The rezoning of the Great Barrier Reef Marine Park (GBRMP) in 2004 increased the number and extent of ‘no-take’ areas within the Park. This project surveys pairs of reefs, one in a ‘no-take’ or green zone and the other a similar reef where fishing is allowed (blue zone), in five regions of the GBRMP. Green and blue zones will be surveyed for the abundance and size of fishery species, particularly coral trout, as well as wider effects on coral reef communities. The results of reef surveys will be used to: 1. Track dynamics of populations of target fish species and by-catch species, such as reef sharks. 2. Track indirect effects of protection from fishing in terms of populations of non-target fish species. Since many exploited species are carnivorous, differences in their numbers may in turn affect the abundance of their prey (and potentially cause more extensive “trophic cascades”) as well as other community components that are related to resilience such as numbers of herbivorous fishes. 3. Track potential ecosystem effects of protection from fishing, such as increased coral recruitment and coral cover due to increased herbivorous fish numbers, and reduced incidence of coral disease (due to lower numbers of coral-feeding butterflyfishes inside no-take areas)

The values of the Great Barrier Reef World Heritage Area (GBRWHA) are threatened by coastal development through habitat loss and runoff of sediment, nutrients and pollutants. Future coastal development is difficult to predict because it depends on volatile socio-economic and political factors. With this in mind, we developed a research project that uses spatially explicit scenario planning to identify plausible futures to 2035 for the GBRWHA coastal zone. The method used to produce maps of these scenarios is land-use change modelling using the GIS Idrisi. A governance analysis for the GBR coast is part of the project and is included in the scenario-planning process. Using a conservation planning approach, this project sets out to identify key priorities for restoring and protecting coastal ecosystems in the GBRWHA coastal zone. The objectives are to: - Compile spatial data on the coastal ecosystems and socio-economic characteristics of the GBRWHA coastal zone - Produce spatially explicit land use scenarios for the GBRWHA coastal zone to 2035 - Analyse the governance system in the GBRWHA coastal zone - Identify conservation goals for the GBRWHA coastal zone - Assess impacts of development for assets related to the conservation goals - Bring all the above information together to determine spatial options for allocating protection and restoration actions to achieve goals

Turbidity is a measure of water clarity that quantifies the amount of small particles suspended in the water, and is a fundamental environmental parameter influencing coastal marine ecosystems. Turbidity reduces the light needed for photosynthesis by corals and seagrasses, and suspended particles also transport nutrients, pollutants and diseases. Previous research based on 3 years of turbidity data collected from 15 inshore reefs by the Reef Rescue Marine Monitoring Program has shown that it can take several months for water clarity to improve after river floods. This project will analyse a 12-year data set to demonstrate the explicit link between variations in discharge (sediments and nutrients) from the major rivers in each Natural Resource Management (NRM) region adjacent to the Great Barrier Reef (GBR) and seasonal and annual variations in water clarity in the inshore GBR. This project will: 1. Determine quantitative relationships between river discharges and seasonal and annual variation in inshore water clarity on the GBR adjacent to each NRM region. This is achieved by processing MODIS/Aqua remote sensing (since July 2002) to calculate euphotic depth (water clarity) for the whole GBR and analysing this against predicted and observed tides, observed waves, wind, rain, river flow data (BOM and DERM daily data) and tidal forcing (Slim model). 2. Strengthen scientific basis for Reef Rescue and Reef Plan and the refinement of water quality targets. 3. Provide data to assist validation and calibration of the Receiving Waters Model and a WQ Risk Analysis. This project is now complete.

Sharks play an important role in marine ecosystems but are facing increasing pressure from fishing and other anthropogenic factors. Along the Queensland coast inshore waters play an important role as nursery areas for sharks. However, the same inshore waters are also most prone to fisheries exploitation and effects of freshwater discharge from coastal streams and rivers. This project will examine the importance of different types of inshore habitat (protected bay vs. open coastline) and marine park zoning (open and closed to fishing), and how environmental factors such as freshwater discharge from rivers effect how these nursery areas function. The project has two broad objectives: A. Investigate the spatial and temporal changes in the biodiversity and abundance of sharks in inshore nursery areas along the central GBR coast. B. Determine the effect of environmental drivers on inshore shark biodiversity along the central GBR coast. Results from the project will be used to improve the information available to fisheries and marine park managers on the relative importance of inshore habitats, the role of areas closed to fishing, and the sustainability of inshore shark populations.

This project will investigate how coral communities along the Great Barrier Reef have historically responded to acute (e.g. cyclones) and chronic (e.g. water quality) disturbances using pioneering high-precision geological dating and palaeoecological techniques, combined with high-resolution geochemical analysis of coral records. This project will determine high resolution chronological records on different time scales over the past 1-2 millennia of parameters such as: 1. Sea-level based on high-precision dating and elevation survey of well-preserved microatolls; 2. Salinity and pH value based on high-precision boron isotope analyses of selected coral cores in conjunction with back-reef sediment cores; 3. Cyclone frequency based on precise dating of transported reef blocks, cyclone ridges and lagoon sediment cores; 4. Sea-surface temperature based on geochemical proxy analyses (Sr/Ca, Mg/Ca, 18O/16O) of U-series-dated coral cores. 5. Variation in coral reef community structure and coral calcification rates.

