The Reef Rescue Marine Monitoring Program (RRMMP) has identified that seagrass meadows along the Great Barrier Reef are in a state of decline. This project will undertake desktop analyses to quantify the exposure of seagrass meadows to flood plumes. Aquaria experiments will measure responses of seagrass to variation in light, nutrients and salinity. This project will also use use True Colour Remote sensing images, to derive flood plume exposure and relate to changes in seagrass abundance and composition. The results will be synthesised to define thresholds of concern of water quality impacts, with a particular focus on flood plumes, and input into the development of guidelines for the protection of seagrass meadows. Tasks include: 1. Quantifying the level of exposure of seagrass meadows to changes in water quality associated with flood plumes (using True Colour Remote sensing) in coastal regions of the GBR. 2. Measurement of changes in biological traits (e.g. growth, biomass) of seagrass in relation to water quality (Light, nutrients, salinity) determined by experimental studies. 3. Experimental testing of indicators of seagrass status adopted in the Great Barrier Reef Marine Monitoring Program (MMP) (e.g. nutrient ratios) in response to changes in water quality. 4. Experimental verification of water quality response models and thresholds, in particular in relation to the MMP.

This project uses genetic parentage analysis, biophysical modelling and information on coral trout larval behaviour to determine patterns of recruitment of coral trout larvae within and among inshore and offshore reefs in the southern Great Barrier Reef. The overall goal of this project will be to assess larval dispersal patterns, demographic connectivity and levels of recruitment subsidies from green zones at a regional scale. Tasks include: 1. Collect tissue samples from adult and juvenile coral trout, develop a new set of hyper-variable microsatellite markers, conduct DNA genotyping analyses of all samples, carry out genetic parentage analysis to examine parent-offspring relationships. 2. Refine the existing biophysical model and assess likely origins of larvae at key recruitment hot spots in the region. 3. Undertake demographic metapopulation analyses using dispersal distances and trajectories derived from this study and available demographic data (growth, natural mortality, fishing mortality) to evaluate long-term persistence of green zone and blue zone populations under different levels of fishing pressure and habitat condition.

This project will determine the movement and habitat use of large predatory fishes such as sharks and coral trout in reef and coastal environments of the Great Barrier Reef. This project will employ acoustic monitoring technology in a series of inshore and offshore environments including coastal bays, inshore reefs and offshore reefs to monitor the presence and movements of predator species (elasmobranchs and teleosts). Mobile predators will be fitted with acoustic transmitters to define their presence and distribution, extent of movement and amount of connectivity between study locations (i.e., movement from bay to inshore reef, movement among reef platforms, etc.). Predator presence and movement will be integrated with habitat mapping and environmental monitoring data to identify factors that lead to changes in movement patterns and to define any preferred locations or conditions that can be targeted for conservation or management. Examination of use of habitats will provide information about the amount of time spent in various GBRMP zones and amount of movement among zones to assess the amount of protection provided under current management arrangements.

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 undertook a scoping study to develop a robust approach that will allow us in Phase 2 to carry out an ecological risk assessment (ERA) of nutrients, fine suspended sediments, and pesticides used in agriculture in the GBR region including ranking the relative risk of individual contaminants originating from priority catchments to the GBR ecosystems using a systematic, objective and transparent approach. The researchers will specifically look at a method able to evaluate relative risk to different ecosystems and their keynote species from the different contaminants, e.g. suspended sediments versus nitrogen (and different forms of nitrogen) versus phosphorus (different forms) versus pesticides (different types). The results of the Phase 1 study were used to secure support to carry out a full risk assessment.

