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Australian Government Transition Funding

The four-year term of the MTSRF officially concluded at the end of June 2010.  The Commonwealth Environmental Research Facilities (CERF) Transition Program for the MTSRF aimed to deliver new and additional synthesis products based on the contemporary information needs of the primary end users through the synthesis and analysis of pre-existing MTSRF outputs.  In addition, the MTSRF Transition Program extended research that is highly relevant to the future CERF key investment areas of the Great Barrier Reef and Torres Strait, northern Australia and terrestrial biodiversity.

The objectives of the CERF Transition Program were to:

  • Build on the outputs of the MTSRF to enable the delivery of synthesis products that reflect the contemporary information needs of major end users;
  • Foster the adoption of science-based knowledge into the policies and operational frameworks of major end users; and
  • Sustain the capacity to conduct environmental research on components of the CERF key investment areas of the Great Barrier Reef and Torres Strait, northern Australia and terrestrial biodiversity.

A total of $1.8 million has been contracted for the delivery of 42 MTSRF transition projects, each outlined below.  Key outputs of transition projects are also indicated, and will be made available via the RRRC website at completion.

Transition Project outputs, such as synthesis reports and fact sheets, are also listed by project number in the Publications section of this website.

Summary of Transition Projects and Key Outputs


Title and Project Leader


Key Outputs


Identification of extent, condition and future trends for threatened species and communities (littoral rainforest) for EPBC purposes, in the Wet Tropics

Dr Dan Metcalfe, CSIRO

This project will build on previous MTSRF projects to deliver a synthesis report combining aspects of cassowary, flying fox and arboreal mammal biology (to contribute to planning for the future of these animals in the Wet Tropics), and improved mapping of littoral rainforest across the bioregion, incorporating field and remote sensing data, including identification protocols and public information resources.

Synthesis Report:  The projected future of cassowaries and arboreal mammals of the Wet Tropics.

Revised map (and associated materials) for littoral rainforest across the bioregion.


The search for water quality stress resistance markers in corals using a population genomics approach

Dr Madeleine van Oppen,
Australian Institute of Marine Science

This project will investigate correlations between genotype and water quality parameters in reef-building corals on the Great Barrier Reef. Findings from this project will provide a genetic tool to measure past impacts of selection and predict the future evolutionary response of corals to changes in water quality.

Map of gene variants in relation to water quality parameters


Incorporation of the high-resolution 3D depth model of the Great Barrier Reef into the e-Atlas for visualisation by end-users

Dr Robin Beaman,
James Cook University

This project aims to develop a new and significantly improved high-resolution depth model (DEM) for the Great Barrier Reef and adjoining Coral Sea at a grid pixel resolution of 3-arc second or about 100 m (see project link at http://www.deepreef.org/).

New high-resolution depth model, the derived datasets and metadata text publicly available via the e-Atlas


Predicted influence of a changing climate on the vulnerable ecosystems of the Wet Tropics: Rates of carbon sequestration, soil and water interactions, phenology and terrestrial biodiversity

Associate Professor Mike Liddell,
James Cook University

This project will be the first to develop a process-based understanding of a typical area of lowland rainforest in the Wet Tropics, by synthesising different datasets that have been collected at the Long Term Ecological Research station at Cape Tribulation.

Synthesis Report: Carbon stock dynamics

Synthesis Report: Physical drivers of the plan community

Synthesis Report: Insect resource use and climate

Modelling Report: Canopy parameters


Guide for design of conservation refugia in the Wet Tropics: practical strategies to minimise loss of biodiversity under climate change

Professor Steve Williams,
James Cook University

This project will synthesise MTSRF research findings on refugia into an accessible form and deliver practical options for local managers to adapt to the threat of climate change in the Wet Tropics, specifically focusing on conservation of existing habitat and/or the restoration of degraded land within refugia.

Synthesis Report: Guide for design of conservation refugia in the Wet Tropics: strategies to minimise loss of biodiversity under climate change


Innovation in invasive species control: Combining science, industry and community knowledge

Dr David Westcott, CSIRO

This project will, (a) prioritise (new) control methods for management and research for application in the development of management programs, and (b) identify future priorities and directions for research to underpin invasive fish management.

