Benthic and substrate cover data derived from photo-transect surveys in Lizard Island, Great Barrier Reef conducted on October 3-7, 2012

Underwater georeferenced photo-transect surveys were conducted on October 3-7, 2012 at various sections of the reef and lagoon at Lizard Island, Great Barrier Reef. For this survey a snorkeler swam while taking photos of the benthos at a set distance from the benthos using a standard digital camera and towing a GPS in a surface float which logged the track every five seconds. A Canon G12 digital camera was placed in a Canon underwater housing and photos were taken at 1 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry bag and logged the position at the surface while being towed by the photographer (Roelfsema, 2009). A total of 1,265 benthic photos were taken. Approximation of coordinates of each benthic photo was conducted based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the GPS coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count for Microsoft Excel program (Kohler and Gill, 2006). Each point was then assigned to 1 of 79 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 55 South.

Stock structure of exploited shark species in north-eastern Australia

The project has provided management and other stakeholders with information necessary to make informed decisions about the management of four of the key exploited shark species caught in the Queensland inshore net fishery and northern New South Wales line fishery. The project has determined that spatial management of milk sharks within Queensland, and scalloped hammerhead, common black tip and Australian black tip sharks within Queensland and New South Wales is appropriate. The project has determined that both black tip shark species are likely to require co-operative management arrangements between Queensland and New South Wales. For scalloped hammerheads separate stocks between the two jurisdictions were identified from the fisheriesdependent samples, however genetic exchange across borders is likely to be facilitated by movement of adult females and perhaps larger males to a lesser extent. This information will greatly assist compliance with the Commonwealth Environment Protection and Biodiversity Conservation Act (1999) for shark fisheries in north-eastern Australia by providing the necessary basis for robust assessment of the status of stocks of the study species, thereby helping to deliver their sustainable harvest. It also helps to achieve objectives of the Australian National Shark Plan. The project provides the appropriate spatial framework for future monitoring and assessment of the study species. This is at a time when shark fisheries are receiving close attention from all sectors and when monitoring programs are being implemented, aimed at better assessment of stock status. This project has provided the crucial information for developing an appropriate monitoring design as well as the necessary basis for making statements about stock status. The project has addressed research priorities identified by the Queensland Fisheries Research Advisory Board, Great Barrier Reef Marine Park Authority and Queensland Fisheries. Previously management has assumed a single stock for each species on the east coast of Queensland, and management of shark fisheries in New South Wales (NSW) and Queensland has been independent of one another. The project has been able to enhance and develop links between research, management and industry. Strong positive relationships with commercial fishers were crucial in the collection of samples throughout the study area and fisheries managers were part of the project team throughout the study period. During the project the study area was extended to include both Queensland and NSW waters, creating mutualistic and positive links between the States’ research and management agencies. Extension of project results included management representatives from NSW and Queensland, as well as the Northern Territory where similar shark fisheries operate and similar species are targeted. The project was able to provide significant human capital development opportunities providing considerable value to the project outcomes. Use of vertebral microchemistry and life history characteristics as stock determination methods provided material for two PhD students based at James Cook University: Ron Schroeder, vertebral chemistry; and Alastair Harry, life history characteristic. The project has developed novel research methods that have great capacity for future application, including: • Development of a simple and rapid genetic diagnostic tool (RT-HRM-PCR assay) for differentiating among the black tip shark species, for which no simple morphological identifier exists; and • Development of laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) methods for analysing and interpreting microchemical composition of shark vertebrae. The study has provided further confirmation of the effectiveness of using a holistic approach in stock structure studies and justifies investment into such studies.

Choosing a fishery's governance structure using data poor methods

Multi-species fisheries are complex to manage and the ability to develop an appropriate governance structure is often seriously impeded because trading between sustainability objectives at the species level, economic objectives at the fleet level, and social objectives at the community scale, is complex. Many of these fisheries also tend to have a mix of information, with stock assessments available for some species and almost no information on other species. The fleets themselves comprise fishers from small family enterprises to large vertically integrated businesses. The Queensland trawl fishery in Australia is used as a case study for this kind of fishery. It has the added complexity that a large part of the fishery is within a World Heritage Area, the Great Barrier Reef Marine Park, which is managed by an agency of the Australian Commonwealth Government whereas the fishery itself is managed by the Queensland State Government. A stakeholder elicitation process was used to develop social, governance, economic and ecological objectives, and then weight the relative importance of these. An expert group was used to develop different governance strawmen (or management strategies) and these were assessed by a group of industry stakeholders and experts using multi-criteria decision analysis techniques against the different objectives. One strawman clearly provided the best overall set of outcomes given the multiple objectives, but was not optimal in terms of every objective, demonstrating that even the "best" strawman may be less than perfect. © 2012.

Stock assessment of the Queensland east coast common coral trout (Plectropomus leopardus) fishery

