MARINE BIODIVERSITY hub

JUNE 2015 2011–2015 A national research collaboration delivering marine FINAL REPORT biodiversity knowledge to the Australian Government Copyright and disclaimer Preferred citation – report The NERP Marine Biodiversity Hub Final Report Bax, N.J. & Hedge, P. [Eds.]. 2015. Marine Biodiversity 2011–2015 is licensed by the University of Tasmania Hub, National Environmental Research Program, for use under a Creative Commons Attribution 4.0 Final report 2011–2015. Report to Department Australia Licence. For licence conditions, see of the Environment. Canberra, Australia. https://creativecommons.org/licenses/by/4.0/ Preferred citation – individual items Acknowledgement Lead author, additional contributors in alphabetical This work was undertaken by the Marine Biodiversity order. 2015. Title. Pages xx-yy in Bax, N.J. & Hub, a collaborative partnership supported through Hedge, P. [Eds]. 2015. Marine Biodiversity Hub, funding from the Australian Government’s National National Environmental Research Program, Environmental Research Program (NERP). Final report 2011–2015. Report to Department of the Environment. Canberra, Australia. Important Disclaimer The NERP Marine Biodiversity Hub advises that the Enquiries information contained in this publication comprises Prof N.J. Bax, Director, Marine Biodiversity Hub general statements based on scientific research. Institute for Marine and Antarctic Studies The reader is advised and needs to be aware that such University of Tasmania information may be incomplete or unable to be used CSIRO Marine Laboratories in any specific situation. No reliance or actions must Castray Esplanade therefore be made on that information without seeking GPO Box 1538, Hobart, TAS 7001 prior expert professional, scientific and technical Phone: (03) 6232 5341 advice. To the extent permitted by law, the NERP Email: [email protected] Marine Biodiversity Hub (including its host organisation, employees, partners and consultants) excludes all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this publication (in part or in whole) and any information or material contained in it. IMAGE: William White, CSIRO MARINE BIODIVERSITY hub 2011–2015 A national research collaboration delivering marine FINAL REPORT biodiversity knowledge to the Australian Government

JUNE 2015 www.nerpmarine.edu.au

National Library of Australia Cataloguing-in-Publication entry Title: Marine Biodiversity Hub, National Environmental Research Program, final report 2011–2014: report to Department of the Environment, Canberra, Australia/editors N.J. Bax and P. Hedge. ISBN: 9781486305261 (paperback) 9781486305254 (ebook : pdf) Subjects: Marine biodiversity conservation–Australia–Management. Endangered species–Australia–Management. Environmental monitoring–Australia. Marine resources–Australia–Management. Marine parks and reserves–Australia–Management. Other Creators/Contributors: Bax, Nicholas J., editor. Hedge, Paul, editor. FRONT COVER: A hard coral in 10─20 m Marine Biodiversity Research Hub (Australia) depth reef habitat at the Houtman Dewey Number: 578.770994 Abrolhos Islands. Image: Reef Life Survey Contents

Chairman’s foreword ...... 1 Director’s overview...... 2 Knowledge brokering...... 5

Section 1: Protecting conservation values in the Commonwealth marine area ...... 7 The need...... 8 Canyons: identifying connectivity patterns for management ...... 9 Improving access to information about fish communities in Commonwealth marine reserves ...... 13 Exploring the origins of Australian marine diversity ...... 14 First maps of biodiversity across Australia’s seafloor ...... 16 Collating existing pressure data for the Commonwealth marine area...... 18 Assessing relative and cumulative impact on the marine environment...... 19 Biodiversity offsets in the marine environment...... 20 Potential for incentive-based management for marine conservation ...... 21 Landscape approaches for managing sharks and rays...... 22 Identifying important areas for pelagic fish...... 23 Predicting benthic impacts and recovery to support biodiversity management in the South-east Marine Region .....24 Collating existing survey data for Commonwealth marine waters ...... 26 Analysis of approaches for monitoring biodiversity in the Commonwealth marine area: Oceanic Shoals...... 27 Analysis of approaches for monitoring biodiversity in the Commonwealth marine area: Houtman Abrolhos Islands .... 30 Analysis of approaches for monitoring biodiversity in the Commonwealth marine area: Solitary Islands...... 32 Putting names to a sea of faces ...... 33 Marine monitoring blueprint: meeting a monumental challenge ...... 35

Section 2: Supporting the recovery of threatened, endangered and protected species ...... 37 The need...... 38 Populations and habitat use of euryhaline sharks and rays...... 39 Partnering with indigenous communities ...... 42 White Shark population and abundance trends...... 44 Estimating population size and characteristics of rare and endangered species ...... 46 Supporting the IUCN Red List ...... 48 Section 3: Management of Commonwealth marine reserves and the Great Barrier Reef World Heritage Area ...... 49 The need...... 50 Applying spatially balanced survey designs to monitor indicators in Commonwealth marine reserves ...... 51 Valuing the South-east Commonwealth Marine Reserves Network ...... 53 Surveys of Commonwealth marine reserves: Flinders...... 54 Southern Rock Lobster thrive in Tasman Fracture CMR ...... 56 Surveys of Commonwealth marine reserves: Geographe...... 57 Sand and granite reef communities revealed at Freycinet CMR...... 58 Surveys of Commonwealth marine reserves: Coral Sea...... 59 Shaping integrated monitoring for the Great Barrier Reef World Heritage Area...... 61

Section 4: International extension ...... 63 The need...... 64 Reef Life Survey global analysis of marine protected areas...... 65 Supporting biodiversity management across the globe ...... 67 Supporting Australian aid to Pacific islands and the Coral Triangle...... 68 Monitoring pelagic fish: from Australia to the Austral Islands...... 69

Science leader reflections ...... 71 Theme 1 – Keith Hayes: National monitoring evaluation and reporting ...... 72 Theme 2 – Tony Smith: Supporting management of marine biodiversity...... 73 Project profile – Peter Kyne, Barry Bruce: Supporting management and recovery of threatened species ...... 74 Theme 3 – Scott Nichol: National ecosystems knowledge...... 75 Theme 4 – Julian Caley: Regional biodiversity discovery to support marine bioregional plans...... 76

People and publications ...... 77 Researchers and staff, past and present ...... 78 Publications...... 82 IMAGE: Matt Curnock IMAGE: Geoscience Australia Ian Cresswell Chairman’s foreword • The Marine Biodiversity Hub has come a long way since The Marine Biodiversity Hub Steering Committee met formally five national research partners were successful in their twice each year. Its membership bid under the Commonwealth Environmental Research comprised an independent chairman Fund (CERF) in 2007. and representatives from each of the partner agencies, the National In 2011, the five partners expanded to seven and were again successful Environmental Research Program, in their bid under the National Environmental Research Program (NERP) the Department of the Environment which is reported on here. More recently, the now nine partners and stakeholder groups. received funding under the National Environmental Science Program (NESP). The expansion of the Hub, and its success in securing funding in a competitive environment, is testament to its increasing national Steering Commitee Chairman’s foreword scope and its alignment with the Department of the Environment to CHAIR Ian Cresswell deliver research that supports evidence-based decision making. As chair of the steering committee for the past eight years, I can attest HUB EXECUTIVE Nic Bax (Director) that it has been an interesting journey. By facilitating collaboration, the Paul Hedge, Vicki Randell Hub has significantly increased the impact of Australia’s major marine research partners, and improved the delivery of scientific information to PARTNERS help understand and solve national issues. Starting with the CERF Marine Australian Institute of Biodiversity Hub, the partners have developed a long-term strategic Marine Science portfolio to reach many stakeholders, as well as delivering directly to the John Gunn, Jamie Oliver Department of the Environment to support the design and planning of the Commonwealth Marine Reserves network. Learning to work more effectively Charles Darwin University Andrew Campbell with the Department and stakeholders has been a key outcome of the Hub. CSIRO Increased impact through collaboration with the Department was the raison David Smith d’etre for the NERP Marine Biodiversity Hub. The Hub research was better aligned to deliver directly to support the Department’s evidence-based Geoscience Australia Brendan Brooke, Adam Lewis decision making. Two new partners joined the Hub to increase our impact in north and north-western Australia, and to start what has become a Museum Victoria highly successful development of research supporting threatened species Tim O’Hara recovery plans. The NERP Hub has strived to understand how to best University of Tasmania provide the right information to individual managers in the Department, as Mike Coffin, Richard Coleman well as to associated agencies and industries. This work is ongoing and has University of Western Australia begun a journey toward fundamental change in the way researchers design, Malcolm McCulloch conduct and deliver research for greater impact on national decisions. STAKEHOLDERS It has been a fascinating and rewarding experience for me to help set that direction at the steering committee, and to support this growth in National Environmental the research partnership and the evolving relationship of the partners Research Program Dave Johnson, Naomi Dwyer, with the Department and other stakeholders. I have been fortunate to Genine Sutton have steering committee members able to leave individual interests at the door and work together to grow the research partnership. I Integrated Marine Observing System Tim Moltmann thank the many steering committee members for their inputs during the past eight years and wish the new NESP Marine Biodiversity Hub Australian Fisheries success under the new chairperson, Peter Cochrane. I will continue Management Authority to take a keen interest in how the Marine Biodiversity Hub evolves its Nick Rayns relationship with the Department and stakeholders and in doing so Department of the Environment fundamentally changes the way that research is developed and delivered Charlton Clarke, Lara Musgrave, to guide the major marine environmental challenges facing Australia. Chris Schweizer

NERP MARINE BIODIVERSITY hub • FINAL REPORT 1 Nic Bax Director’s overview • The overall objective for the NERP Marine Biodiversity Hub was Fisheries, the New South Wales Department of Primary Industries, to ‘provide scientific information and advice that will support the New South Wales Office of (the Department of the Environment) in decision making in the Environment and Heritage, and the marine environment, specifically to: Department of Fisheries Western Australia, in addition to IMOS. Other • implement and monitor marine bioregional plans; collaborators are listed on page 80. • develop the National Representative System of Marine To ensure relevant and appropriate Protected Areas (NRSMPA); research outputs, research leaders and especially the Hub Director and Director’s overview • support the information needs of the Environmental Knowledge Broker endeavoured Resources information Network (ERIN) and Approvals and to understand the decision making challenges that face departmental Wildlife Division (AWD); and officers, and the associated • provide key baseline information for the Heritage Division’. information needs. A peer-reviewed journal paper, essential to scientific For four years, the seven NERP Marine Biodiversity Hub partners have worked development, is of little direct use to closely with departmental officers, adjusting research and deliverables to a manager required to make rapid suit a changing policy environment. The research was coordinated by a decisions, unless the data have also Research Leadership Team comprised of theme and project leaders, and been provided in a form suitable representatives from all partners. This ensured the adoption of research for the internal information system. advances, such as the application by the Regional Biodiversity Discovery Consequently, the Hub Knowledge Theme of survey design approaches developed in the Monitoring Theme. Broker developed communication Stakeholder and partner representatives on the Hub Steering Committee products useful to departmental oversaw the program and provided guidance to the Director, and many officers and increased the managers’ collaborators have been integral to the research. Infrastructure provided capacity to use them. When the through the Integrated Marine Observing System (IMOS) was vital to the success Plan for a Cleaner Environment was of projects investigating seabed condition, while threatened species projects released in October 2013 setting the depended on the infrastructure and personnel resources of Northern Territory new government’s environmental management strategy, we mapped the Hub’s ongoing research to this new strategy (see figure opposite), and were encouraged to see that our research portfolio still met Australia’s marine biodiversity research needs. Scientists still frequently believe that good science will be adopted and are surprised when frontline managers have not used the latest available scientific information. This is because we often focus on what science can deliver, rather than what the customer wants. But what does the customer want? A clear summary of Departmental research priorities can be difficult to find. This is perhaps understandable as we are asking managers to step into our shoes and show us what ABOVE: Marine Biodiversity Hub surveys have provided baseline research they would find valuable. descriptions to support future monitoring of CMRs. What if, instead, we ask what