Synthesis Report: Prioritising control methods for the management of invasive fish in the Wet Tropics Region


Maintaining and maximising rainforest resilience in the face of change

Professor Steve Turton,
James Cook University

Synthesising the large quantity of MTSRF-generated information into a form that is useful for key end users – locally, regionally, nationally, and internationally – has been identified as an important step towards generating the maximum benefit from several decades of intensive research into the basis of rainforest resilience, and practical ways in which resilience of the ecosystem, and the human communities which depend on them, can be built and maintained by managers at a range of spatial scales.

Synthesis Report: Maintaining and maximising rainforest resilience in the face of change


Adapting current integrated management strategies for protecting tropical biodiversity from invasive weeds to vertebrate pests

Dr David Westcott, CSIRO

Despite decades of on-ground activities and research focused on invasive species management and the huge economic and environmental costs associated with biological invasions, invasive species management programs can still be characterised as having only limited success.  This project will assist managers in incorporating current integrative approaches into the invasive species programs currently operating in the region.

Synthesis Report: Integrated invasive species management for the protection of tropical biodiversity


Enhanced analysis of existing coral cores to improve historical understanding of water quality in the Great Barrier Reef lagoon

Dr Stephen Lewis,
James Cook University

Preliminary data suggest that phosphorus records in coral cores may provide a long-term (e.g. multi-decadal), high resolution (e.g. weekly-monthly) record of phosphorus inputs from adjacent catchments. Additional work is required to confirm these findings and expand results with 2009 cores collected from mid-shore and off-shore reefs. Nutrient and sediment records in these coral cores will be examined to see if the influence of terrestrial sediment and nutrient runoff has influenced coral health and calcification rates. 

Several high quality scientific publications on the geochemical records from coral cores from the Townsville to Cairns region and the Whitsunday Islands


Hindcasting water quality and climate change from benthic foraminiferal communities in sediments from inshore areas of the Great Barrier Reef using existing data

Dr Sven Uthicke,
Australian Institute of Marine Science


Fourteen sediment cores from inshore reefs of the Whitsunday area have been collected, sliced, and their foraminifera sampled and identified. This transition project will provide evidence of the influence of changes in water quality and ocean pH on marine assemblages by relating these parameters to historical changes in foraminiferal communities in sediments of the inshore Great Barrier Reef.

Report on the use of foraminifera communities in sediment cores for hindcasting of water quality and CO2 concentrations in the inshore Great Barrier Reef


Biofilms as indicators of water quality: Changes in microbial diversity and activity in coastal biofilms in the Great Barrier Reef

Verena Witt,
Australian Institute of Marine Science


MTSRF-funded experiments suggest that dominance shifts in key microbial groups in biofilm communities may be useful bioindicators of tropical coastal water quality. This project will provide advice on the efficacy of using changes in microbial diversity and activity as indicators of changes in water quality and ocean pH, which could be adopted in future marine water quality monitoring programs.

Two scientific papers: Microbial Biofilm Community Structure in Response to Water Quality and Substrate Specificity; The Effects of Ocean Acidification on Microbial Diversity and Activity in coastal marine Biofilm Communities in the GBR


Fine sediments in the Burdekin catchment: from catchment source to plume processes

Dr Zoe Bainbridge,
James Cook University


Given the importance of the Burdekin catchment as the single largest contributor of sediment to the Great Barrier Reef lagoon (thirty percent of all Reef catchments), the findings of this MSTRF transition project are directly applicable to the considerable funding currently being invested in this catchment through the Australian Government's Reef Rescue Initiative. Transitional funding will allow for MTSRF-funded research on sediment transport processes from the catchment to the plume to be published in a scientific journal. 

Journal Article describing the sediment transport processes in the Burdekin River from the catchment to the plume

Communication of the outcomes of this work to managers and policy makers involved in the Reef Rescue Initiative and the Paddock to Reef Program.


Changes in inshore turbidity in the Wet Tropics region following river runoff

Craig Humphrey,
Australian Institute of Marine Science

Do increased river loads of suspended sediments lead to repeated or prolonged regional turbidity from repeated resuspension in shallow (generally <10 m deep) inshore areas of the Great Barrier Reef lagoon? This transition project aims to harvest, process and interpret and report data from a two-year deployment of oceanographic instruments in order to answer the question of whether sediment import alters inshore water clarity in this region.