Common coral trout Plectropomus leopardus is an iconic fish of the Great Barrier Reef (GBR) and is the most important fish for the commercial fishery there. Most of the catch is exported live to Asia. This stock assessment was undertaken in response to falls in catch sizes and catch rates in recent years, in order to gauge the status of the stock. It is the first stock assessment ever conducted of coral trout on the GBR, and brings together a multitude of different data sources for the first time. The GBR is very large and was divided into a regional structure based on the Bioregions defined by expert committees appointed by the Great Barrier Reef Marine Park Authority (GBRMPA) as part of the 2004 rezoning of the GBR. The regional structure consists of six Regions, from the Far Northern Region in the north to the Swains and Capricorn–Bunker Regions in the south. Regions also closely follow the boundaries between Bioregions. Two of the northern Regions are split into Subregions on the basis of potential changes in fishing intensity between the Subregions; there are nine Subregions altogether, which include four Regions that are not split. Bioregions are split into Subbioregions along the Subregion boundaries. Finally, each Subbioregion is split into a “blue” population which is open to fishing and a “green” population which is closed to fishing. The fishery is unusual in that catch rates as an indicator of abundance of coral trout are heavily influenced by tropical cyclones. After a major cyclone, catch rates fall for two to three years, and rebound after that. This effect is well correlated with the times of occurrence of cyclones, and usually occurs in the same month that the cyclone strikes. However, statistical analyses correlating catch rates with cyclone wind energy did not provide significantly different catch rate trends. Alternative indicators of cyclone strength may explain more of the catch rate decline, and future work should investigate this. Another feature of catch rates is the phenomenon of social learning in coral trout populations, whereby when a population of coral trout is fished, individuals quickly learn not to take bait. Then the catch rate falls sharply even when the population size is still high. The social learning may take place by fish directly observing their fellows being hooked, or perhaps heeding a chemo-sensory cue emitted by fish that are hooked. As part of the assessment, analysis of data from replenishment closures of Boult Reef in the Capricorn–Bunker Region (closed 1983–86) and Bramble Reef in the Townsville Subregion (closed 1992–95) estimated a strong social learning effect. A major data source for the stock assessment was the large collection of underwater visual survey (UVS) data collected by divers who counted the coral trout that they sighted. This allowed estimation of the density of coral trout in the different Bioregions (expressed as a number of fish per hectare). Combined with mapping data of all the 3000 or so reefs making up the GBR, the UVS results provided direct estimates of the population size in each Subbioregion. A regional population dynamic model was developed to account for the intricacies of coral trout population dynamics and catch rates. Because the statistical analysis of catch rates did not attribute much of the decline to tropical cyclones, (and thereby implied “real” declines in biomass), and because in contrast the UVS data indicate relatively stable population sizes, model outputs were unduly influenced by the unlikely hypothesis that falling catch rates are real. The alternative hypothesis that UVS data are closer to the mark and declining catch rates are an artefact of spurious (e.g., cyclone impact) effects is much more probable. Judging by the population size estimates provided by the UVS data, there is no biological problem with the status of coral trout stocks. The estimate of the total number of Plectropomus leopardus on blue zones on the GBR in the mid-1980s (the time of the major UVS series) was 5.34 million legal-sized fish, or about 8400 t exploitable biomass, with an 2 additional 3350 t in green zones (using the current zoning which was introduced on 1 July 2004). For the offshore regions favoured by commercial fishers, the figure was about 4.90 million legal-sized fish in blue zones, or about 7700 t exploitable biomass. There is, however, an economic problem, as indicated by relatively low catch rates and anecdotal information provided by commercial fishers. The costs of fishing the GBR by hook and line (the only method compatible with the GBR’s high conservation status) are high, and commercial fishers are unable to operate profitably when catch rates are depressed (e.g., from a tropical cyclone). The economic problem is compounded by the effect of social learning in coral trout, whereby catch rates fall rapidly if fishers keep returning to the same fishing locations. In response, commercial fishers tend to spread out over the GBR, including the Far Northern and Swains Regions which are far from port and incur higher travel costs. The economic problem provides some logic to a reduction in the TACC. Such a reduction during good times, such as when the fishery is rebounding after a major tropical cyclone, could provide a net benefit to the fishery, as it would provide a margin of stock safety and make the fishery more economically robust by providing higher catch rates during subsequent periods of depressed catches. During hard times when catch rates are low (e.g., shortly after a major tropical cyclone), a change to the TACC would have little effect as even a reduced TACC would not come close to being filled. Quota adjustments based on catch rates should take account of long-term trends in order to mitigate variability and cyclone effects in data.

Phototoxicity of photosystem II (PSII) herbicides to coral

Recent reports of contamination of the Great Barrier Reef Marine Park by herbicides used in antifouling paints and in agriculture have caused concern over the possible effects on corals in nearshore areas. Pulse-Amplitude Modulated (PAM) chlorophyll fluorescence techniques were used to examine changes in the maximum effective quantum yield (ΔF/Fm′) of symbiotic dinoflagellates within the host tissues (in hospite) of the coral Seriatopora hystrix exposed to a number of Photosystem II (PSII) inhibiting herbicides in short-term toxicity tests. The concentration of herbicide required to reduce ΔF/Fm′ by 50% (median effective concentration [EC50]) differed by over 2 orders of magnitude: Irgarol 1051 (0.7 μg l-1) > ametryn (1.7 μg l-1) > diuron (2.3 μg l-1) > hexazinone (8.8 μg l -1) > atrazine (45 μg l-1) > simazine (150 μg l-1) > tebuthiuron (175 μg l-1) > ionynil (> 1 mg l-1). Similar absolute and relative toxicities were observed with colonies of the coral Acropora formosa (Irgarol 1051 EC50: 1.3 μg l-1, diuron EC50: 2.8 μg l-1), Time-course experiments indicated that ΔF/Fm′ was rapidly reduced (i.e. within minutes) in S. hystrix exposed to Irgarol 1051 and diuron. On return to fresh running seawater, ΔF/Fm′ recovered quickly in diuron-exposed corals (i.e. in minutes to hours), but slowly in corals exposed to Irgarol 1051 (i.e. hours to days). Time-course experiments indicated that the effects of diuron (3 μg l-1) on S. hystrix were inversely related to temperature over the range 20 to 30 °C, although initially the effects were less at the lower temperatures. Repeated exposure to pulses of Irgarol 1051 (daily 2 h exposure to 30 μg l -1 over 4 d) resulted in a 30% decrease in the density of symbiotic dinoflagellates in the tissues of S. hystrix.