2 NERP MARINE BIODIVERSITY hub • FINAL REPORT Impact of research

Focus areas of research > Performance indicators for managing CMRs > National data catalogue for CMRs Drivers of research > Collating marine survey and pressure > Baseline surveys for the Flinders and Oceanic Shoals CMRs data for CMRs > Enhanced national capacity for sustained Commonwealth Marine > New surveys of selected CMRs data collection Reserve network (CMRs) > National capacity for sustained data > Blueprint for monitoring management collection in CMRs > National data catalogue for KEFs • > Baseline surveys for selected KEFs > Collating survey and pressure data for KEFs > Blueprint for monitoring EEZ ecosystems Marine Bioregional Plan > New surveys of selected KEFs > Tools for evidence-based decision-making implementation > Supporting evidence-based decision-making > Data collection standards for multiple sectors and jurisdictions

> Aligning management priorities with existing Reef 2050 monitoring > GBRWHA integrated monitoring framework > Integrating monitoring with management > Guidance to integrate monitoring for other marine regions or programs

Recovery of EPBC listed > Status trends and habitat use of species threatened species > More targeted and effective Director’s overview implementation of recovery plans > Evidence base for recovery of threatened sharks

is valuable in their daily routines? What decisions are made and what data A landscape approach to marine are routinely used? We have had good results using this approach. We management identified the areas have collaborated with the Department to develop a blueprint for marine used by multiple vulnerable shark ecosystem health monitoring in Commonwealth waters. We have worked species. Further management with ERIN and marine managers in the Department to map where and how attention in such areas could benefit data are used to support decision making. We have also led the development multiple species while reducing the of an integrated monitoring framework for the Great Barrier Reef World impact on fisheries, compared with Heritage Area. This intensive engagement driven by specific questions asked a species-by-species approach. A by departmental officers has required substantial effort and resources, second approach used predictions but has been instrumental in increasing the impact of research outputs. of the distributions and commercial uses of benthic habitats in South- Adapting to changing policies east Australia to estimate the impact The Hub’s efforts to help the Departmentimplement and monitor of alternative management tools marine bioregional plans met with mixed success. Ironically, some of (such as fisheries closures and CMRs) the research areas most tightly linked to departmental decision making on habitat destruction and recovery. – such as marine implementation of the revised offsets policy – have The tools and techniques developed been challenged by a changing policy environment. This is a reminder in these landscape projects are being that if our goal is to influence decision making, we cannot assume advanced outside the Hub to support that Department and stakeholder goals and objectives will remain commercial fisheries management. constant. Other areas have met with much more direct success. Threatened species research was We have improved the understanding of conservation values identified in initially focussed on projects that marine bioregional plans, including Commonwealth marine reserves (CMRs) would enable recovery plans to be and Key Ecological Features (KEFs). We have also cultivated the collaborations implemented more cost effectively. and developed the standardised approaches required to monitor CMRs and Euryhaline elasmobranchs were marine ecosystem health, and contribute to State of the Environment reporting. selected to examine whether new A marine blueprint is being developed with the Department to understand our genetic and telemetry approaches capability to monitor status and trends of marine biodiversity in deep waters, effectively support decision-making and the opportunities to extend that capability. This will provide a foundation and appraisal of recovery plans. for integrating existing and new monitoring programs to cost-effectively Early success with this approach support planning, regulation and management. It complements the integrated has led to its extension to White monitoring framework developed in collaboration with two other Hubs, the Sharks and Grey Nurse Sharks, and is Great Barrier Reef Marine Park Authority and the Queensland Government providing the first estimates of adult that has been incorporated into the REEF 2050 Long-Term Sustainability Plan. population size.

NERP MARINE BIODIVERSITY hub • FINAL REPORT 3 Ongoing developments existing museum samples indicate may soon enable measures that movements of the Earth’s of adult population size, tectonic plates contributed to and the size one generation ago, all from the speciation of marine fauna. • contemporaneous samples. This promises The Hub would not have achieved a fundamental change in the information that the successes that it has without can be provided on these threatened species. the many dedicated researchers in Our research capability built on earlier fisheries partner institutions, or without our research and supported the Department in decision- many collaborators. It is a pleasure making under the Environment Protection and Biodiversity Act 1999. for me to recognise the many and It supported the development and implementation of recovery plans, diverse inputs from such a talented the international convention in trade on endangered species and the and creative group of people. Finally, evaluation of potential impacts of proposed activities and developments. I would like to take the opportunity Hub research has helped the Department to develop the NRSMPA, providing to thank the Steering Committee baseline descriptions for CMRs (Oceanic Shoals, Flinders, Freycinet, Tasman which has unfailingly been available Fracture, Geographe, and Coral Sea) to support future monitoring. Robust to provide sound guidance that has Director’s overview survey designs were developed that will withstand both funding and oceanic improved the outcomes of the NERP conditions. Social and economic studies are helping to identify how the public Hub and laid the foundations for identifies with and values the marine environment and marine protected the NESP Marine Biodiversity Hub. areas, and how different forms of communication and information affect perceptions of management options. We had less success in working with the Department to operationalise management objectives for the CMR Research leadership team network, partly because the Department needed to focus on a changing policy environment that included the CMR Review. Adding to this was the Director challenge of prioritising management objectives for a representative network Nic Bax, UTAS covering more than a third of Australia’s Exclusive Economic Zone, from Knowledge Broker high tropical species richness in the north to high endemism in the south. Paul Hedge, UTAS Improving data access PROJECT LEADERS Data discovery and access has improved during the course of the Hub, Australian Institute of Marine Science contributing to the objective to support the information needs of ERIN and Julian Caley AWD (now Environmental Assessment and Compliance). We have worked Charles Darwin University with the Australian Ocean Data Network (AODN), the Atlas of Living Australia Peter Kyne and partners and collaborators to make data available soon after collection. At the same time we have helped to increase the relevance of these data CSIRO portals to environmental managers and researchers by enabling searches on Barry Bruce, Piers Dunstan, conservation values including CMRs and KEFs. National maps of pressures Keith Hayes, Tony Smith and how they have changed over time (aggregated to match the State of Geoscience Australia the Environment reporting cycle) are now available through the AODN and Scott Nichol will be an important input to State of the Environment 2016. We have also Museum Victoria developed a search tool that extracts previous survey information relevant Tim O’Hara to monitoring CMRs and the use of KEFs for monitoring marine ecosystem health. We have worked with ERIN to identify marine policy and management University of Tasmania decisions being made in the Department, and the supporting data portals Sarah Jennings and processes. Further work remains in this area, including through the PARTNERS National Plan for Environmental Information, but we are confident that we are developing a deeper understanding of the Department’s information University of Western Australia needs. Scientists’ information needs, including longer term data archival, Jessica Meeuwig are also being met through existing national research data infrastructure. University of Tasmania In providing key baseline information for the Heritage Division, Hub scientists Neville Barrett have developed new national datasets and classifications to identify and assess areas of natural heritage. An accurate map and classification of Australia’s 750 marine canyons (many previously unrecognised) will identify CONTACT canyons that may have higher biodiversity value. New national and global Nic Bax biogeographies provide the basis for moving beyond the Integrated Marine [email protected] (03) 6232 5341 and Coastal Regionalisation of Australia (IMCRA 4.0). New genetic analyses of

4 NERP MARINE BIODIVERSITY hub • FINAL REPORT Paul Hedge Knowledge brokering • Collaborative research conducted through the NERP Marine Understanding the nature of research projects, the policy setting, Biodiversity Hub provided evidence and advice to support the people and their capacity management decisions relating to the conservation values of for engagement was important. Australia’s marine environment. Research drivers focused on adaptive management and the monitoring and Knowledge brokering was integral to this process, ensuring projects evaluation of conservation value, were appropriately designed and scoped to meet the needs of end- and marine reserves were a focus users, in particular the Department of the Environment, and that results of collaboration, capacity building were provided in a format that would be used by decision makers. and, in some cases, co-production of project outputs. Policy drivers were Approach Marine Bioregional Planning, including A knowledge broker was appointed to help develop and exchange managing the CMR network, species brokering Knowledge knowledge between scientists and policy makers. The knowledge broker, recovery plans and REEF 2050. The also the Deputy Director of the Hub, worked closely with the Director and marine monitoring blueprint and the Research Leadership Team. A broad group of scientists, policy makers Great Barrier Reef World Heritage and communicators supported the exchange of knowledge, including Area monitoring framework are the Hub’s Steering Committee, project leaders, senior executives, policy examples of products that tailored the officers, marine reserve managers, technicians and data managers. best available science to meet policy Knowledge brokering under the NERP built on previous success with the objectives. Knowledge brokering Commonwealth Environment Research Facility (CERF) Marine Biodiversity Hub. also supported project leaders to Under the CERF program, knowledge brokering activities generally focused on forge relationships with end-users. informing and engaging scientists and policy makers so that scientific outputs Lessons learned could be understood and used. Under NERP, we extended this approach to inform, engage, collaborate and build capacity, regularly revisiting important Marine Biodiversity Hub scientists areas to ensure that the outcomes remained integral to Departmental and end-users, particularly activities. The five stages of knowledge brokering under NERP were: policy makers and managers from the Department, embraced • scoping and refining research projects in collaboration with the Department; and participated in knowledge • describing research outputs and indicators of impact to identify key users; brokering. This was most evident • communicating progress toward outputs to maintain engagement; in their commitment to plan and • delivery of outputs in an agreed format; and

• evaluating impacts on Departmental activities. BELOW: Marine reserves were a focus of collaboration and capacity building during the NERP Marine Biodiversity Hub. Images: Reef Life Survey (left) and University of Western Australia

NERP MARINE BIODIVERSITY hub • FINAL REPORT 5 implement strategies designed to inform, engage, collaborate and build capacity sensitivities and expectations for for applied marine research. The great example of this was the scoping and research in social and economic progressing of research to support plans for the recovery of listed species. disciplines was another challenging In these instances, well structured policy problems, clearly defined data and area (also experienced during the • information needs, and established relationships between researchers and CERF Hub). The knowledge broker policy makers, enabled effective engagement and knowledge exchange. also maintained the momentum of research collaborations affected Considerable capacity was built in the area of marine monitoring, particularly by restructures and staff changes in terms of understanding how policy and research are central to developing in the Department, a shared language and logic for monitoring and environmental reporting. and identified This is a challenging arena in which the interests and resources of policy opportunities to expand makers and researchers converge. Ongoing knowledge brokering will enhance agreed research outputs to the contribution of monitoring to evidence-based decision making. meet the needs of end users. The knowledge broker played an important role in interpreting the Australian Government’s environmental policies and conservation values for the marine CONTACT Paul Hedge research community. This was particularly important for projects operating in an [email protected] ambiguous, broad, or evolving policy context, such as marine offsets. Managing (03) 6232 5023 Knowledge brokering Knowledge

Building a framework for the world’s largest living structure

Establishing an integrated monitoring framework for the Great Barrier Reef World Heritage Area (GBRWHA) presented a significant knowledge brokering challenge amid tight timeframes set to meet processes under the Environment Protection Biodiversity Act 1999. Developing a more strategic approach to reef monitoring involved collating a wealth of information on management needs and 65 existing monitoring programs, and harmonising the needs and views of diverse specialists and stakeholders in the complex setting of adaptive management. Policy makers, scientists, and data and natural resource managers helped to define and prioritise steps towards integrating management and monitoring approaches, and distilled this into practical guidance applicable in any coastal or marine region. The guidance was subsequently applied to the GBRWHA to develop an integrated monitoring framework tailored for GBR managers. This provided the basis for further collaborative efforts to build the monitoring program (see story on page 61). Stakeholder commitment to participation has been vital to successful knowledge brokering in this project and has involved developing a shared language and logic for integrating monitoring, including the identification of key management and science inputs, essential monitoring functions and options for engaging experts and stakeholders. The monitoring framework contributed to the strategic assessment of the World Heritage Area in 2014 and is guiding development of a reef-wide integrated monitoring and reporting program to review the success of the Reef 2050 Long-Term Sustainability Plan (draft released for public comment in September 2014). It will build on and coordinate existing monitoring and reporting activities and will ABOVE: The Great Barrier Reef World Heritage Area. be linked to the outcomes and targets identified in the plan. Image: Great Barrier Reef Marine Park Authority

6 NERP MARINE BIODIVERSITY hub • FINAL REPORT Protecting conservation values in the Commonwealth marine area 1 Geoscience Australia IMAGE:

NERP MARINE BIODIVERSITY hub • FINAL REPORT 7 The need

Commonwealth marine areas are protected as a matter of national environmental significance under the Environment Protection and 1 Biodiversity Conservation Act 1999 (EPBC Act). The Australian Government has developed marine bioregional plans for five Commonwealth marine planning areas to help government and industry manage and protect the marine environment. The plans describe the marine environment and conservation values of each marine region, set broad biodiversity objectives, and identify regional priorities, strategies and related actions. Conservation values are defined in the plans as species or places that are listed under the EPBC Act, (such as threatened species or heritage areas), or Key Ecological Features considered important for a region’s biodiversity or ecosystem function and integrity. Marine Biodiversity Hub research on these conservation values is covered in this section of the report. Hub research on listed species is covered in Section 2, and research on Commonwealth marine reserves and the Great Barrier Reef World Heritage Area is covered in Section 3. Research was designed to contribute to the following strategies identified in marine bioregional plans: • provide relevant, accessible and evidence- based information to support decision-making with respect to development proposals that come under the jurisdiction of the EPBC Act; • increase collaboration with relevant industries to improve understanding of the impacts of anthropogenic disturbance and address the cumulative effects on the region’s key ecological features and protected species; and • improve monitoring, evaluation and reporting on ecosystem health in the marine environment. Responding to the need An important research focus was to make better use of existing physical and biological data to better understand biodiversity in the Commonwealth marine area. Museum collections were reinterpreted to characterise the spatial structure of marine habitats and communities at national scales and to identify prehistoric processes that influence contemporary biodiversity patterns. Further Protecting conservation values in marine the Commonwealth Protecting area data were used to identify habitats inside and outside CMRs that support multiple species of vulnerable elasmobranchs and may benefit from refinements to management. The impact of fisheries and biodiversity conservation management interventions in the past three decades on the predicted state of benthic communities was also investigated. Surveys were used to gather information about how the public values the marine environment, existing data were collated on environmental pressures and their potential for cumulative impact. Hub scientists worked to improve monitoring and reporting on ecosystem health through an enhanced understanding of KEFs and by extending Australia’s capabilities to collect and analyse relevant biological data in deep water environments. Finally, this new knowledge and capability was combined with an extensive review of existing data relevant to KEFs as input to a blueprint for monitoring ecosystem health. This was developed in concert with the Australian

Government Department of the Environment and other stakeholders. CSIRO IMAGE:

8 NERP MARINE BIODIVERSITY hub • FINAL REPORT Canyons: identifying connectivity patterns for management

Submarine canyons are areas of high biological productivity Approach and aggregating marine life, from deep-sea corals to foraging Tools and methods were developed blue whales. to examine the relationships between canyons, large-scale ocean 1 A better understanding of how the physical, biological and ecological currents and biodiversity values. New characteristics of canyons are shaped on a national scale would help to bathymetric maps were generated, prioritise their conservation and sustainable use. This project generated a and indicators of ocean productivity better understanding of how submarine canyons may influence biodiversity across the Exclusive Economic Zone patterns across marine regions, including within and between CMRs. It mapped (EEZ) were derived from time-series and measured Australia’s submarine canyons, classified their structure, and maps of sea-surface properties determined how they are linked: to each other, to the deep ocean, and to (temperature, chlorophyll-a, the continental shelf. A central question was whether all canyons functioned turbidity). Remote sensing similarly with respect to the physical processes that influence biodiversity. techniques were also used to define the spatial and temporal variability of Connectivity modelling enabled the strength and direction of population the Leeuwin Current, as a case study links between canyons to be examined: for example, whether the exchange is for the South-west Marine Region. upstream, downstream or both ways. The degree to which an area contributes Spatial statistical methods were to other areas is its source capacity; the degree to which it receives from used to classify canyon types (such other locations is its sink capacity. Canyons with high sink capacity encourage as shelf-incising and slope-confined) larval settlement, and are likely to have high resilience due to their strong and fish distribution patterns, to connectivity with larval sources. Canyons with a high source capacity examine relationships between can boost ecological resilience by exporting larvae to other locations. canyons, canyon types, and other seabed features, and to identify NATIONAL MAP OF SUBMARINE CANYONS IN RELATION areas of conservation priority. TO COMMONWEALTH MARINE RESERVES Protecting conservation values in marine the Commonwealth Protecting area : Geoscience Australia IMAGE

NERP MARINE BIODIVERSITY hub • FINAL REPORT 9 A new acoustic methodology that can consistently differentiate hard from soft substrate was developed to classify potential benthic habitats associated with canyons. A uniform scoring method was used to classify 1 epibenthic fauna in these habitats from seafloor video imagery (656,649 records from 12 voyages). Shelf- incising canyons were analysed and their habitat types and fauna compared to the surrounding slope, with the expectation that relatively high proportions of hard substrates and associated fauna would be found where canyons incise the shelf edge. An individual-based dispersal model (see story on page 12) was used to simulate the movement of marine larvae from the coastline to the 200 nautical mile limit of the EEZ (excluding external territories). Their connectivity – the degree of exchange between two ABOVE: Simulated dispersal of brittle star different populations or areas – was measured at local (canyon), regional larvae originating in north and north- and continental scales according to the scale of larval transportation. The western CMR waters for 2009–2012. model was used in case studies exploring the source/sink capacity of canyons Warm colours indicate relatively high in CMRs of the South-west and North-west marine planning regions. larval densities, and cooler colours show areas where lower larval densities are Key findings expected. Image: Geoscience Australia More than 750 canyons were mapped across the Australian margin, including Norfolk Island and Cocos Island Territories. This is many more than to be depth stratified and higher previously known. Almost 40% of the canyons were in a marine reserve, inside canyons. Seabed hardness was and of the 29 canyons that were identified as having high biodiversity value, an important habitat classifier for 24 are located in existing Key Ecological Features (KEFs) and CMRs. a large subset of the fauna. Based on the video imagery, the shelf Hard ground habitats in the 150-700 m depth range were both infrequent and incising canyons did not support quite highly variable between canyons for the 60 shelf incising canyons for significantly different epibenthic which data were available. Video imagery showed benthic epifauna abundance macrofauna when compared to other upper slope hard and soft substrate. Canyon-specific metrics of ALBANY CANYONS: CAPACITY TO ACT AS epifauna biomass and distribution, A SOURCE FOR MARINE LARVAE and finer taxonomic resolution of fauna, appear to be needed to resolve biodiversity distribution patterns within and outside canyons. This will be necessary for any prioritisation of individual features or areas for management attention. Protecting conservation values in marine the Commonwealth Protecting area A study of connectivity in the South- west Marine Region conducted as part of this project found the Albany Canyons off south-western Australia to be an important sink and source for marine larvae transported eastward by the Leeuwin Current. Twenty-five of the 81 Albany canyons had medium to high sink and source capacity: mostly the larger, topographically complex canyons such as Wilson and Bremer canyons, suggesting ABOVE: Albany Canyons showing the capacity for each canyon to act as a source for that these two canyons may have marine larvae, modelled for larval release across the South-west marine region a larger role in maintaining the in 2009 (represented by the grey dispersal cloud). Image: Geoscience Australia

10 NERP MARINE BIODIVERSITY hub • FINAL REPORT biodiversity of this area than the other canyons. The strong connectivity capacity for marine larvae. This of these Albany Canyons is driven by the Leeuwin Current and augmented variability in sink and source capacity by secondary flows that recirculate the larvae dispersal cloud westward, across a relatively small area reflects providing additional opportunity for larval settlement. Smaller canyons the ‘decay’ of the dispersal cloud to the east, at the downstream end of the current’s dispersal path, and along the direction of the Leeuwin 1 outside CMRs, tended to have a low relative sink and source capacity. Current and with distance offshore. Similarly, the shelf-incising canyons The individual-based model also showed that time-series earth observations that intersect Ningaloo CMR have are effective in mapping the Leeuwin Current and to quantitatively low sink capacity due to their weaker investigate the temporal variability of its oceanographic and geographical links with the Leeuwin Current. characteristics. The findings indicate that the Leeuwin Current has strong seasonal and inter-annual variation in its area of influence and cross-shelf New knowledge migration. The Leeuwin Current also has a significantly positive influence over the nutrient characteristics of the South-west Marine Region. and opportunities A study of canyons in the North-west Marine Region conducted as part of this Datasets and models produced in project focussed on canyons that intersect several CMRs offshore from Cape this project provide a foundation Range Peninsula (Gascoyne, Carnarvon Canyon and Ningaloo). The connectivity for targeted studies aimed at model showed a higher sink and source capacity for canyons in the northern testing/validating components half of the group, with most of those canyons intersecting the Gascoyne CMR. of the connectivity patterns In contrast, canyons within the Carnarvon Canyon CMR had low sink and source identified by the dispersal model. This project is producing a CAPE RANGE CANYONS: RELATIVE CAPACITY comprehensive assessment of TO ACT AS A SOURCE FOR MARINE LARVAE Australian canyons as habitat for benthic and pelagic species. The assessment is using biodiversity surrogates, (such as seafloor rugosity, upwelling strength and current velocity), to classify habitat complexity, productivity and disturbance. Geomorphometrics, (measures of seafloor complexity), such as canyon distribution and seafloor rugosity have an important influence on the movements of large fish predators over macro-ecological scales. The connectivity model and canyon maps can be used to identify data gaps and priority areas for future observations and sampling, either to reduce uncertainty in lesser known areas such as the North-west Marine conservation values in marine the Commonwealth Protecting area Planning Region, or to confirm the presence of locally important biodiversity values inside and outside the CMR network. The modelling can also explore connectivity patterns between marine regions and interdependent geographic regions, and reveal areas that may have a relatively higher role in maintaining the biodiversity of the area. For example, the models predict strong ophiuroid connectivity between the Oceanic Shoals and Kimberley CMRs. ABOVE: Cape Range Canyons showing the relative capacity of each canyon to act as a source for marine larvae, modelled for larval release across the North-west marine region for 2009 (represented by the grey dispersal cloud). Image: Geoscience Australia

NERP MARINE BIODIVERSITY hub • FINAL REPORT 11 Modelling connectivity

Outputs and outcomes Well-connected populations can ameliorate habitat The study produced national canyon and Leeuwin Current fragmentation by reaching 1 datasets in GIS format, a time series out to one another during MODIS dataset in GIS and remote difficult times. Connectivity also sensing formats, and a national- lets species reach previously scale point cloud database of unoccupied changing habitat, simulated marine larval dispersal. and can generate concentrated This database is incorporated in pockets of diversity through the connectivity model, and can be used to determine expected overlap and accumulation. levels of connectivity among This study developed an user-defined geographic areas and individual-based dispersal depths (such as CMRs and KEFs). model to simulate the A nationally consistent map movement and connectivity of canyons on the Australian of marine larvae in four margin, and maps of hard and soft dimensions (three-dimensional substrate for shelf incising canyons and compiled video annotation space over time). The model data, were also produced. This simulates the interactions of information can be used to billions of individual larvae develop a better understanding with their environment, of how topographic features enabling studies of their influence biodiversity patterns collective behaviour. in areas such as Ningaloo Reef, and can also be applied in studies Three-dimensional ocean of ecosystem processes, such as currents and larval behaviour studies of population connectivity are combined in the model to among these features. map the expected flow patterns Outputs from the connectivity (for a pelagic larval phase of model are publically available and 90 days). Australia’s national have been applied to a range of supercomputer at the Australian resource management challenges: by the Australian Fisheries National University performs Management Authority Slope ABOVE: Depth slices taken through three- the trillions of calculations Resource Assessment Group to dimensional larval dispersal clouds at the sea required, and the connections it investigate geographic stocks of surface (upper) and 3000–3500 m water depth traces can be sliced or grouped (lower) spanning the Gascoyne, Carnarvon Blue Eye Trevalla; by James Cook and Abrolhos CMRs. Warm colours represent by geography (such as canyons, University to study Wideband high larval concentrations. Note the broader marine reserve, Key Ecological Anemonefish; and by the University dispersal at the sea surface and trapping effect Protecting conservation values in marine the Commonwealth Protecting area Feature, or volume) and time. of Western Australia to study of canyons at depth. Image: Geoscience Australia coral dispersal from the Abrolhos Connectivity modelling can Islands. Cross-agency information help to guide management sharing and collaboration has also decisions by detecting covered science-management interdependent areas such communication, ocean currents and upwelling processes. as clusters of canyons, exchanges between regions, CONTACT and areas of high ‘source’ Scott Nichol capacity. It can also point to [email protected] critical links that maintain the (02) 6249 9346 resilience of marine systems, and predict the potential spread of invasive species.