Report: The effects of river runoff on water clarity in the inshore marine region of the Wet Tropics


Testing the type of cumulative or additive impact of nutrient enrichment and increases in sea surface temperature

Florita Flores,
Australian Institute of Marine Science

Transition funding will permit analysis of the results of a pilot laboratory experiment assessing changes in the temperature tolerance in corals exposed to (1) nutrient-enriched flood plume waters with more mature plankton communities and suspended solids (facilitating heterotrophic feeding as well as nutrient and sediment stress), and (2) to unprocessed nitrate. The results of these experiments will be an important first step in providing insight into the complex interactions of climate change and water quality.

Report:  The influence of water quality on the temperature tolerance thresholds of corals


Freshwater-marine connectivity indicators

Professor Richard Pearson,
James Cook University


Connectivity is a fundamental property of integrated systems, and important to understand if management is to address it appropriately. This project aims to collate and analyse data (some from MTSRF projects, some from elsewhere) to examine the important ecological linkages that are governed by connectivity through waterways feeding into the Great Barrier Reef lagoon.

Synthesis Report:  Freshwater-marine connectivity in the Great Barrier Reef catchment:  A review of current knowledge and a case study of the Tully-Murray floodplain


Prioritised input of water quality data into the e-Atlas

Dr Glenn De’ath,
Australian Institute of Marine Science

While the e-Atlas currently holds a growing number of text pages and more than 600 maps, the value of the e-Atlas can be enhanced with a dedicated program to incorporate water quality data that is a direct priority for major end-users including the Australian Government's Reef Rescue Initiative, the GBRMPA, the Commonwealth Department of Sustainability, Environment, Water, Population and Communities (DSEWPaC), and Paddock to Reef. The objective of this project is to collate, analyse and incorporate priority water quality data from monitoring programs and water quality-related research projects conducted on the Great Barrier Reef.

Prioritised water quality-related data publicly available via the e-Atlas


Integrating landholder research and Natural Resource Management (NRM) program appraisals for enhanced NRM arrangements

Dr Nick Emtage and Associate Professor John Herbohn,
The University of Queensland


Institutional arrangements for NRM are being constantly established and reviewed towards achieving desired environmental outcomes.  There is now an opportunity to integrate research on landholder engagement and NRM governance at multiple scales with NRM program design and delivery data to draw overall conclusions about effective arrangements for NRM. 

Synthesis Report: Integrating landholder research and NRM program appraisals for enhanced NRM arrangements


Innovative governance arrangements for Natural Resource Management at a regional scale

Dr Cathy Robinson, CSIRO

This project builds on the integrated NRM governance assessment framework that has been successfully developed at a regional scale and applied under MTSRF Project 4.9.6 to assess NRM grant delivery partnerships in the Wet Tropics region. This framework will be synthesized to compare the strengths, challenges and strategic NRM outcomes delivered through integrated governance models being used throughout the Wet Tropics region

Synthesis Report

Communication of results via an Essential Science Session


Delivering improved outcomes for threatened species in economically and environmentally high value ecosystems under development pressure: The case of the Cassowary at Mission Beach

Dr Ro Hill, CSIRO

This transition project will synthesise the outcomes of MTSRF-funded research focused on cassowary conservation at Mission Beach, and distil lessons relevant to species conservation in economically and environmentally high value ecosystems elsewhere.  The synthesis will help inform the development of Wet Tropics-wide cassowary habitat conservation projects.

Synthesis Report: Innovations in strategic planning and institutional frameworks to deliver improved outcomes for threatened species in economically and environmentally high value ecosystems under development pressure: case study on the cassowary at Mission Beach

Communication of results via an Essential Science Session


An analysis of existing data to quantify the influence of region, habitat, zoning and take on deep and shallow targeted fish populations of the Great Barrier Reef

Mike Cappo,
Australian Institute of Marine Science

This transition project will compile all the existing MTSRF intelligence to enable managers to develop an holistic picture of the regional effects of the Great Barrier Reef Zoning Plan amongst the Pompeys, Swains and Capricorn-Bunkers management zones.

