This dataset contains the catch data from seasonal gillnet and longline surveys of shark nursery areas in the Central Section of the Great Barrier Reef Marine Park (2011-2014). Methods: Sampling occurred seasonally in nine bays along ~ 400 km of the tropical north Queensland coastline: Rockingham, Halifax, Cleveland, Bowling Green, Upstart, Abbott, Edgecumbe, Woodwark/Double and Repulse Bays. Of these nine bays, five were sampled regularly, the others (in italics) were sampled only once as part of a broader survey. Sampling sites were dominated by silty substrates, and mudflat and/or mangrove-lined foreshores. Between October 2011 and November 2013 eight rounds of fisheries-independent surveys were undertaken to collect data on the shark community across the study region. Within each bay sampling occurred randomly within sixteen 0.9 km wide strips running perpendicular to the shore. Two groups of eight strips were placed within each bay to spread the sampling across different habitat types and management zones (i.e. gill-net fishing allowed and gill-net fishing prohibited) where possible. During each round, each bay was sampled over four days allowing for two days of sampling in each group of strips. The bays vary in size and so the relative proportion of area sampled varied between bays. Two methods were used to sample across a broad range of shark sizes. During a total of 183 days of sampling, 453 longline shots and 343 gill-net shots were deployed totaling 370 and 310 h, respectively. Bottom-set gill-nets, comprised of 11-cm-stretched mesh, were deployed for ~ 1 h and checked every 15 min to facilitate tagging and release. In accordance with the Great Barrier Reef Marine Park Authority’s Dugong Protection Areas, multiple panels of net were joined to create a total net length of either 200 m or 400 m. In addition, some 100-m gill-nets were used during the Jan/Feb round in 2012. Bottom-set longlines were comprised of 800 m of 6-mm nylon mainline with an anchor and float at both ends. Gangions were attached to the mainline ~ 8–10 m apart; and were comprised of 1 m of 4-mm nylon cord, 1 m of 1.5-mm wire leader, and a baited 14/0 Mustad tuna circle hook. A variety of fresh and frozen baits were used including butterfly bream (Nemipterus sp.), squid (Loligo sp.), blue threadfin (Eleutheronema tetradactylum) and mullet (Mugil cephalus). Up to two longlines were deployed simultaneously for 40–90 min sets. Environmental data (water temperature, salinity, depth, turbidity and oxygen saturation) were recorded for all sets. Captured sharks were identified to species level, tagged on the first dorsal fin (Rototag or Superflex tag; Dalton, Oxfordshire, UK), measured, sexed, assessed for clasper calcification, examined for umbilical scar condition, and released at their capture site. Stretch total length was determined according to Compagno (1984). Small sharks (? 1 m) were placed ventral side down on a measuring board and measured to the nearest mm with the upper lobe of the caudal fin depressed in line with the body axis. Larger sharks were secured beside the boat and measured to the nearest cm using a measuring tape. Additional measurements of fork length and pre-caudal length were recorded. Format: CSV File, 4432 rows (~1MB), Shapefiles (4409 Points) Each line of data represents the catch of an individual shark, ray, fish, etc. Multiple lines exist per shot if more than one animal was caught. The shapefile was created by the eAtlas for visualisation purposes. It retains most of the information in the CSV as a point shapefile. The point shapefile was created from the CSV using the Start_Lat and Start_Long as the coordinate for points. If rows which did not have a valid Start_Lat or Start_Long (29 rows) then the End_Lat and End_Long were used instead (6 rows). If neither of these were available then the row was ignored. This removed 23 rows. Attributes Lat and Long were added to contain the coordinates used in the shapefile, leaving the

Ningaloo Marine Park extends southward from North West Cape along 230 km of coastline. In most places, the seaward margin of the reef is generally less than 3 km from the shoreline, with a sandy lagoon between the reef edge and the shoreline.During this first AIMS survey of fish and coral communities within the Ningaloo Reef system, 26 sites were visited. Systematic surveys of coral and fish community structure were carried out at five locations along the length of the Ningaloo Reef (separated by 10s of km). Within each region, surveys were made at two sites on both the outer reef slope and within the shallow lagoon. In response to a request from the Western Australian Department of Conservation and Land Management (CALM), surveys were also carried out at six sites within the Ningaloo Dugong Sanctuary. There was scant biological information available regarding coral and fish populations within the Ningaloo Marine Park. Veron (1993) recorded 214 species of corals in Ningaloo Reef. Hutchins (1994) recorded 482 fish species, making it the most diverse mainland reef habitat along the Australian coast. The first quantitative assessments of coral and fish populations were carried out in the late 1980s (Ayling and Ayling, 1987).Prior to the AIMS surveys, no baseline ecological data had been collected on benthic and fish communities within the Ningaloo Dugong sanctuary zone. Fish were surveyed using actual counts on 20 minute timed transects (three transects per site). Video surveys were carried out on 20 metre transects (5 transects per site). The starting point for fish and video transects were the same, but observers moved in different directions from that point.Lists were made of fish and coral species observed at each site and specimens of coral and algae were taken for taxonomic reference collections.