12 NERP MARINE BIODIVERSITY hub • FINAL REPORT Improving access to information about fish communities in Commonwealth marine reserves

Under the Integrated Marine and Coastal Regionalisation of Australia (IMCRA v4.0), Australia’s marine environment was classified into bioregions that make sense ecologically and are at a scale useful for regional planning. 1 The bioregions under IMCRA were an important input to Australia’s marine bioregional planning program and the subsequent identification of a network of Commonwealth marine reserves. Fish distribution data were an important part of IMCRA’s classification process. This project has improved the accessibility and utility of existing and new information about fish distributions for environmental managers, scientists and the general public. This is expected to support the understanding of biodiversity values in Commonwealth marine reserves, in Key Ecological Features (KEFs) and across broader Commonwealth waters. Approach NERP Marine Biodiversity Hub scientists worked with the Atlas of Living Australia (ALA) to compile, centralise and streamline access to existing fish data derived from field research and museum collections. The project drew on an improved knowledge of historic and present-day processes that relate to marine fish distributions (developed in associated research). The resulting data extend the knowledge-base to more than 4500 species of marine fishes. Data are being made available through the FishMap search interface previously developed by CSIRO and the ALA. Outputs, outcomes and opportunities FishMap generates customised, illustrated lists of fishes by area, depth, family or ecosystem that can be used for research, planning, management, fisheries, conservation, recreation and citizen science. It is the only resource of its kind in the world that covers virtually all species of marine fish found in the marine waters of an entire continent. The service is being revised to include further data compiled within the NERP program that are relevant to support assessment and monitoring of CMRs and KEFs. For example, information on fishes within each reserve in the CMR network and KEFs will include the number of families, genera and endemic or listed species, and species of commercial interest. The continuing development of FishMap and the underlying datasets can provide tools to generate slices of data tailored for environmental managers: for example, endemics only, species represented in only one

CMR, or species with a high proportion of their range within CMRs. conservation values in marine the Commonwealth Protecting area Tailored lists of fishes within each of the CMR reserves will highlight each area’s unique values and contributions to conservation management. This can help to identify key species for demographic and genetic connectivity assessment (whole-of-organism approach) across CMRs, and circumstances in which off-reserve management would support conservation and sustainable-use objectives. A wide range of information is available only to scientists or other specialists. Making data publicly and freely available through FishMap and the ALA is an example of the Hub’s provision of broader access to scientific data: through interpretation and synthesis, and more accessible methods of data delivery. ABOVE: Examples of tailored maps and lists generated by FishMap, in CONTACT this case for the Zeehan CMR. Daniel Gledhill [email protected] (03) 6232 5363

NERP MARINE BIODIVERSITY hub • FINAL REPORT 13 Exploring the origins of Australian marine diversity

An evolutionary understanding of Australia’s marine fauna can help to explain modern biogeographic patterns and assess the 1 vulnerability-risk of fish families to present and future change. Historical climatic and geological processes, as the architects of evolutionary change, offer a means of predicting the environmental conditions that promote changes in distribution, extinction or persistence. Because of its geological, climatic and geographic history, the Indo Australian Archipelago (IAA) is an ideal arena for examining the origins, speciation, diversification and colonisation of species across ecological climatic gradients, particularly in coastal habitats. This project used selected fish families from the IAA and southern Australia to examine large-scale geological events or climatic changes that occurred millions of years ago, (such as the collision of the continents, or rising sea levels) for their influence on species creation and distribution. The findings highlight Australia’s iconic endemisms: a the origins of Australia’s endemic marine fauna and the role of the continent persistent source of diversity as a biodiversity reservoir, from geological periods to the present day. Southern Australian endemic Approach fish in the family Labridae (genus Notolabrus) were estimated to Specimens from the CSIRO Australian National Fish Collection were tissue- have evolved six million years ago. sampled for DNA extraction and sequencing to evaluate the genetic distances Monacanthids (leatherjackets) among species. Species evolution was placed into a timescale by calibrating diverged as early as 16 million the phylogenies with fossil records and a molecular clock to identify peaks of years ago, possibly in parallel with speciation or extinction. (The molecular clock hypothesis asserts that molecular Australian labrid taxa. On the sequences evolve at a relatively constant rate, so genetic differences between other hand, the stingarees, genera species can be related to the time since they last shared a common ancestor.) Urolophus and Trygonoptera (family The resulting calibrated phylogeny is a reconstruction of the evolutionary Urolophidae), began speciation history of each taxonomic group. Additional evidence, such as species in the late Oligocene (27 million distributions and habitat associations, were used to identify functional shifts. years ago). Modern members of these groups, such as Urolophus Key findings bucculentus and U. flavomosaicus Australia and the mega diversity of the Indo-west Pacific appeared as recently as two million years ago. Patterns of sympatric The maskrays, genus Neotrygon (Dasyatidae), originated following the diversification (along latitudinal collision of the Australian and Eurasian plates, with the ancestral, narrow- gradients) and parapatric speciation, ranging endemic species appearing Austral in origin. Evidence from (gradual speciation from populations the Neotrygon kuhlii species complex, the most derived and dispersed with overlapping zones of contact), group of the genus, suggests that mid-Miocene (15.7 million years ago) assisted by depth preferences, and Plio-Pleistocene falls in sea level (2–5 million years ago) may have were common, suggesting local accelerated species formation. Genetically distinct lineages survived in speciation supported by sea level isolated refugia following the geographic fragmentation of a once large, fluctuations and habitat preference. continuous population into distinct genetic variants of different colours. Protecting conservation values in marine the Commonwealth Protecting area The tuskfishes, genusChoerodon (Labridae), diverged from their New knowledge ancestral group, the Odacines, when extensive shallow water habitats Glaciation cycles of the Pleistocene formed at the onset of the Miocene (20 million years ago). Today, the had important biotic consequences widespread species in the group occupy a broad range of habitat types, in temperate and tropical waters, with peripheral endemics in specialised reef or non-reef habitats. causing range shifts, extinctions and the formation of unique endemic Platycephalid flathead subfamilies Onigociinae and Platycephalinae diverged species. Sea-level fluctuations in the Eocene (35 million years ago) into mainly tropical and temperate in the past two million years, species. Onigociins appear to have remained in the tropics and diversified however, have not significantly since the early Miocene, while Platycephalins remained in temperate accelerated the evolution of regions with only a few derived taxa reaching the tropics, possibly reaching groups such as the temperate the tropical Indo West Pacific from the Australian continent via tectonic wrasses and leatherjackets, and the rafting and shallow-water environments. Centrifugal speciation appears stingarees. On the contrary, since to have shaped diversity in both subfamilies across tropical regions.

14 NERP MARINE BIODIVERSITY hub • FINAL REPORT LEFT: A fossil of an extinct ray. The maskrays originated after the collision of the Australian and Eurasian plates and their speciation may have been accelarated by falls in sea level millions of years ago. Image: John Adamek

diversification was static for the past Outputs and outcomes two to three million years, it appears This project mapped the origins of that extreme climatic events over selected Australian marine fauna, geological time scales were necessary in particular its endemic species, to achieve radical modifications in 1 providing knowledge that may the distribution and composition help to guide realistic expectations of Australia’s unique fauna. for long-term sustainable Under the present-day climatic management of Australia’s marine scenario, range shifts have been natural resources. The Australian detected for some Australian marine continent emerged as a reservoir of species, especially with the southwards biodiversity for the indo-Pacific in penetration of boundary currents. geological periods and as a Noah’s This could represent the beginning Ark’ for biodiversity in modern days. of rapid and drastic shifts in Australia’s marine biodiversity, however accurate A conceptual framework and estimates of the severity of climatic alterations necessary for new species to practical toolkit (molecular develop, or for existing species to vanish, cannot be realistically determined. markers, genetic analysis protocols, The genealogical history in each of the analysed fish groups was biogeographic inference and influenced by multiple geological and climatic episodes. Each episode modelling) has been created that is has left a distinct signature in the groups’ ecological function, transferable to other marine groups. morphology and genome. The patterns observed point to the integrative importance of environmental affinities, ecological conditions and CONTACT biotic interactions in shaping modern biogeographic patterns. Nikos Andreakis [email protected] Synchronic speciation and the comparable biogeographic patterns (07) 4753 4124 in Australia’s wrasses, leatherjackets and stingarees demonstrate the evolutionary and tectonic stability of the Australian southern marine platform over geological times and the importance of Australia’s unique fish endemisms to the global marine diversity.

MAJOR GEOLOGICAL EVENTS AND THE TIMING OF DIVERSIFICATION WITHIN THE LABRIDAE, MONACANTHIDAE AND UROLOPHIDAE

Notolabrus species Labridae Monacanthidae Urolophidae

Monacanthid species

Monacanthid genera

Diversification stasis Urolophus / Trygonoptera Urolophus – Trygonoptera species

PALEOCENE EOCENE OLIGOCENE MIOCENE PL – P - H

60 MYBP 50 40 30 20 10 0 conservation values in marine the Commonwealth Protecting area Oi-1 Glaciation Mi-1 Glaciation Deeping of the Tasman gateway Collision between Australian and South-East Asian plates Breakup of Australia and Antarctica

Opening of the Drake passage Australian plate collides with Ontogon Java plateau Periodic glacial extensions

Development of the Antarctic circumpolar current

ABOVE: Selected fish families from the Indo Australian Archipelago were used to examine large-scaleFigure geological 2. Schematic events representation or climatic changes of main that geological occurred events millions and of the years timing of diversi cation within Labridae, Monacanthidae and ago for their influence on species creation and distribution.Image: Nikos Andreakis Urolophidae. Plate tectonic evolution of the last 60 MY are extracted from the literature (Hall, 2002). (plate tectonic evolution of the past 60 million years from Robert Hall, 2002). NERP MARINE BIODIVERSITY hub • FINAL REPORT 15 First maps of biodiversity across Australia’s seafloor

Few national maps of marine biodiversity exist for Australia. data suggest that species on the abyssal plain have relatively recently evolved Marine planning, and assessments of potential developments from those on the continental slope. and conservation actions therefore have been based on a 1 Seafloor communities within each limited biological dataset. depth biome are structured into This project accumulated new and comprehensive biological datasets for latitudinal bands (tropical, temperate, the Australian Exclusive Economic Zone (EEZ) including Antarctica, from polar). Within each of these bands depths of 0–2000 m. The datasets provided the basis for mapping seafloor there are variations in community fauna and species richness and turnover across the EEZ and neighbouring composition by longitude and waters, and determining the best way to interpolate species distributions habitat. In shallow water, the south- from existing records. It also examined the role of environment and history western fauna differs by up to 50% in forming biological communities, mapping evolutionary diversity, and from the south-eastern fauna. identifying areas with clusters of phylogenetically distinct species. On the shelf and upper slope, species The mapping contributes an improved knowledge and understanding of offshore richness peaks at tropical/subtropical seabed communities and can be used to identify areas of biological and genetic latitudes for both taxonomic groups, diversity that may require special consideration during planning decisions. It declining at temperate latitudes, also supports future updates to the marine bioregionalisation for Australia. and substantially declining at polar latitudes. The pattern is different Approach on the middle and lower slopes and Australian and overseas museum records, international databases, and the abyss, where species richness taxonomic literature were collated into a comprehensive distributional dataset peaks at temperate latitudes. for two groups of benthic invertebrates: brittlestars and squat lobsters. Species at bathyal depths (200–2000 m) Distributional datasets were analysed to map species richness and species can occur across extensive longitudinal turnover around Australia, taking into account the variation in sampling ranges. For example, the seamount density and collection techniques between different regions. A genetic fauna of Tasmania is closely related dataset was developed at the same time for these groups to ensure that to seamount faunas around southern conservation activities can prioritise taxa in divergent evolutionary lineages. New Zealand, and species on the A synthesis of the distributional and phylogenetic datasets will be mapped as southern Australian continental slope a means of incorporating phylogenetic diversity in conservation planning.