Synthesis Report:  Reasons for observed regional differences in effectiveness of the Representative Areas Program 2004 Zoning Plan

Presentation of results at regional fora (see above mentioned Synthesis Report)

Scientific publication of synthesis


Quantifying the risk to fish spawning aggregations from commercial and recreational fishing

Dr Andrew Tobin,
James Cook University

Though the current management of the Coral Reef Fin Fish Fishery (CRFFF) includes an input control of seasonal fishing closures, the efficacy of the timing and duration of these closures has not previously been quantified due to a lack of appropriate data. This project will allow for the first truly quantitative assessment of the efficacy of the current CRFFF seasonal closures.

Scientific publication on the species-specific risks to fishes that aggregate to spawn from fishing exploitation, with a view to global utility


Long-term trends in the abundance and composition of major inshore shark groups

Associate Professor Colin Simpfendorfer,
James Cook University

The Queensland Shark Control Program has collected data on shark catches since the early 1960s, but these data have not been analysed to examine long-term trends in shark populations or the changes in the composition of the shark community. This project will build on preliminary work and will be useful in understanding the current status of shark populations.

Report detailing the results of analyses and their interpretation


Interdependency of reef and rainforest tourism - a comprehensive contemporary review

Professor Bruce Prideaux,
James Cook University

MTSRF support for visitor monitoring in North Queensland (Great Barrier Reef, Wet Tropics Rainforests and Cairns Domestic Airport exit surveys) over a four-year period has provided a comprehensive database that can now be integrated to identify underlying drivers for travel to North Queensland.

Synthesis Report:

Patterns of Reef and Rainforest Tourism in North Queensland from Exit Surveys Conducted at Cairns Domestic Airport (2010)

Patterns of Rainforest Tourism in the Wet Tropics World Heritage Area, North Queensland (2012) 

Rainforest Tourism Drivers Trends and Management Tools (2012)

Workshop and fact sheets


Identifying the strengths of a community monitoring program for describing the human-use impacts of recreational fishing: CapReef as a case study

Dr Andrew Tobin,
James Cook University

Serious data gaps and insufficient knowledge of recreational fishing activities occur at many levels within the Great Barrier Reef World Heritage Area (GBRWHA), making effective management problematic. This project will utilise an extensive dataset collected by CapReef, a community based monitoring program of recreational fishers activities within the Capricornia region of the GBRWHA.

Scientific publication describing the influences of demography, habitat and season on catches taken by recreational fishers and the vulnerability of exploited components of the fishery


The structure, usefulness and limitations of social networks for regional co-management and stewardship of fisheries

Dr Renae Tobin,
James Cook University

Research has identified social networks as important factors in determining whether multiple sectors can come together to discuss and decide on natural resource management issues. This project will deliver a literature review aimed at understanding the roles of social networks in regional areas and exploring methods of building essential capacity in this field for northern Australia.

Literature review examining the structure, usefulness and limitations of social networks for regional co-management and stewardship of fisheries


Communicating science to stakeholders

Dr Steve Sutton,
James Cook University


With 750,000 fishers in Queensland, recreational fishing has a significant impact on the fisheries resource, and management authorities (e.g. the GBRMPA) have begun to realise the importance of engaging recreational fisheries in the management process.  The results of this study will allow social scientists, management bodies and science communicators to construct more focused and efficient communication programs for recreational fishers. 

Literature review of methods to communicate the results of complex scientific studies stakeholders


Expansion and maintenance of the e-Atlas

Dr Eric Lawrey,
Australian Institute of Marine Science


The value of the e-Atlas can be enhanced with a dedicated program to incorporate additional information generated by the MTSRF program that is of direct priority for major end-users including the Department of Sustainability, Environment, Water, Population and Communities (DSEWPaC). This project will increase automation, deliver more synthesis and improve coordination with key synthesis projects, for example, the GBRMPA Outlook Reports.