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

This project will act as an integrating focus within the rainforest theme to strategically target research gaps and thereby increase our understanding of the drivers of rainforest biodiversity. We will generate high resolution maps and landscape scale estimates of temporal trends in the condition of biodiversity and environmental changes. The project consists of four subprojects: A. Monitoring: Tasks include a microsensor network, standardised vertebrate surveys, habitat structure monitoring and data harvesting from other projects. A comprehensive review of regional literature followed by extensive stakeholder consultation identified long-term monitoring data as the most important knowledge gap in the region (Welbergen et al. 2011). This sub-project is aimed at maintaining and significantly improving a regional-scale, long-term environmental monitoring program that provides biodiversity and environmental data that has a demonstrated value to a wide range of users including the research community, regional/state/national management agencies and conservation policy development, and national / international bioinformatic infrastructure initiatives (e.g. ALA, TERN). Data collected and maintained here will provide the primary input for the other sub-projects described below with flow-on inputs to many of the other proposed projects across the rainforest node. These data will include but not be limited to: 1. Regional microclimate sensor network at more than 30 sites established under MTSRF that are strategically placed across elevational and latitudinal gradients in the region. o Replace and upgrade existing microclimate stations (now defunct/worn out) o Establish standardised microclimate logging stations in new sites in gaps in environmental coverage, identified climatic refugia, peripheral habitat isolates and increased coverage of the rainforest edge habitats (e.g. wet sclerophyll). Data: temperature (air, soil, microhabitats), humidity, soil moisture, cloud interception. 2. Standardised vertebrate surveys across all long-term sites (>30) including: o 2-4 complete surveys per year for three years with 6 replicated sampling points within each site and including standardised surveys of: birds, reptiles, spotlighting (mammals and other nocturnal fauna) and microhylid frogs, with potential to add specific other groups dependent on student projects. o These surveys follow well-established and extensively published methodologies within the CTBCC (e.g. Williams et al. Ecology 2010). 3. Habitat structure monitoring will be continued and improved at all monitoring sites both directly by this project and via site-based collaboration with other projects including rainforest dynamics project (Project 10 - Laurance) and plant genetics (Project 9 -Crayn). 4. Link to Project 14: potential monitoring of vegetation structure and thermal properties using UAV technology to capture aerial photos, multispectral remote sensing, Lidar vegetation structure, thermal imagery of habitat and fauna, cyclone damage and canopy condition. 5. Additional monitoring data will be harvested across the node for increased regional and taxonomic coverage and baseline data improvements via links and data exchange with Projects 4, 5, 7, 9, 10, 11, 15, 16, 18, 20 and 25. B. Climate change vulnerability and adaptation: Includes the production of downscaled regional climate projections, projected changes in species distribution models, composite biodiversity maps, identification and mapping of climate refugia, predictive models of impacts on biodiversity including extreme events. Climate change is arguably the single largest threat to biodiversity in Australia and the unique biodiversity of the Wet Tropics rainforests is recognised as one of the most threatened ecosystems globally (IPCC 4th AR). This subproject will build on previous and existing research to provide cutting-edge predictions on climate change impacts, vulnerability assessment and adaptation options for rainforest biodiversity. We will link closely with the National Climate Change Adaptation Research Network to ensure that outputs, tools and approaches are distributed across this network for maximum national and regional benefit and outcomes. Specific objectives and collaborative links include: 1. Produce and make available downscaled regional climate projections using eight Global Climate Models across multiple (at least 3) emission scenarios at 10 year time steps from 1970-2080 for more than 50 bioclimatic variables; 2. Projected changes, including uncertainty estimates, in species distribution models and composite biodiversity maps for the majority of rainforest vertebrates, 500+ species of invertebrates, major vegetation types and some key ecosystem processes (baseline data for these analyses were collected under MTSRF and ongoing projects within the CTBCC); 3. Identify and map climatic refugia (extension of previous MTSRF work that mapped landscape-scale temperature refugia by Shoo et al. 2010a, 2010b). This analysis will expand previous work to include finer scale microhabitat refugia and also increase the generality of the analyses by examining moisture refugia and dry season drought events that have been shown to have significant impacts on biodiversity (Williams & Middleton 2008, Middleton & Williams in review). 4. Produce predictive impact models on biodiversity that explicitely include a consideration of extreme events rather than just environmental means/averages. Project will link closely with the extreme climate events project (Project 16 – Welbergen) to incorporate the impacts of changes in the frequency, intensity, duration and extent of extreme events, such as heat waves and droughts, as a major component of assessing relative vulnerability and adaptation actions; 5. Project will closely collaborate with Project 15 (Phillips, Llewelyn) examining the potential for useful local adaptation to climate changeextremes in isolated populations. This link explores the potential to utilise existing adaptive potential as a means to increase species resilience to climate change. 6. Other external links: • NCCARF Refugia project (National) - proposed • NCCARF Terrestrial Biodiversity Research Network • Northern Biodiversity NERP Hub • AEDA Hub – Restoration project and Future Fellowship (Wintle) examining demographic modelling and climate change. 7. Incorporate IPCC 5th Assessment Report climate models and scenarios into all above analyses, once they become available. C. Synthesis, analysis and integration: Determinants of biodiversity: Includes mapping of almost all rainforest vertebrates and 200+ species of invertebrates, identify key monitoring locations, examining the relationships between biodiversity and vegetation and landscape structure. An understanding of the drivers of biodiversity in the region is crucial to predicting impacts from a variety of threats and ensuring effective conservation planning and management that aims to maintain a resilient landscape. We will use data collected in subproject A in combination with our existing extensive vertebrate and invertebrate database to examine the drivers of biodiversity in the region and to provide the resources and knowledge to make this useful to stakeholders. Specific objectives will include, but not be limited to: 1. Mapping of almost all rainforest vertebrates and >500 species of invertebrates (distribution and abundance) with emphasis on threatened species; 2. Identify key locations and taxa where we have long-term count data and/or high frequency of repeat count surveys over time periods that have encompassed important environmental change. We will undertake statistical power analyses to evaluate condition and trends of species (e.g., range shifts, change in population size); 3. Analyses will also inform the design of our ongoing monitoring program (subproject A) to maximise the detection of change in a cost-effective manner. 4. Comprehensive habitat/vegetation type vulnerability assessment; 5. Examine a range of environmental and evolutionary drivers of biodiversity to provide the basic scientific underpinnings for evidence-based policy and management in the region including paleostability of habitat; seasonal habitat and climatic stability, relationships to ecosystem processes such as net primary productivity, habitat structure and heterogeneity, species and habitat compositional turnover and evolutionary biology. 6. Examine relationships between biodiversity and vegetation and landscape structure (vegetation type and structure, habitat extent, connectivity etc.) D. Status, trends and future projections: Includes Producing a spatial and temporal resources tool that allows web-based query of all the above datasets. No practical measure currently exists to evaluate trends in biodiversity values at the ‘whole-of-region’ scale in near real-time on a regular, repeatable and affordable basis (WTMA Research Strategy 2010-2014). We will generate high resolution maps and landscape scale estimates of temporal trends in the condition of biodiversity and environmental changes. This will be the major vehicle for synthesizing, integrating and communicating data from all projects. This project will make use of extensive computing power represented by the collaboration between the CTBCC and the James Cook University eResearch group and High Performance Computing Facility. Specific objectives: 1. Produce and make publicly available a spatial and temporal resources tool that allows web-based query of all the above datasets based on a user-defined spatial area that will return all predicted and observed data within the query area for climate (past, current and future projections), habitat, species (predicted and observed), biodiversity values, terrain, ecosystem processes and, where available data is site-based, the tool could query the temporal patterns in the data (e.g. changes in abundance of a species) with “approaching real-time” updates (expected bi-annual upload of all new biodiversity and environmental data with temporal resolution dependent on the specific data stream, example quarterly for the standardised vertebrate surveys). 2. Automatic upload, synthesis and visualisation in JCU eResearch group (Tropical Data Hub) including time series examination of trends; 3. Automated upload via Tropical Data Hub onto National (ALA, TERN, NPEI) and international (GBIF) data infrastructure. This means that as data is entered into our system from the monitoring program and other projects, it will be uploaded and available via national and international data portals; 4. Future forecasting of trends and forecasts via combination of modelling and workshopping to conduct future horizon scanning. Once established, these bioinformatic tools could form the basis for UNESCO, and Queensland and Australian government reporting on the state of the Wet Tropics World Heritage Area, and could easily be utilized more generally across other ecosystems in Australia.