Key findings BELOW LEFT: This shallow water crab Depth (or rather correlated factors such as pressure and temperature) is species (Liomera edwardsi) was collected in the Oceanic Shoals CMR off northern the first order environmental predictor for species turnover/community Australia, and is widely distributed composition on the seafloor. Fortunately, this means that fine-scale bathymetry across the Indo-West pacific. It may data can be used as a (partial) surrogate of community composition. represent a cryptic species complex. Communities on the continental shelf and slope have evolved independently. BELOW: Uroptychus spinirostris is an endemic These two biotas should be considered as inhabiting separate biomes, although species of squat lobster that occurs across northern Australia at about 400 m depth. they can overlap at outer shelf/upper slope depths (100–400 m). Preliminary Images: Anna McCallum, Museum Victoria Protecting conservation values in marine the Commonwealth Protecting area

16 NERP MARINE BIODIVERSITY hub • FINAL REPORT are also found at similar depths around New Zealand. The hard substratum Outputs and outcomes fauna on the Macquarie Ridge is more related to the seamount faunas of south- Maps of seafloor fauna and species eastern Australia and New Zealand than to seamounts adjacent to Antarctica. richness and turnover have been ‘Species’ with extensive bathymetric ranges are often composed of suites of developed for the Australian EEZ 1 cryptic species, each distributed into their own depth band. The magnitude and neighbouring waters, providing of bathyal diversity has almost certainly been considerably underestimated. an improved knowledge base for identifying, assessing and managing New knowledge and opportunities biodiversity in Commonwealth Datasets collated in this project can be used to predict seafloor waters. A deeper understanding of community composition in most unsurveyed areas of the Australian EEZ. the origins of selected Australian Exceptions include the Cocos Keeling and Christmas Island territories marine fauna can help to explain and the entire EEZ at lower bathyal to abyssal depths (3000–6000 m). modern biogeographic patterns and They can also contribute to the future refinement of the Integrated assess the potential impacts of future Marine and Coastal Regionalisation of Australia (IMCRA) classification change (see story on page 14). scheme, a spatial framework that supports bioregional planning. CONTACT MODELLED SPECIES TURNOVER Tim O’Hara [email protected] (03) 8341 7441

LEFT: Modelled species turnover across the EEZ and Antarctic Territories. The darker colours indicate areas of most rapid species change. Image: Skipton Woolley, Museum Victoria.

BELOW LEFT: This species of brittle-star (Astrogymnotes hasmishi) lives upside down with its back to the host corals.

BELOW: Sigsbeia oloughlini, a new species described from the continental shelf off Esperance, Western Australia. Australia’s shelf and slope fauna are not well known. Images: Caroline Harding, Museum Victoria Protecting conservation values in marine the Commonwealth Protecting area

NERP MARINE BIODIVERSITY hub • FINAL REPORT 17 Collating existing pressure data for the Commonwealth marine area

Understanding the pressures on the marine CHANGE IN SEISMIC SURVEYS environment and their change over time is an important part of developing and prioritising 1 management actions. In the past, however, pressure data have not been collated, nor provided in formats that made them easy to compare. In addition, commercially sensitive data have often not been available for general display. This project mapped environmental pressures in Commonwealth waters (such as fishing, shipping, seismic surveys and oil and gas infrastructure) on a national scale and identified the associated risks and impacts in relation to marine biodiversity. The resulting capacity to assess the impacts of human activities on the marine environment will help the Department of the Environment to assess cumulative and relative impact and risk, and support the implementation of marine bioregional plans. SHIPPING ACTIVITY AND SEISMIC SURVEYS Approach Existing data and information on key threats were sourced from the Commonwealth Environment Research Fund Marine Biodiversity Hub (the forerunner of the NERP Hub), national bioregional planning, CSIRO marine indicator and threat mapping projects, the Integrated Marine Observing System and the Australian Fisheries Management Authority. The data were analysed or aggregated to improve interpretation. For example sea-surface-temperature data were analysed and presented as long-term change, and commercial fisheries data were aggregated to obscure individually-confidential data points. The distribution of pressures was mapped, and options were explored for SEA-SURFACE TEMPERATURE CHANGE combining qualitative and quantitative analyses of impact. Approaches and statistical tools were developed to investigate interactions between biodiversity assets and pressures and between multiple pressures as a stage in the development of cumulative impact indices. New knowledge and opportunities A simple data viewer was developed and deployed on the NERP Marine Biodiversity Hub website to provide simple access for Departmental staff to all the outputs of the Hub, including the pressure maps. Pressure maps were aggregated and displayed in five-year bins to match the State of the Environment reporting interval and to allow Protecting conservation values in marine the Commonwealth Protecting area straightforward assessment of whether the footprint for individual

pressures had increased or decreased in the past few decades. ABOVE: Examples of collated pressure data for Outputs and outcomes Commonwealth waters (from top). Images: CSIRO Change in seismic surveys (red: pre-1996; One hundred and twenty six different layers of pressure data, blue: 2006─2010). The collated data show the with associated metadata records, have been collated for the extensive surveying done before 1996, and Commonwealth Marine Reserve network. They include summaries the reduced seismic footprint in later years. of the current status of oil and gas extraction and infrastructure, All shipping activity for shipping greater than seismic surveys, shipping movements, aquaculture leases, pollution 200 tonnes around Australia: 2006─2010 (green events, trends and variability in changes on ocean temperature. The to red, low to high activity) and the sum of all data have been archived on the Australian Ocean Data Network to the seismic surveys for the same period (blue). ensure their long-term availability to Departmental databases. Estimated sea-surface temperature average long-term linear change, (°C per decade). Areas CONTACT of orange and red indicate warming during Piers Dunstan 1993–2013 (south-western Australian and eastern [email protected] Tasmania); areas of green and blue indicate cooling (03) 6232 5382 (eastern Australia and northern Australia).

18 NERP MARINE BIODIVERSITY hub • FINAL REPORT Assessing relative and cumulative impact on the marine environment

Pressures on the marine environment are steadily increasing low cost approaches to more complex and costly approaches. with new uses including renewable energy and new pressures This hierarchical approach to including warming and more acidic seas. estimating cumulative impact supports timely decision making 1 Some of these pressures will threaten conservation values and the impacts can be cumulative. Predicting the location and magnitude of these based on available information, impacts can be challeging. A scientifically robust and pragmatic approach enabling additional scientific is needed that can estimate the overall cumulative impact of pressures, understanding to be incorporated as well as detect how different pressures contribute to the overall impact when available, and identifying (their relative impact). This will provide managers and regulators with potential research investments. information to underpin policy, regulatory or management responses. In this project, fisheries and biodiversity conservation scientists worked New knowledge with the Department of the Environment to examine and advise on the and opportunities development of cost-effective approaches to understanding and estimating The application of many tools cumulative impact on marine biodiversity assets in South-east Australia. and approaches for assessing cumulative impact is limited by Approach the availability of knowledge, data The project team identified three broad approaches that have been applied and resources, and uncertainty. It to understand and estimate cumulative impact on biodiversity assets might be desirable to have a single on the continental shelf in South-eastern Australia: expert elicitation, tool that could always be used to qualitative mathematical models and quantitative mathematical models. meaningfully assess cumulative Expert elicitation is a relatively simple, low cost approach used by the impact and attribute relative Department in marine bioregional planning to assess the potential for impact, but the circumstances in cumulative impact on conservation values, including biodiverse submarine which this is possible are limited. canyons and shelf rocky reefs (identified as Key Ecological Features). The hierarchical approach developed Qualitative mathematical models were used by CSIRO to identify ecological here provides a framework for indicators sensitive to cumulative impact on submarine canyons and shelf identifying the minimum set of reefs. They identified important ecosystem components, and how these are tools required to understand the linked and affected by pressures. High-resolution statistical models were used potential for cumulative impact to retrospectively predict the cumulative impacts of 20 years of trawling on and progress to more sophisticated demersal fish communities on the continental shelf of South-eastern Australia. approaches to assess cumulative and relative impact where this is An examination of these three approaches highlighted their relative required and possible. For example, strengths and weaknesses in terms of simplicity, cost, data requirements the project identified three different and uncertainty. It also demonstrated how each approach can complement processes to produce a three-level each other when arranged in hierarchical manner, from simple, rapid and hierarchical approach to assess the 20-YEAR CUMULATIVE EFFECT OF TRAWL FISHERIES cumulative impact of trawling. Outputs and outcomes Collaboration with the Department

and fisheries scientists has conservation values in marine the Commonwealth Protecting area enabled the Hub’s researchers to propose a hierarchical approach to understanding and estimating cumulative impacts and relative impacts that is scientifically robust, practical and incorporates tools already used to inform decision making processes.

CONTACT Piers Dunstan [email protected] (03) 6232 5382 ABOVE: The 20-year cumulative effect of trawl fisheries on four groups of demersal fish species. Darker areas indicate higher cumulative impact. KEFs identified in the south east are overlaid in green.

NERP MARINE BIODIVERSITY hub • FINAL REPORT 19 Biodiversity offsets in the marine environment

On land, biodiversity offsets are an established instrument ABOVE: Choice modelling elicited community preferences for offsetting for reconciling economic development with biodiversity in relation to seagrass habitat in WA conservation. In the marine environment, however, the waters. Image: Curtin University 1 potential is still being explored. threshold level of damage to occur This research examined issues associated with the design and implementation before requiring offsets, (depending of marine biodiversity offsets. First, the performance of offset strategies on their perception of habitat status). (comprising a management approach and offset objective) when cumulative impacts are present, and second, community preferences for aspects of Respondents had strong preferences offset design (such as location/distance from the impacted site and direct for offsets close to the original or indirect offsets). The effect of offsetting on developers’ social licence to project, and a strong aversion to operate was also explored. These issues are pertinent to agencies responsible shifting the offset overseas, even if for conserving marine biodiversity and regulating activity, particularly the costs of implementing the offset given the complexity of the marine environment, uncertainty around were much lower there. Distant impacts, and increasing pressures and demands for use. Such issues have offsets were only acceptable if the potential to generate community concern about resource allocation. the pay-off (additional shorebirds protected) was sufficiently high. Approach Also, respondents were willing Different approaches and methods were used to address each issue. A simple to accept protection of a smaller socio-ecological model was used to simulate the effect of annual development number of endangered shorebirds projects occurring over five consecutive years on habitat and resource recovery, as compensation for losing numbers human utility and offset costs under four different offsetting strategies. Choice of common species. Indirect offsets modelling was used to elicit community preferences for biodiversity offsets (such as research and education) for migratory shorebirds (Queensland and Western Australia) and seagrass were considered acceptable if more (Western Australia), and a four-dimensional framework was used to evaluate birds were protected as a result. the effect of offsetting on the Western Australian oil and gas industry social Offsetting does not have a negative licence to operate. Data were collected through online public surveys. effect on a developer’s social licence to operate, (conditional Key findings upon the offsets achieving the Socio-ecological modelling highlighted the importance of adopting an offsetting stated ecological outcomes). approach that either took a strategic assessment approach to development approvals, or explicitly accounted for cumulative impacts in project-by-project Outputs and outcomes assessments. The link between alternative offsetting approaches and the This research has begun building distribution of offset costs across developers was also shown. A novel aspect of the knowledge required for the the research was that it accounted for the possibility that societies may allow a effective design and implementation of offsets in the marine environment. MARINE SYSTEM OFFSET MODEL The socio-ecological marine system offset model is being enhanced to biological resource society address additional questions, such as the uncertainty assumptions under ecosystem Protecting conservation values in marine the Commonwealth Protecting area which offsets portfolios are designed. services Research on public attitudes to offsetting, including its effects on management social licence to operate, and on preferences for offset attributes, can help policy makers, managers offsets and developers identify socially habitat developer acceptable approaches. It can also contribute to communication and education strategies that align biological sub-system human sub-system public preferences for offsets with ABOVE: The marine system offset model links biological and human systems. environmental effectiveness. The arrows denote positive effects, and the lines ending in dots denote negative ones. The habitat element supports a biological resource exploited by society in a predator-prey relationship. Habitat is damaged by development, but may be CONTACT remediated by offsets. The relative strength of this remediation is determined by Sarah Jennings management, which in turn is influenced by a social process that allows a threshold [email protected] level of ecosystem service loss before offsets are required (dashed blue lines). 0459 069 250