The delivery ofall priority MTSRF data, synthesis and text contributions to the e-Atlas

A stable software platform and functional web-based mapping components

Statistical analyses of priority data

Strengthened links to the GBRMPA Outlook Online System


Combining landscape ecology, palaeoecology and plant function analyses to determine the impact of changed fire regimes and/or changing climate on the landscape matrix: a case study of rainforest boundary dynamics

Professor David Bowman,
University of Tasmania

Does the perceived expansion of rainforest ecosystems constitute a departure from historical variability and is it a threat to biodiversity?  This project has evolved from a workshop conducted by the Wet Tropics Management Authority in June 2008 focusing on appropriate management responses to the perceived expansion of rainforest into wet eucalypt forests.

Report of analyses using advanced geospatial statistics to resolve the rate, direction and magnitude of boundary changes across landscape settings with contrasting nutrient status to test hypothesis that rainforest boundaries are uniformly expanding throughout the Wet Tropics


Ecosystem water and carbon balance in upland and lowland tropical forests

Professor Michael Bird,
James Cook University

This project will deploy newly available state-of-the-art instrumentation that, in combination with current and planned future installations, will enable whole system monitoring of carbon and water storage and flux at the small catchment scale. This will in turn provide area-averaged time-series that can be used for validation of remote sensing techniques aimed at developing indicators for assessing the health of the Wet Tropics bioregion.

Synthesis Report


Implementing the Cassowary Recovery Plan:  Population estimation and monitoring

Dr David Westcott, CSIRO

The critical need in cassowary management has been the development of a monitoring method that allows estimation of cassowary population sizes and of the type and magnitude of the errors associated with those estimates.  This project will use newly-developed methods to conduct sub-regional population surveys for key areas.

Report on estimation of sub-regional population size


Biodiversity conservation in a changing climate

Professor Steve Williams,
James Cook University

The aim of this project is to both harvest and extend outputs from previous MTSRF projects by integrating and synthesising biodiversity and climate change vulnerability data collected in the Australian Wet Tropics rainforests. We will use the incredible depth of data available for the region to develop cutting-edge tools and applications that can be generalised to other ecosystems.

Development of automated and analytical tools for spatial analysis of extreme climate events

Mapping and quantification of extreme climate regimes (intensity, frequency, duration) in the Wet Tropics rainforests, particularly heat waves and dry season severity (drought)

Report: Optimisation analysis for competing objectives in the Wet Tropics: protection of current species diversity, future species diversity and climate change refugia


Restoring resilience to tropical forest landscapes

Dr Carla Catterall,
Griffith University

Building landscape-scale ecosystem resilience depends on the restoration of forest habitat to reverse past loss and fragmentation and also to provide key habitat for climate-sensitive species. This project consists of the following two components: (a) harvesting existing information from current MTSRF research about the effectiveness of past restoration efforts, and (2) identification of important knowledge gaps and future priorities.

Report: Analyses of recovery of plant regeneration processes in restored rainforest sites

Synthesis Report: Opportunities to integrate science and practice to fill important knowledge gaps about restoring Australian tropical rainforest


Conceptualising, evaluating and reporting social resilience in vulnerable regional and remote communities facing climate change in tropical Queensland

Dr Allan Dale and Dr Margaret Gooch,
James Cook University

If we are to better manage biodiversity values in the face of climate change, strategic investment in building the regional-scale resilience of vulnerable communities will require a clear set of indicators for benchmarking resilience, for targeting the priority interventions required, and for measuring progress arising from these interventions. This project will collaboratively establish an effective set of regional scale indicators that agencies and Natural Resource Management bodies can use to monitor and evaluate regional-scale community resilience in the face of climate change.

Monograph/journal article on multidisciplinary approaches to community resilience

Synthesis Report: Findings across the MTSRF social resilience projects to date and the social science and resilience literature to design and a clear indicators framework

Scoping paper that desribes ways of spatially representing resilience


Ichthytoxicological studies of Indigenous plant poisons on freshwater fish – validating traditional ecological knowledge in fish management

Dr Damien Burrows,
James Cook University

Working in close cooperation with Traditional Owners, this project will test the effects and efficacy of traditional plant poisons against a range of native and pest freshwater fish to determine tolerance to varying concentrations of toxins. Results from this work will not only validate traditional ecological knowledge and give greater impetus to Indigenous involvement in Natural Resource Management, but will also trial/operationalise the suitability of this technique as a potential control method for invasive tilapia.