Two field surveys were undertaken for this study. In June 2003, Mermaid Reef (Rowley Shoals, unfished MPA) and Scott Reef (MOU74 Box, currently fished) were surveyed. In October 2004, Ashmore and Cartier Reefs (MOU74 Box, historically fished) and Clerke and Imperieuse Reefs (Rowley Shoals, unfished MPAs) were surveyed.In both field surveys, BRUVS (TM) were deployed in 2 modes. Firstly, at all reefs they were deployed along depth contour lines with each unit separated by approximately 400m in the shallow (5-30m) reef crest and deeper reef slope (40-70m) on the outside of reefs, and on the lagoon floor (20-30m) where these could be accessed by surface vessels. Secondly, at Scott, Ashmore and Mermaid Reefs a zodiac was allowed to drift in deep (50-300m+) water 500 m off the edge of drop offs and BRUVS (TM) hung from the side at 15 m depth.The total numbers of benthic BRUVS (TM) deployments at each locality were: Ashmore Reef, 58; Cartier Reef, 6; Scott Reef, 24; Mermaid Reef, 30; Clerke Reef, 24; and Imperieuse Reef, 41. The majority of reef deployments occurred in deep (40-70m) water and all deployments (including zodiac deployments) were spread throughout daylight hours from 07.00 - 16.00 hrs.In the 2003 pilot surveys, at Mermaid and Scott Reefs, interrogation of each tape provided the time the BRUVS (TM) settled on the seabed and for each shark: its species; the time of first sighting; time of first feeding at the bait; a coarse initial estimate of length; and a list of fish species. This enabled the identification of different sharks on each tape for cumulative summaries of shark visits to be developed for each BRUVS (TM) set. In the 2004 surveys at Ashmore, Cartier, Clerke and Imperieuse Reefs, interrogation of each tape provided the time the BRUVS (TM) settled on the seabed and, for each species of shark and fish, the time of first sighting, time of first feeding at the bait, the maximum number seen together in any one time on the whole tape (MaxN), the time at which MaxN occurred, and the intraspecific and interspecific behaviour. No attempts at measurement were made in these 2004 surveys, but fish and sharks were classified as 'adult' or 'juvenile', based on their size. A 'reference collection' of images of each species was made from the BRUVS (TM) tapes, and identifications based on these images were verified by taxonomists and other fish biologists. The benthos visible in each BRUVS (TM) set was classified and an image was stored for later reference. In 2003, the deployment of BRUVS (TM) was investigated as part of a pilot study to develop non-destructive techniques for rapid assessment of shark abundance in northern Australia.These data were later included in a larger study of reefs within the MOU74 Box and the Rowley Shoals, with the following aims:1) to sample fish and shark assemblages at Ashmore and Cartier Reefs within the MOU74 Box (historically fished reefs, now Marine Protected Areas - MPAs) and Clerke and Imperieuse Reefs (unfished reefs) in the Rowley Shoals.2) to integrate data from the 2003 BRUVS (TM) surveys (Scott Reef- presently fished, MOU74 Box, and Mermaid Reef, MPA, Rowley Shoals) into results to provide a comprehensive picture of the status of shark stocks within the MOU74 Box in comparison to unfished reefs (Rowley Shoals) nearby.3) to provide a preliminary assessment of the status of reef fishes on Ashmore and Cartier Reefs within the MOU74 Box (historically fished reefs, now MPAs) in comparison to Clerke and Imperieuse Reefs (unfished reefs) in the Rowley Shoals. In recognition of the long standing use of marine resources of northern reefs as a small scale, traditional fishery, the Australian and Indonesian governments negotiated a memorandum of understanding (MOU74) that allows access by Indonesian fishermen to an area of 50,000 km² within the Australian Exclusive Economic Zone (AEEZ). Within this area lie 6 coral reef systems, the northern most of which are Ashmore and Cartier Reefs. Concern

Coral reef underwater visual census (UVC) survey of reef fish species between northern Ningaloo and the Dampier Archipelago. The data include: * Fish UVC database - short transects 25x5m: Fish Counts * Fish families excluding cryptic benthic groups eg gobies. Sharks and rays are included.