20 NERP MARINE BIODIVERSITY hub • FINAL REPORT Potential for incentive-based management for marine conservation

Incentive-based management is increasingly being used to manage industries that interact with the environment. Fundamental to the concept is the notion that environmental damage could be reduced if the costs were borne by the individual or industry 1 responsible. Appropriate incentives – either an explicit price (such as a tax) or a market-based opportunity (such as a tradeable quota) – can provide efficient ways to reduce or limit environmental damage. Incentive-based marine management has largely been limited to fisheries quotas. These have been applied to limit turtle and mammal bycatch in the United States, Canada and New Zealand with mixed success, partially due to quota type and low-frequency species interactions. Some tourism-based industries pay a bond to operate in environmentally sensitive areas (such as dive and day-trip boats in the Great Barrier Reef). ABOVE: Some tourism-based industries, such as dive and day boat trips in This research explored the potential for incentive-based the Great Barrier Reef, pay a bond to management to limit environmental damage in two areas: the operate in environmentally sensitive dumping of dredge spoils at sea, and interactions between areas. Image: Matt Curnock fisheries and high-conservation-value species and habitats. In the case of fisheries environmental Approach and methods impacts, the optimal incentive-based The research was largely review-based, with a qualitative assessment of management measure depended how a range of existing Commonwealth and State incentive-based measures on the frequency of impact and the may work (in the dredging and fishing industry), and an exploration of how impacted matter. For infrequent different instruments might change these incentives. International experiences bycatch species (such as seabirds), a in marine environmental management were also reviewed. In the case levy based system was most likely to of fisheries impacts to habitats and species, most reviewed studies were be effective, but this approach has largely theoretical or model based, as relatively few countries have adopted had little international application incentive based management approaches for non-target species or habitats. internationally due to a reluctance to use tax-related management Key findings measures. In contrast, for high- In the case of dredging, Commonwealth and State legislation is largely frequency bycatch species, individual based on a permit system, the granting of which depends on the expected quotas offered benefits. For habitats, environmental impact. Once approved, it generally provides no incentives assurance bonds and/or insurance to minimise the quantity of spoils dumped at sea. In some cases, limits on based systems were most appropriate the amount of spoils are set as part of the approval process. Based on other when impacts were relatively studies, a combination of a bond and levy based system to provide incentives to infrequent. Model based analyses minimise the impact (in terms of volume and where dumped) was considered suggest individual habitat quotas an optimal outcome. An offset system should form part of the package. were likely to be most suitable when impacts were likely to be frequent.

RELATIONSHIP BETWEEN THE FREQUENCY OF IMPACT conservation values in marine the Commonwealth Protecting area AND THE MANAGEMENT APPROACH Outputs and outcomes This research has clarified the management measure potential of incentive-based measures frequency of impact bycatch habitats as tools for policy makers. It has infrequent charge/penalty assurance provided guidance on incentives (low divisibility for quota) bonds/insurance faced by commercial operators with respect to unpriced outputs of the production process, and the measures available to manage these, as well as mixes of incentives appropriate for specific circumstances. quota (better divisibility/too many individual frequent notices to issue penalties) habitat quota CONTACT Sean Pascoe ABOVE: Individual quotas can offer benefits for managing [email protected] high frequency impacts on bycatch species and habitats. (07) 3833 5966

NERP MARINE BIODIVERSITY hub • FINAL REPORT 21 Landscape approaches

for managing sharks EAGLE RAY DISTRIBUTION IN SOUTH-EASTERN and rays AUSTRALIA Many species of sharks and rays are slow-growing, long-lived, and have low rates of reproduction. These characteristics make them vulnerable to the impacts of 1 human activities, and populations can take decades to recover once they have declined. Nine species of sharks and rays are protected in Australia under the Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act), and the population status of more than 10 further species offers cause for concern. Marine spatial planning for sharks and rays is challenging because many species traverse inshore areas managed by different states, offshore waters managed by the Commonwealth, and spatial closures covering both. Cost-effective, integrated spatial management requires identifying areas in which several species co- occur. Importantly, proposed management measures for individual species need TOP: Eagle Ray distribution in south-eastern to be jointly evaluated as they could help one species while harming another. Australia. Green: adult core range; orange: adult minor range. Image: Ross Daley Approach ABOVE: The Eagle Ray, Myliobatus This project improved species mapping, identified areas shared between tenuicaudatus. Image: CSIRO species, and measured the overlap with existing marine spatial planning areas, with a focus on temperate waters off south-eastern Australia. New knowledge Species maps from the Atlas of Living Australia were improved using and opportunities updated seafloor bathymetry overlaid with fishery catch data (where Many species of sharks and rays available). The maps were refined in workshops attended by 23 specialists share similar breeding grounds, who also helped to group species according to movement patterns. feeding grounds and corridors. It is possible to gain better management Shared areas were mapped by overlaying species maps in each group. outcomes by integrating existing This simple, biogeographic approach avoids some of the (time and areas identified for marine spatial spatial) scale issues with alternative approaches. For example, while planning with areas used by many geomorphology has been used as a proxy for critical habitat, shark breeding species. This would improve the and foraging ranges occur at finer scales than the available mapping. general conservation of sharks Key findings and rays while limiting reductions in resource access. Marine Common corridors, feeding patches and breeding patches were identified spatial planning alone is not a full around temperate Australia. Several feeding patches were within CMRs, and solution, however, and corridors most breeding areas were in state waters. Corridors stretched for hundreds of will be difficult to manage. kilometres and these are only partially protected by marine spatial planning. The landscape approach was found to have higher utility for benthic sharks, Outputs and outcomes skates and rays, which often are overlooked in conservation activities This project generated improved such as recovery planning. It was species maps and maps of common

Protecting conservation values in marine the Commonwealth Protecting area not as useful for highly migratory corridors, feeding patches and species such as white sharks. breeding patches, identifying areas used by many species that will assist future fisheries and biodiversity management.

CONTACT Ross Daley [email protected] (03) 6232 5352

The Scalloped Hammerhead Shark, Sphyrna lewini. Image: CSIRO

22 NERP MARINE BIODIVERSITY hub • FINAL REPORT Identifying important areas for pelagic fish

Seabed features such as canyons, seamounts, banks PREDICTIONS OF PELAGIC FISH ABUNDANCE and shoals provide aggregation points for ocean (pelagic) predators such as tunas and mackerels. 1 Learning more about this relationship can offer insight into the distribution patterns of these wide-ranging species, and may present opportunities for monitoring programs and the assessment of management initiatives such as Commonwealth Marine Reserves (CMRs). This research sought to identify relationships between pelagic predators and seabed geomorphology to support the management and monitoring of conservation values inside and outside the CMR network. Approach A literature review assessed knowledge of predator dynamics in relation to seabed geomorphology. Of particular interest were relationships between predator species and seabed features and methods used to quantify these relationships, as well as the use of landscape metrics (standard measures) by ecologists. Model simulations determined which metrics best captured seabed complexity and showed promise for monitoring the responses of predators to seabed features. The distribution of oceanic predators such as tunas and mackerels was modelled in relation to seabed geomorphology such as canyons to find continental-scale patterns in marine biodiversity. Key findings The study of long-term commercial catch data off Western Australia found geomorphology to be a key predictor of the distributions of tunas, marlins ABOVE: Modelled predictions of pelagic fish and mackerels. Data for other pelagic predators including marine mammals abundance, showing three main regional- scale hotspots (red areas): one in the north, and sharks were less available (no fishery data, or poor bycatch data). Many one in the south-west and one along the areas of predicted high pelagic fish diversity fell outside the CMR network, southern coast. Submarine canyons are particularly those in the Gascoyne Coast, South and West Coast bioregions. shown in black. Image: Phil Bouchet, UWA Where predicted areas did fall within in CMRs, they often fell within multiple use zones, indicating the importance of how these multiple use zones are managed. Outputs and outcomes Historical, global fisheries datasets – such as those produced by the Sea This project has contributed an Around Us Project – are among the most extensive information sources increased understanding of the available for many marine organisms. They can be a useful avenue for relationship between geomorphology identifying important biological processes, and a continental-scale view and pelagic fish that can be applied of predatory dynamics, in the data-deficient pelagic ocean. With careful to CMR monitoring and assessment, treatment, they can act as a foundation for determining conservation conservation values in marine the Commonwealth Protecting area environmental impact assessments priorities on scales much broader than local surveys could capture. Identified for offshore oil and gas, and hotspots can then be refined and further studied on local scales. fisheries management. A pelagic New knowledge and opportunities fish and sharks dataset linked to an environmental dataset including A new understanding of relationships between geomorphology and static (geomorphometric) and pelagic fish assemblages can support the effective design, internal dynamic data is now available for the zoning, management and monitoring of CMRs in the open ocean. EEZ adjacent to Western Australia. Fisheries-derived data relating to large fish such as tunas provide a valuable tool to support marine conservation and ecology and further analyses of these CONTACT data across Australia’s Exclusive Economic Zone (EEZ) would help to identify Jessica Meeuwig opportunities for conserving pelagic megafauna inside and outside CMRs. [email protected] (Similarities between the predicted hotspots of tunas and those of other 0400 024 999 large predators such as blue whales and tiger sharks have been observed in other studies, suggesting tunas can be used as proxies for pelagic diversity.)

NERP MARINE BIODIVERSITY hub • FINAL REPORT 23 Predicting benthic impacts and recovery to support biodiversity management in the South-east Marine Region

Many animals and plants live attached to the seabed where addition to their exposure to fishing and levels of protection (derived they form benthic habitats used by a diversity of other species. from existing data sources). These habitats can be affected by human uses in the marine environment Survey data were collated for benthic 1 and a range of management measures have been implemented to reduce species on the continental shelf and these impacts. This project sought a better understanding of the types of taxa upper slope, as well as information that form benthic habitats: their distribution, sensitivities and management on impact and recovery rates in measures that provide protection from pressure. It produced the first regional- relation to human uses. Biophysical scale distribution maps for benthos in the South-East Marine Region (SEMR), modelling was used to characterise, and assessed the impacts of human uses (including cumulative effects) and predict and map patterns of the efficacy of existing management strategies for epibenthic fauna. biodiversity assemblages (spatially Approach unique mixtures of all species, including mobile invertebrates and A trawl-simulation model developed for tropical regions was reconfigured to fishes), and the distributions and quantify and assess cumulative threats, risks to benthic biodiversity, and the abundance of the major habitat- effects of discrete management actions in the SEMR. The model incorporated forming taxa such as sponges, predictions of biodiversity assemblages and habitat-forming benthos, in coral, gorgonians and bryozoans.

CLOSURES, ASSEMBLAGES AND TAXA TYPES IN THE SOUTH-EAST MARINE REGION RIGHT: (a) Post-1985 footprints of the main bottom fisheries (cross- hatching) over four main 2013 trawl closure types: [D] Deep water closure, [C] CMRs, [B] Bass Strait closure and [G] Gulper shark closures. (Light grey shading: open areas.) The inset plot shows actual trawl effort time-series and alternative effort scenarios. (b) Bio-physical characterisation with 15 predicted species assemblages (environments in which biological composition is expected to be relatively similar, and between which composition is expected to vary). Their degree of similarity is indicated by the proximity and colour of the legend Protecting conservation values in marine the Commonwealth Protecting area symbols. Assemblages may not be spatially continuous. The inset plot shows the inclusion of assemblages in closed areas, and exposure to trawling. (c─l) Images and predicted distributions of 10 major taxa types of habitat forming benthos (relative density: blue=low through to red=high). Each inset plot shows predicted abundance time-series, relative to 1985, from simulation modelling of trawl effort on the taxa type distribution (from no management interventions to all interventions).

24 NERP MARINE BIODIVERSITY hub • FINAL REPORT INCLUSION OF BENTHIC BIODIVERSITY IN CMRS AND FISHERY CLOSURES, AND EXPOSURE TO HUMAN USES

15 spatially unique Overlap with habitat- SEMR shelf and slope: assemblages: area forming benthos taxa area affected affected types (by abundance)* 9% (excluded 1.1% of historical CMRs ~ 0–41% 7–19% trawl effort) 39% (excluded 5.5% of historical Trawl closures ~ 1–81% 33–60% trawl effort) 44% (excluded 6.2% of historical CMRs and closures ~ 1–83% 40–63% trawl effort) 1–9% (most-exposed taxa 1 0–43% (3 most exposed Exposure to trawl effort 6% of seabed trawled (across trawled 2 times yearly on ~ assemblages trawled 2–3 times ~ since 2007 23% of the region) average; annual overall trawling ~ yearly on average) impact ~1–8%) Longlining (widespread, 0.03% of seabed long-lined 0.01–0.03% ~ 0–0.12% but lighter impact) (spread over ~17% of the region) (annual impact 0<0.01%) Scallop dredging 0.01% dredged (spread over 0–0.02% ~ 0–0.05% (Commonwealth only) 0.38% of region) (annual impact 0–0.01%) Oil and gas facilities 0.05% (spread over 0.52% of ~ 0–0.20% 0–0.05% and pipelines region)

* Survey data for habitat-forming benthos are sparse and patchy, thus prediction maps have high uncertainty.