This project will conduct a biodiversity assessment of coral communities on Torres Strait reefs to establish a baseline of coral condition and start a longer-term monitoring program of selected coral reefs in the region. The monitoring will look for changes in the condition of coral reefs and document factors that might contribute to changes incl COTS, disease, bleaching, temperature anomalies etc. As part of this project, an early warning system will be established for coral bleaching. This will give the Torres Strait Regional Authority (TSRA), Torres Strait communities, industry and other stakeholders, the ability to predict, prepare for and respond to coral bleaching. This project will: 1. Consult with TSRA and community to design a monitoring program for reefs of Torres Strait that addresses community needs and involves training TSRA LSMU rangers in field activities so that they can continue the reef monitoring program once this project is completed. During the project a biodiversity survey will be completed along with a baseline monitoring survey (Feb 2013) and a repeat monitoring survey (Feb-March 2014). 2. Establish an early warning system for coral bleaching based on the best-available knowledge of bleaching thresholds and a real-time environmental observing system for key parameters, including temperature and light. One real-time observing station will be located in the western Torres Strait and a second for the eastern TS subject to sufficent funds being available. 3. Establish a network of non real-time temperature loggers at up to 15 sites (two loggers/sites at different depths) at sites representative of the Torres Strait to capture the range of thermal regimes in the Torres Strait. LSMU rangers will be trained to exchange loggers on a 6-12 monthly basis (depending on site accessibility). 4. Provide regular updates on current coral reef conditions and summer forecasts for bleaching risk. These updates are a compilation of all available satellite and in-situ data together with forecasts from POAMA and NOAA bleaching risk models and will be provided to key stakeholders.

The project seeks to improve understanding of practices that can underpin co-management arrangements for conservation areas, including the Wet Tropics World Heritage Area (WTWHA). A co-research team of CSIRO scientists, Rainforest Aboriginal peoples, protected area managers and other key partners will investigate the potential of Indigenous Protected Areas (IPAs), and other collaborative models and tools, to engage Indigenous values and world views. The team will focus on the conditions under which these arrangements lead to effective joint management. The overall goal of the project is to identify the means for effective engagement of Indigenous knowledge and co-management for biodiversity and cultural protection in the region; and for joint management of the Wet Tropics World Heritage Area between governments and Rainforest Aboriginal peoples, in partnership with communities. The project will deliver tested mechanisms for co-governance and collaboration between Traditional Owners, government managers, and other key partners, for biodiversity and Indigenous cultural conservation in the Wet Tropics region. This project is now complete.

This project is providing a direct assessment of the ecological effects of multiple-use zoning on inshore reefs of the GBRMP. Underwater visual census (UVC) monitoring of fish and benthic communities is being carried out at 50 no-take marine reserve (green zone) sites and at 50 sites that have remained open to fishing within the Palm, Magnetic, Whitsunday and Keppel Island groups. Long-term monitoring surveys are providing information on: 1. The effects of no-take marine reserves on populations of both species that are fished and other non-fished species. 2. Variations in structure of fish communities due to the reserves and natural disturbances. 3. Structure and dynamics of marine species on the sea bed. 4. Coral health, bleaching, incidence and severity of coral disease and coral predators. 5. Temporal monitoring of the relative number of fishing lines recorded at each site will be used to assess the distribution of fishing effort and provide information on the levels of non-compliance with zoning regulations.

This project will implement monitoring programs for the endangered southern cassowary, Casuarisus casuarius, and the vulnerable spectacled flying-fox, Pteropus conspicillatus. Cassowary monitoring will be based on regular surveys to collect dung. DNA fingerprinting of the bird dung will provide data on cassowary abundance and distribution, the influence of habitat type and the structure and phylogeography of cassowary populations across the region. For spectacled flying-fox monthly surveys of all known spectacled flying-fox camps in the Wet Tropics Region will be conducted. Resulting data will be used to describe population distribution, population size and trends to build upon the long term database already established.

This project focuses on improving methods to detect the introduction of exotic animal diseases into the Torres Strait. The researchers will examine the environmental factors that influence the establishment and persistence of wildlife diseases in the region. They will study insect disease vectors and the incidence of disease in birds in a range of habitats in order to identify where disease risk is greatest. Field studies will be conducted using replicated mosquito trapping and mist netting of birds in Torres Strait, at sites identified from previous projects. Outcomes include: 1. Developing a model of disease dynamics across the Torres Strait based on past and ongoing epidemiology and ecological studies on vectors, reservoir hosts and known disease prevalence including the influence of inter-island and PNG traffic on insect vectors. 2. Undertake a fieldwork program that tests and improves upon our understanding (the model) of how diseases are maintained and dispersed across the islands. 3. Use the results to identify appropriate responses for minimizing the risks associated with disease incursion. 4. Develop capacity in north Queensland in the identification and sampling of vectors and diseases