Coral reef survey of target fish species and large grazing fish between northern Ningaloo and the Dampier Archipelago. The data include: * Fish UVC database - long transects 100x10m - Fish Count Numbers

Coral reef survey of target fish species and large grazing fish between northern Ningaloo and the Dampier Archipelago. The data include: * Fish UVC database - long transects 100x10m

Coral reef underwater visual census (UVC) survey of reef fish species between northern Ningaloo and the Dampier Archipelago. The data include: * Fish UVC database - short transects 25x5m: Biomass Estimate * Abundance and size of fish. * Fish families excluding cryptic benthic groups eg gobies. Sharks and rays are included.

The abundance of newly settled corals following the 2009 and 2010 annual coral spawning peaks was measured in the northern half of Ningaloo Reef at eleven locations between Coral Bay, Tantabiddi and Bundegi. An annual influx of coral recruits were detected at all locations, using terracotta tiles deployed by divers on the reef using permanent tile mounting fixtures, then subsequently retrieved and counted under a dissecting microscope. This study has measured annual coral recruitment rates at Ningaloo Reef using deployed tiles, but has also had a particular focus on evaluating some alternative methods for coral juvenile census. Deploying, recovering and assessing tiles is labor intensive, requires use of SCUBA and a specialist using a microscope in the laboratory for census of the tiles. A key aim of this project has been to understand the tradeoffs associated with simplified and more cost-effective approaches. The objective was to assess methods that could still yield robust research data, yet utilize non-specialist regional DEC staff for routine field surveys, maximizing the effectiveness of Perth-based specialist research staff for more complex analytical tasks.

This dataset describes the predicted occurrence of juvenile sharks around Northwest Australia, mapped over a 0.01 degree spatial grid. Juvenile sharks were mapped at two taxonomic levels: order by including all juvenile sharks sampled (all juveniles) and species by considering the three most abundant species sampled separately (grey reef (Carcharhinus amblyrhynchos), sandbar (Carcharhinus plumbeus), and whitetip reef (Triaenodon obesus) sharks). The data cover the period 2003-2013 and are derived from an analysis of count data derived from baited remote underwater videos deployed through various sampling programs. Further detail can be found in the following peer-reviewed publication: Oh, BZL, Sequeira, AMM, Meekan, MG, Ruppert, JLW and Meeuwig, JJ (2017), Predicting occurrence of juvenile shark habitat to improve conservation planning. Conservation Biology, 31: 635–645. doi:10.1111/cobi.12868 Below is a full list of species, with contributions to the total counted (%): Silvertip shark / Carcharhinus albimarginatus – 4.14% Grey reef shark / Carcharhinus amblyrhynchos – 28.06% Bronze whaler / Carcharhinus brachyurus – 0.18% Galapagos shark / Carcharhinus galapagensis – 0.09% Bull shark / Carcharhinus leucas – 0.18% Common-Australian blacktip shark / Carcharhinus limbatus-C.tilstoni – 1.38% Blacktip reef shark / Carcharhinus melanopterus – 1.56% Sandbar shark / Carcharhinus plumbeus – 4.78% Spot-tail shark / Carcharhinus sorrah – 0.18% Tiger shark / Galeocerdo cuvier – 2.39% Sliteye-Sharpnose shark / Loxodon macrorhinus-Rhizoprionodon spp. – 6.35% Lemon shark / Negaprion acutidens – 1.01% Whitetip reef shark / Triaenodon obesus – 18.95% Tawny shark / Nebrius ferrugineus – 0.83% Grey carpetshark / Chiloscyllium punctatum – 1.38% Taselled wobbegong / Eucrossorhinus dasypogon – 0.09% Scalloped hammerhead / Sphyrna lewini – 0.46% Great hammerhead / Sphyrna mokarran – 3.86% Zebra shark / Stegostoma fasciatum – 0.83% Sicklefin houndshark / Hemitriakis falcata – 1.01% Grey gummy shark / Mustelus ravidus – 0.28% Archived BRUVS video files used in this study are the intellectual property of multiple institutions and industry partners and are not published in this record. See credits for further information.

Snorkel and SCUBA underwater visual surveys were conducted as part of four field trips to Ningaloo in April and June 2007 and August and December 2008. The June and August surveys were restricted to the reef edge on SCUBA, while the April and December surveys were mainly on snorkel and in the lagoon. While the original intention was to provide coverage through the different seasons, poor weather conditions coincided with most of the planned fieldwork (including cyclone ‘Nicholas’) resulting in re-scheduling of some trips. A total of 137 sites were surveyed between Vlaming Head on the northeast of the Cape to Gnaraloo in the southern part of the Marine Park (see thumbnail picture). Of these surveys, 89 were in sanctuary zones and 48 in non-sanctuary zones (sanctuary zones are shown as hatched in the picture).