Fishing and other human activities that affect the SEMR seabed were data gaps in the map of benthos taxa mapped from collated data. For the fishing industry (particularly types, by conducting new surveys trawling) this included historical annual fishing effort by area, fishing of the distribution and abundance operations and management actions (including effort reductions, of habitat-forming benthos taxa. closures to fishing and the Commonwealth marine reserves system). Information was also collected in relation to oil and gas infrastructure. Outputs and outcomes An unprecedented level of data Key findings integration led to improved The effects of fishing were modelled for 15 spatially unique species assemblages knowledge and understanding of and 10 habitat-forming benthos taxa types that had been predicted and benthic biodiversity distribution, mapped from survey data*. Simulation of the bottom trawl fishery from ~1985, protection, vulnerability and status. (when consistent logbook records were available), showed that all 10 benthos It enabled the first regional scale taxa types declined in abundance in trawled areas until the mid-2000s. At quantitative analysis of pressures this time fishing effort reduced due to economic pressures and licence buy- and cumulative impacts, and the backs, and large areas were closed to trawling. A complex picture emerged, first quantitative evaluation of with patterns and responses varying spatially according to the distribution of management strategies for benthic benthos taxa types, trawling distribution, and type of management action. biodiversity conservation. This advanced capacity to evaluate The lowest total regional abundance (status) of habitat-forming benthos existing and potential alternative taxa types across the SEMR was ~80–93% of pre-trawl status, after effort biodiversity management options peaked during 2000–2005. Subsequently, all taxa were predicted to recover on and off reserves, as well as by varying extents (~1–3%) in the following decade. Had none of the the relative impact of alternative management actions been implemented, benthos status was predicted to pressures including marine stabilise or recover slowly, and with all management actions in place, the rate industries, supports evidence-based conservation values in marine the Commonwealth Protecting area and magnitude of recovery was greater. Reductions in trawl effort universally decision making in these difficult- improved the status of habitat-forming benthos, with the larger 2006 licence to-observe offshore environments. buy-back leading to greater improvements than the 1997 buy-back. In some cases, spatial management that excluded trawling, (particularly CONTACT Roland Pitcher deepwater fishery closures), led to improved status of some benthos [email protected] taxa types. Most fishery closures and CMRs had little detectable (07) 3833 5954 influence on status, though in some cases they worsened the status of some taxa in some locations. This was because displaced trawl effort moved to areas in which some taxa were more abundant. New knowledge and opportunities The new approaches can be used to evaluate existing and potential future management measures, and also be applied to assess the status of benthos in other marine regions. There are opportunities to reduce the uncertainties and

NERP MARINE BIODIVERSITY hub • FINAL REPORT 25 Collating existing survey data for Commonwealth marine waters

The Australian Government has identified 58 Commonwealth Improved KEF boundaries will enhance the assessment of existing Marine Reserves (CMRs) and 54 Key Ecological Features (KEFs) data sources for each KEF. in Australia’s Commonwealth marine area. Collating existing 1 data and information about these areas is critical to effective Outputs and outcomes Data summaries are available for 50 biodiversity management and protection. regions associated with KEFs, and 173 Approach zones in CMRs. The ARMARDA webpage enables the rapid spatial and temporal An overarching catalogue equipped with powerful, standardised search tools summary of existing data sources for was needed to integrate and enhance the value of disparate marine databases all Australian KEFs and CMRs. Data rich relevant to Australia’s CMRs and KEFs. The catalogue developed in this and data poor areas can be identified. project, the Australian Region MARine Data Aggregation (ARMARDA) facility, provides a single entry point to databases held by a suite of national research ARMARDA aggregates data for networks and agencies and has an unprecedented level of functionality. irregular-shaped areas, includes the spatial and temporal resolution ARMARDA is able to upload physical and biological observation data of the data, and caters for users via websites from CSIRO, the Australian Institute of Marine Science, the who are new to an area of interest. Australian Ocean Data Network, Geoscience Australia, the Integrated This is a significant advance on the Marine Observing System, the Institute for Marine and Antarctic Science functionality of previous search and the Terrestrial Ecosystem Research Network (TERN). ARMARDA is tools for marine databases. not yet able to search all existing marine data from these providers, but there is strong potential to make more data from these sites visible. www.cmar.csiro.au/data/armarda In consultation with staff from the Department of the Environment and CONTACT Environmental Resources Information Network, a protocol for updating and Jeff Dambacher editing shape files (a file format used for storing geographic information [email protected] data in GIS computer programs and databases) for KEFs is being established. (03) 6232 5096

Inside the data NINGALOO CMR catalogue biological data graph A preliminary analysis of the data catalogue shows that most observations in the past biological data map

50 years have targeted oceanographic hydrological data map variables, with some biological sampling of upwelling and eddy systems, canyons, deep hydrological data graph and shelf seabeds. These data are unlikely

Protecting conservation values in marine the Commonwealth Protecting area to support baseline status assessment, TASMAN FRONT AND EDDY FIELD KEF although community composition data may serve as a reference point for contemporary changes associated with climate change. Most biological sampling has been at shelf reefs biological data graph and areas of enhanced pelagic productivity. biological data map These data, augmented by satellite ocean colour observations, are likely to support baseline status assessment in some areas. The maps and graphs are sample outputs hydrological data graph hydrological data map from the data catalogue. At Ningaloo Commonwealth Marine Reserve, biological Both datasets show a relatively patchy distribution. At the sampling records are primarily from baited Tasman Front and Eddy Field KEF, sampling is also patchy, but remote underwater video stations in 2005, with greater intensity dating back to the 1950s. Biological while hydrological sampling spans 50 years. sampling has targeted pelagic fish and plankton communities. 26 NERP MARINE BIODIVERSITY hub • FINAL REPORT Analysis of approaches for monitoring biodiversity in the Commonwealth marine area: Oceanic Shoals

Carbonate banks and terraces of the Van Diemen Rise and the Sahul Shelf, and pinnacles of the Bonaparte Basin (North and North-west marine regions) are Key Ecological Features (KEFs) 1 represented in the Oceanic Shoals Commonwealth Marine Reserve (CMR). These features, with their abrupt bathymetry presenting a range of substrates, aspects and depths, were considered potential biodiversity hotspots, and merited further investigation. This project explored and discovered new marine biodiversity information, with a ship-based expedition in the RV Solander to previously unsampled carbonate banks and pinnacles in the western part of the Oceanic Shoals CMR. The information is being integrated with existing data to ABOVE AND RIGHT: Benthic biological material was better understand biodiversity distribution and sensitivity in sampled with epibenthic this area of active offshore exploration and development. sleds. Twenty-nine sponge species collected are new Approach to science, with as many as 100 potential new species The collaborative nature of this project capitalised on the unique yet to be confirmed. expertise of the research partners. A 25-day voyage involving Sediment-dwelling animals the Australian Institute of Marine Science, Geoscience Australia, were highly diverse with the Museum and Art Gallery of the Northern Territory, and 266 observed species, including newly discovered the University of Western Australia targeted three rectangular species of sea spider, areas. Each rectangle covered approximately 200 km² of squat lobster and worm. seabed and contained one or more banks or pinnacle features and contrasting non-KEF habitats. Multibeam sonar and other 127°25’E 127°25’E acoustic tools were used to create high-resolution seabed maps and benthic biological material was sampled with epibenthic sleds. The project also observed seabed habitats and fish 12°5’S communities with cameras including towed video (and associated stills cameras) and benthic and pelagic baited video stations. Key findings The Western Oceanic Shoals CMR contains more banks and 12°10’S pinnacles than previously thought, with high resolution mapping in four survey areas revealing 41 banks and pinnacles covering an area of 152 km², an increase from 105 km² (~33%). This finding suggested that the number of banks and pinnacles is likely to be significantly greater throughout the CMR than previously 0 2 4km 0 2 4km had been indicated by available charter or the bathymetric conservation values in marine the Commonwealth Protecting area data in the 250 m grid national bathymetric database. ABOVE: A bathymetry map before the 2012 survey with a spatial resolution of 250 m (left) compared with the In general, open, low-relief areas of continental shelf same area mapped by this project at a spatial resolution supported very low abundances of macrobenthos. The of 2 m. The high resolution sonar mapping revealed 41 banks and pinnacles covering an area of 152 km2, an sampled biotas were dominated by sponges, with soft corals increase of 33% from 105 km2 of previous surveys. the next dominant group, and much lower numbers of other The carbonate banks, terraces and pinnacles of the major taxa. Sponges and soft corals were mostly associated outer Sahul Shelf were built by repeated episodes of reef with the sides and plateau areas of banks and pinnacles. growth during high sea level (interglacial) phases of the Benthic biodiversity and abundance on banks and pinnacles past two million years. These features were then shaped decreased with water depth and across the transition, from by erosion and weathering during the low sea level of a following ice age. Today, tidal currents shape and score the hard substrate of banks to soft sediment plains. the seabed around these hard ground features. Banks and The high diversity of sponges, in particular on raised pinnacles provide important habitat for living organisms. Benthic biodiversity decreases with water depth and geomorphic features (banks, pinnacles, ridges, terraces) across the transition from the hard substrate of banks compared to subdued features (plains, valleys), adds to the to soft sediment plains.Images: Geoscience Australia

NERP MARINE BIODIVERSITY hub • FINAL REPORT 27 BATHYMETRY OF THE JOSEPH BONAPARTE GULF AND SURROUNDING AREAS

Pinnacles of the Bonaparte Basin

Oceanic Shoals CMR

1

Carbonate banks Carbonate banks and terraces of the and terraces of the Sahul Shelf Van Diemen Rise

ABOVE: The Oceanic Shoals CMR contains components of three KEFs considered 0 m regionally important for biodiversity or ecosystem function and integrity: the carbonate banks and terraces of the Sahul Shelf and the Van Diemen Rise, and the pinnacles of the Bonaparte Basin. (Visualised depths fall between 0 and 300 m.) Image: Geoscience Australia 300 m

growing awareness that Australia is a global diversity hotspot for sponges. area also supports a wide range Distinct regional faunas, including differences from east to west across of pelagic animals, with 32 species the Oceanic Shoals CMR, and high levels of endemism are evident. observed: 11 shark species, black marlin, barracuda, Olive Ridley Shallower banks that rose to within 45 m of the sea surface supported turtle, sea snakes and orca. greater biodiversity, including isolated hard corals of limited diversity. It is noteworthy that other studies of more seaward, clearer water shoals in New knowledge the same CMR, undertaken in 2014 by AIMS, found much more abundant and diverse hard coral communities more similar to shelf edge shoals. and opportunities Biological samples collected in

Protecting conservation values in marine the Commonwealth Protecting area This indicates the CMR boundary has captured a broad range of shoal and pinnacle features and associated environmental conditions, and the the Oceanic Shoals CMR clearly diversity of biota associated with these physical environmental gradients. demonstrate the region’s high biodiversity values. The abrupt Tidal currents are important in shaping the seabed by scouring holes bathymetric features such as into soft sediments around the base of banks and pinnacles and by pinnacles and shoals appear to be extending the length of pockmarks. Levels of suspended sediment locations of species and biomass (turbidity) appear higher in the western part of the CMR than the accumulation for macrobenthos, east, with some smaller pinnacles partly buried by sediment. and other demersal and pelagic Demersal fish communities appear to correlate with the spatial patterns species relative to the broader shelf observed for the benthic biodiversity, occurring in larger and more diverse environs. The greater abundance of communities on the shallower, less turbid banks. Given that water clarity shoals than previously thought and limited the utility of the demersal, camera-based methods deployed, better the variety of their sizes, depths and sampling of fish diversity across more turbid, mid-shelf regions of the CMR is shelf positions indicates a complex likely to require extractive sampling such as trawls and traps. The surveyed mosaic of biodiversity hotspots.

