum at reef base) and its benthic community (dominant benthic group, dominant hard coral, dominant coral life form). To facilitate causes of coral mortality including juvenile and adult Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, and the mollusc Drupella. To assess the amount of coral bleaching and disease. Bleaching is recorded as a percentage of the total hard coral cover: 0=absent, 0+ = individual colonies, -1= 1-5%, +1= 6-10%, 2=11-30%, 3=31-50%, 4 =51-75%, 5=76-100%

The purpose of this study is to detect and quantify spatial and temporal changes in reef fish assemblages of the Great Barrier Reef (GBR). Between 1993 and 2005, reef fish assemblages of 46 reefs were monitored annually along permanent transects within a standard habitat using visual census. The selected intensive survey reefs are distributed across three positions of the continental shelf and among six sectors each representing one band of latitude. These reefs continue to be surveyed in odd years as part of the Long Term Monitoring Program (LTMP). The survey pattern changed in 2006 in response to the implementation of a new zoning plan for the GBR Marine Park in 2004. In order to assess the effects of re-zoning on the biodiversity of reefs, a different selection of reefs are surveyed in even years as part of the Representative Areas Program (RAP). Surveys are carried out for 28 pairs of reefs, with each pair comprising one reef which was re-zoned as a no-take area in 2004 and another nearby reef which remained open to fishing. The RAP survey reef pairs are distributed among four of the same sectors in the original LTMP survey design and two different sectors. The cross-shelf distribution of reefs differs, though, as inshore reefs were not included in the RAP sampling design. Fishes of 214 species are counted along the permanently marked transects. Larger mobile fishes (141 spp.) are counted in a 5m wide belt and damselfishes (73 spp.) are counted in a 1m wide belt. Total lengths of any coral trout species (Serranidae, Plectropomus spp.) recorded within transect belts have been estimated from 1996 onwards. Length estimates of other species within the Serranidae, Lethrinidae and Lutjanidae families have been recorded in RAP surveys since 2006. To demonstrate spatial variation in fish community assemblages of the GBR, spatial distributions of a number of relevant variables were mapped in Google Earth using the long term average. Monitoring data collected up until and including the 2008 field season are included. Spatial variation in species richness and in total fish abundance are displayed. Fish species have also been divided into trophic groups and the spatial variation in abundance of each group is mapped accordingly. As part of the Reef Atlas project (now the eAtlas) the fish observations were interpolated over the whole GBR by Glenn De'ath using Generalized Additive Models with a Quasipoisson fit. This produced a gridded version of the dataset and is available as a KML. Data units: Richness: number of species per transect Density: Number of fishes per transect Resource Constraints: Copyright remains with the data owner(s) References: Cheal A, Wilson S, Emslie M, Dolman A, Sweatman H (2008) Responses of reef fish communities to coral declines on the Great Barrier Reef Marine Ecology - Progress Series 372:211-223 Emslie M, Cheal A, Sweatman H, Delean S (2008) Recovery from disturbance of coral and reef fish communities on the Great Barrier Reef, Australia. Marine Ecology - Progress Series 371:177-190 Sweatman H, Cheal A, Coleman N, Emslie M, Johns K, Jonker M, Miller I, Osborne K (2008) Long-term monitoring of the Great Barrier Reef. Australian Institute of Marine Science, Townsville 379

Water Quality Data from the AIMS Long Term Monitoring Program. Water and sediments (another dataset) were sampled at the same sites adjacent to all 52 reefs where fish and benthic transects are conducted. Sampling occurs in open water within 500 metres of the reef, on both sides (north and south flanks) of the reef. Sampled reefs occur throughout the Great Barrier Reef, and the reefs of the North West coast of Australia. To track change. Data recorded includes temperature, salinity, Secchi depth, suspended solids, silicates, ammonium, nitrite, dissolved nitrogen (organic, inorganic and total), dissolved phosphorus (organic, inorganic and total), chlorophyll-a and phaetophytin pigments. Observations commenced in August 1990 and ceased in 1996.

64 'key' reefs in 11 sectors of the Great Barrier Reef (Cape Grenville, Princess Charlotte Bay, Cooktown/Lizard Island, Cairns, Innisfail, Townsville, Cape Upstart, Whitsunday, Pompey Complex, Swain and Capricorn Bunker) are annually surveyed for crown-of-thorns starfish using the manta tow technique. An additional 117 reefs from the sectors (excluding the Whitsunday, Swain and Capricorn-Bunker sectors) are scheduled for survey every third year ('cycle' reefs). The cycle manta tow reefs take second priority if surveys are unable to be completed because of bad weather and limited ship time. Results of manta tow surveys around the perimeter of reefs assessing populations of Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris. Historical data are held from a number of projects - P. Moran's post-doctoral work, CCEP scheme, COTSAC, COTSREC, LTMP. All data are stored in the Oracle database table RM_MANTA, and data from all but the first listed program are generally consistent and systematic. In the latest and ongoing program - the Long Term Monitoring Program (LTMP) - about 50 reefs throughout the Great Barrier Reef and NW Australia have been sampled. Observations started in January 1982 and are ongoing. For each two-minute manta tow the variables recorded are: Number and size of COTS; Percentage cover of live coral, dead coral, and soft coral; Visibility; Any other observations of note. The ambient variables recorded include, information about the survey (reef name, time, date, data collectors), and the weather conditions:(Wind strength; Cloud cover; Sea state; and Tide). Information is also recorded about the reef environment of each survey (e.g. reef slope, substratum at reef base) and its benthic community (dominant benthic group, dominant hard coral, and dominant coral life form). To assess populations of Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, on reefs. Coral Reef - Feeding Scar, Crown of Thorns Starfish - Diameter, Crown of Thorns Starfish - Outbreak Status, Percentage Cover, Count - Individuals, Turbidity Number and size of COTS. Size is recorded as follows: J = less than or equal to 5cm, early juvenile, <1 yr; A = 6-15cm Juvenile, 1-2 yrs; B = 15-25cm Sub-Adult, 2-3 yrs; C = >25cm Adult, >3 yrs). If no COTS are seen, then the column is left blank. When several size categories are seen, the category with the most numerous counts is recorded, and a note is made of the other size categories in the 'other' column. Percentage cover of live coral, dead coral, and soft coral. Categories are: 0 = 0%, 1- = 1-5%, 1+ = 5-10%, 2 = 10-30%, 3 = 30-50%, 4 = 50-75%, 5 = 75-100%. Presence of COTS feeding scars: absent (A: 0), present (P: 1-10) or common (C >10). The ambient variables recorded include, information about the survey (reef name, time, date, data collectors), and the weather conditions: Wind strength categories: 1 = 0-5 knots; 2 = 6-10 knots; 3 = 11-15 knots; 4 = 16-20 knots; 5 = 21-25 knots Cloud cover unit of measure is the okta. One okta = one eigth of the sky. Sea State. A modified Beaufort scale describes sea state: Calm = Mirror-like to small ripples; Slight = Small waves, some whitecaps; Moderate = Moderate waves, many whitecaps; Rough = Large waves 2-3 m, whitecaps everywhere, some spray Tide is recorded as low (1.5 hrs either side of Low water), high (1.5 hrs either side of High water), falling (between High and Low water) or rising (between Low and High water), determined from a Tide Table. Data have been used for the e-Atlas: http://e-atlas.org.au/content/large-scale-manta-tow-surveys-densities-crown-thorns-starfish-and-benthic-cover-aims-ltmp