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

Long-term social and economic monitoring helps reef managers understand the current status of marine park users, industries and communities. It also helps build a picture of how industries and communities are likely to respond and cope with changes associated with environmental degradation, climate change, regulatory frameworks, and changes in culture. It can also assist in evaluating the effectiveness of management interventions.This project will establish and collect a unique data set that documents long-term social and economic trends in communities and users of the Great Barrier Reef (GBR). In 2011-12 a number of existing datasets were collated and relevant information extracted. Additionally data gaps were identified, which then formed the primary survey questions. In 2012-13 and 2013-14 primary data will be collected via surveys conducted on mini iPads from Bundaberg to Cooktown. Outcomes of this project include: * Providing GBR management and industries with better access to social and economic information necessary for planning purposes. * Strong liaison with GBR stakeholders on the social and economic status of the region. * An annual snapshot of the social and economic indicators for the entire GBR region.

This project involved working with a range of stakeholders to identify the most effective governance systems for managing climate change adaptation in the Wet Tropics through the emergence of new ecosystem service markets, including Carbon Farming. The project will directly contribute to: Regional climate change adaptation policies and planning processes, Regional Natural Resource Management (NRM) organisations’ role in guiding emerging carbon markets in Australia and the region. This project developed: 1. Detailed Practical Manuals for NRM Bodies concerning planning and carbon market integration in place and training delivered across Queensland regional NRM bodies. 2. Defined partnership arrangements for refinement of Governance systems, institutional and planning reforms maintained. 3. Theory based publication on governance systems required for application of ecosystem service market activities against NRM plan objectives.