Report on project outputs


Initiating interdisciplinary research on wildlife disease in Australia’s tropics with practical implications for conservation, biosecurity and human health: a case study of forest fragmentation and vector-borne avian diseases

Dr David Hilbert, CSIRO

International research has demonstrated that disease can have a significant impact on wildlife populations that can affect their conservation, but there has been little research in the Wet Tropics or tropical Australia on disease. This project will shift and broaden previous MTSRF-based disease research toward the interactions between landscape structure, conservation biology and epidemiology with a greater emphasis, in the longer-term, on identifying possible management interventions that can reduce disease threats to both endemic wildlife and humans

Workshop including researchers in the areas of conservation biology, landscape ecology, biosecurity, and epidemiology of wildlife and zoonotic diseases, including key land managers

Report: Preliminary assessment of haemoprotozoan disease prevalence in  birds in relation to anthropogenic modifications to rainforest landscapes


Biodiversity planning - capturing multiple values in decision-making

Dr Ro Hill, CSIRO

This project will scope out a research project in the tropical landscapes within Great Barrier Reef catchments to improve the ability of existing planning and decision-making systems to deliver biodiversity conservation. It will deliver a synthesis of the current status, and a theoretically-robust framework and design for ongoing research.

Report: Identification of planning systems, governance structures and institutions that capture the diversity of human values and world views associated with biodiversity: A framework for research

Peer-reviewed publication


Culturally diverse communities and sustainable natural resource use

Professor Hurriyet Babacan,
James Cook University


This research will explore the elements around the key themes of 'cultural practice' resource use and biodiversity conservation.

Report on project outputs

Journal article


Landscape scale outcomes from market based instruments

Dr Anthea Coggan, CSIRO

The purpose of this transition project is to develop a set of rules of thumb or guidance principles which can be applied by end users (managers) to determine what type and design of offset market is most suitable in what circumstances, particularly when the objective is for landscape scale outcomes. Rules of thumb will be developed based on data from existing Australian and international experiences with offset schemes but will be designed to apply specifically to offsets for biodiversity in Far North Queensland.

Report: Rigorous and practical rules of thumb available to guide current and potential offset scheme selection, design, implementation and refinement

Report: Plan for future research for expansion of rules of thumb for landscape scale outcomes to include mixes of instruments beyond offsets


Rainforest plant identification training for Wet Tropics QPWS and IPA/Working on Country Indigenous Rangers

Professor Darren Crayn,
Australian Tropical Herbarium

In partnership with the Wet Tropics Management Authority (WTMA) and the CSIRO Plant Industry (CPI), the Australian Tropical Herbarium (ATH) has developed a series of Plant Identification Workshops that provide hands-on training to learn and develop skills in identifying Wet Tropics flora. This project will deliver these workshops 'On Country' to Wet Tropics rangers as part of their Natural Resource Management (NRM) Cultural and Land Management training programs.

Modification of course modules appropriate for this training program

Training workshops


Assessing environmental research needs across the Torres Strait

Dr Karen McNamara,
James Cook University

This project will seek to conduct an assessment, including a gap analysis, of environmental research needs across the Torres Strait. This project will attempt to ensure that knowledge generated from future applied research arrangements is appropriate and useful for end-users throughout the Torres Strait.

Synthesis Report: Assessing environmental research needs across the Torres Strait

Fact sheet on environmental research needs in Torres Strait


Sustained end user engagement facilitating delivery in the Torres Strait – the Research Support and Indigenous Engagement (Uncles) program

Vic McGrath,
Torres Strait Regional Authority

Sustained, effective engagement with end users has been critical to the success of the MTSRF in delivering for the Torres Strait region. This project will maintain this culturally appropriate engagement capacity for the benefit of current and future research programs in the region.

Progress report


Gap analysis of environmental research needs in the Australian Wet Tropics

Professor Steve Williams,
James Cook University

Strengthened linkages between terrestrial biodiversity researchers and end users across northern Australia are desirable to reduce duplicative effort and achieve maximum return on public investment in applied research. To assist this process, this project will facilitate a significant review, synthesis and consultation process with the aim of identifying end user needs, research gaps and possible synergies, delivering an accessible and useful resource for terrestrially focussed end user groups.

Report: Gap analysis of environmental research needs in the Australian Wet Tropics


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