28 NERP MARINE BIODIVERSITY hub • FINAL REPORT First qualitative Pinnacles of the Bonaparte Basin models for the KEFs Oceanic Shoals CMR of Oceanic Shoals

The research voyage extended Key Ecological Features (KEFs) are part of the marine understanding of biodiversity environment considered regionally important for patterns on shoals into more turbid biodiversity or ecosystem function and integrity and mid-shelf environs than previously are represented in the Commonwealth Marine Reserve assessed. The results confirm the 1 Network. Qualitative modelling can be used to represent importance of these features in relationships between the physical and biological supporting diversity, and elaborate the role of light reaching the seabed components of KEFs, and to assess potential threats. in shaping the dominant benthos. New information gained from this Oceanic Shoals voyage They also support the notion that made it possible for the first time to construct such models as turbidity increases, the depth at for its resident KEFs. The qualitative modelling was used to which autotrophic species are able characterise ecosystem dynamics for the carbonate banks, to dominate the seabed decreases. In the CMR this may be particularly terraces and pinnacles, and to predict future threats. It the case for habitat-engineering revealed no fundamental differences between terrace, bank species such as hard corals and large and pinnacle communities, but the location of these features macroalgae. An opportunity exists to varied with respect to physical factors such as turbidity, develop predictive models – based water depth or shear stress associated with cyclones. Carbonate banks Carbonate banks on data for depth, water quality and and terraces of the and terraces of the shelf position – to better understand Attached invertebrate communities support fishes and Sahul Shelf Van Diemen Rise the nature of benthic communities mobile reef invertebrates through trophic interactions on the majority of shoal and pinnacle and habitat-effects, including refuge from strong features yet to be surveyed. currents and protection from predators. Invertebrate and 0 m plankton eating fishes are consumed by both benthic and Outputs and outcomes pelagic predatory fish species. This latter predator-prey This project exercised strong, relationship links the benthic and pelagic ecosystems. national, multidisciplinary collaboration in marine science Based on the ecosystem structure, five key threats were considered plausible within a 50-year time frame. They 300 m to build a greater understanding of marine connectivity, both included oil and gas spills, (affecting algae and planktivorous within the CMR and across the fishes), illegal fishing, (affecting benthic and pelagic broader region. It produced high- piscivores), ocean acidification, (affecting tall algae), increased resolution bathymetry, geochemical water column shear stress through increased storm intensity, and geophysical data, biological and increased turbidity through increased agricultural collections, and a new qualitative run-off. The model, and the associated direct and indirect model of the KEFs of the Oceanic effects of the above five threats, will be used to identify Shoals CMR. The results confirmed ecological indicators of use to monitoring and management. the value of the KEFs in terms of the biodiversity they host and their regional significance. They were communicated in scientific and

non-technical formats, to raise the conservation values in marine the Commonwealth Protecting area understanding of marine biodiversity in Australia’s poorly known north and north-western waters, (including the potential effects of fishing, and oil and gas exploration and extraction). www.nerpmarine.edu.au/rv-solander-blog

CONTACT Julian Caley [email protected] (07) 4753 4138

NERP MARINE BIODIVERSITY hub • FINAL REPORT 29 Analysis of approaches for monitoring biodiversity in the Commonwealth marine area: Houtman Abrolhos Islands

A suite of complementary, non-extractive survey Integrated Marine Observing System autonomous underwater vehicles methodologies is required to identify and monitor change in (AUVs) identified the presence/ habitats and species across areas identified by the Australian absence and abundance of coral, kelp 1 Government as Key Ecological Features (KEFs) of the marine and associated benthic communities. environment. The proportion of coral genetic variation (a key component of The Commonwealth marine environment surrounding the Houtman Abrolhos resilience) attributable to ocean Islands is a KEF in the South-west Marine Region. This complex of 122 islands circulation was determined by and reefs, some 60 km off the mid-west coast of Western Australia, form the linking genetic data from a panel largest seabird breeding area in the eastern Indian Ocean. Many of the islands’ of coral microsatellites (short biodiversity features, most notably seabirds and rock lobster, are supported repeated DNA sequences at a by benthic and pelagic ecosystems in surrounding Commonwealth waters. particular locus on a chromosome) The shelf rocky reefs in the vicinity of the Houtman Abrolhos islands mark the to a three-dimensional model that northern border of kelp, and the southern border of coral, in Australia. Because simulated coral dispersal over time. of this they are associated with very high biodiversity. Any changes in the A single tail feather (from each distribution of kelp or corals in this region may signal climate-change induced adult) and approximately 5–10 pin shifts in species distribution. This project located shelf rocky reef coral-kelp feathers (from each chick) were communities that form part of this KEF, examined regional influences on gene collected from two species of terns flow between coral populations, and assessed isotope analysis of seabird in a non-lethal and minimally- feathers as a means of monitoring and evaluating changes in food webs. invasive way. Individual amino acids Approach were extracted from the feathers and profiled using stable isotope A survey designed using the Generalised Random Tessellation Stratified analysis. Differences in the natural Technique (see story on page 51) identified the presence and patterns of benthic isotopic ratios for nitrogen (δ15N) and habitats in Commonwealth waters between the Houtman-Abrolhos Islands carbon (δ13C) were used to identify and the coast. Shelf rocky reefs (coral-kelp communities) in Commonwealth the bird’s position in the food chain, waters adjacent to the Houtman-Abrolhos Islands were located by a drop as well as the sources of nutrients camera survey. Multi-beam sonar was used to delineate their boundaries. important for primary productivity. Protecting conservation values in marine the Commonwealth Protecting area

ABOVE and ABOVE RIGHT: Amino acids extracted from feathers provide information on the bird’s trophic level, or position in the food chain, as well as the sources of nutrients important for primary productivity.Images: CSIRO

30 NERP MARINE BIODIVERSITY hub • FINAL REPORT 1

Key findings Analysis of compound-specific stable nitrogen isotopes extracted from Shelf rocky reefs were located in the Commonwealth waters of bird feathers was demonstrated as this KEF (these had previously only been identified in State waters, a possible cost-effective monitoring but were predicted to be an important habitat of this KEF). tool for offshore pelagic ecosystems Stable isotope analysis enabled the feeding niches of sooty terns, bridled terns which would enable the long- and crested terns to be differentiated for the first time. The results suggest term monitoring of ecosystem that the absolute value of, and changes in, this nitrogen ratio may indicate health for this pelagic productivity the trophic level for several important seabird species, while the carbon KEF. The technique could be ratio indicates the source of nutrients utilised by phytoplankton at the base combined with new approaches of the food web. The technique may have potential for tracking fluctuations to evaluating population-level or trends in these variables over time providing a remote and cost-effective plastics ingestion and identifying measure of the trophic status of offshore mid-water fish populations. foraging habitats of seabirds. Regional oceanographic circulation patterns are a better predictor of gene flow between coral populations at the Houtman Abrolhos Islands than the distance (as the crow flies) between them. TOP: High resolution bathymetry of New knowledge and opportunities a shelf rock reef in Commonwealth waters adjacent to the Houtman Shelf rocky reefs, previously unknown, were located in the Commonwealth Abrolhos Islands, derived from waters of this KEF, and the composition of coral-kelp communities multibeam sonar swath.Image: CSIRO will be characterised during the analysis of AUV imagery. TOP RIGHT: Pentagonaster dubeni (seastar) in 8 m coral reef habitat at the Houtman Abrolhos Islands. Image: IMAS/Reef Life Survey Protecting conservation values in marine the Commonwealth Protecting area

ABOVE: Parrotfish school over typical reef habitat in depths of CONTACT 10─20 m at the Houtman Abrolhos Islands. Image: Reef Life Survey. Keith Hayes ABOVE RIGHT: A Spangled Emperor (Lethrinus nebulosus) [email protected] at 0─15 m depths. Image: IMAS/Reef Life Survey (03) 6232 5260

NERP MARINE BIODIVERSITY hub • FINAL REPORT 31 Analysis of approaches for monitoring biodiversity in the Commonwealth marine area: Solitary Islands

An important part of establishing monitoring protocols is to determine the optimum sampling regime for seabed biodiversity. This project inventoried shelf rocky reef habitats, benthic communities and 1 demersal fish at the temperate Shelf Rocky Reef Key Ecological Feature (KEF) near the Solitary Islands off New South Wales. Underwater imaging equipment was tested and improved during the process, and protocols were developed to improve the efficiency and rigour of future monitoring. Approach Non-extractive survey methodologies were developed, deployed and evaluated under a range of conditions. In addition, an experimental, two-day deployment of 30 baited remote underwater video (BRUV) systems located at varying distances apart examined spatial autocorrelation (the degree of clustering) between ABOVE: Thicklip Trevally (Carangoides orthogrammus), Solitary Islands. observations of selected fish assemblages. This evidence will help to determine Image: Reef Life Survey the minimum distance between BRUVs at which samples are statistically independent and therefore useful for detecting trends. The effect of habitat characteristics (such as reef rugosity) on fish communities was also examined. New knowledge Key findings and opportunities High-resolution multibeam sonar swath mapping and analysis of 40 km² The distribution and importance of seafloor habitat identified ancient-coastline reefs and mobile sands of rocky reefs in this area appear on the seafloor south of South Solitary Island. The abundance of fish to part of a larger complex of reefs at every trophic level was strongly related to the three-dimensional associated with ancient coastlines structural complexity of reefs: generally, abundance increased with that occur around Australia. complexity. At small-scales, complexity influenced the abundance Fine-scale BRUV data on the and composition of four of the five trophic groups examined. distribution of selected fish are Data from the experimental BRUVs deployment proved inconclusive, so the being combined with broader-scale project team analysed a much larger data set from Queensland’s Moreton Bay. (swath acoustic) mapping to predict Initial model results indicated that the spatial correlation between observations the occurrence of different species of snapper was negligible after about 300 m (indicating that for statistical over the broader area of the KEF efficiency in these areas BRUVS should be placed at least 300 m apart). that will be useful in determining its ecological values and status. The project examined how to streamline the manual scoring process of complex, underwater video images, and defined a ‘stopping rule’ Some 30,000 image labels have after which little further information would be gained by further been provided to University of analysis. With 25 points per image, 20 images were sufficient to Sydney researchers to ‘train’ characterise benthic biodiversity in the Solitary Islands KEF. supervised automatic image classification algorithms. Outputs and outcomes

Protecting conservation values in marine the Commonwealth Protecting area This project has generated an improved understanding of the location and morphology of shelf rocky reefs in Commonwealth waters near the Solitary Islands and key determinants of demersal fish community composition in this KEF. It has inventoried demersal fish and benthic communities and identified effective methods of design, collection and analysis of underwater imagery in rocky reef habitat.

CONTACT Keith Hayes [email protected] ABOVE: Additional multibeam sonar data acquired in the Solitary Islands KEF.Image: CSIRO (03) 6232 5260

32 NERP MARINE BIODIVERSITY hub • FINAL REPORT Putting names to a sea of faces

Photographs and video provide a safe, non-destructive and with automated image analysis to ensure the consistent annotation of efficient way to examine and monitor marine habitats, and are datasets used to ‘train’ automatic particularly useful in areas protected for their biodiversity values. image analysis algorithms. 1 To be useful on a national scale, however, the life forms they reveal must be The CCS provides the framework named in a consistent way. This project established a national standard for for nationally-consistent annotation classifying the substrates, flora and fauna visible in marine photos and video. The of marine imagery data. This will Collaborative and Automated Tools for the Analysis of Marine Imagery (CATAMI) support national marine monitoring classification system now provides that common vocabulary for Australia. by streamlining data collated by different organisations, including Approach through government contracts, The CATAMI classification system (CSS) was funded by the National eResearch environmental impact assessments Collaboration Tools and Resources and supported by the Australian and long-term monitoring. National Data Service. It was established and refined during workshops involving software engineers, programmers, and benthic ecologists from Outputs and outcomes state and Commonwealth agencies and universities, under the direction An agreed, national standard for of the CATAMI Technical Working Group. For longevity, the CCS was classifying substrates and biota in incorporated into the Codes for Australian Aquatic Biota database. marine imagery has been developed and provided online through the New knowledge and opportunities Australian Ocean Data Network. The CCS employs a standardised combination of high-level taxonomy (phylum, Standardised, quantitative estimates order, class) and morphological (shape, growth-form) characteristics that such as the presence and percentage can be determined from a picture. This provides more consistency than cover can now be made from video traditional classification approaches. In future, the system could be combined and photographic images, improving the efficiency of marine ecosystem research and the ability to compare BIOTA COMMUNITY: OUTCROPPING ROCK AND SEDIMENT results from different studies. POCKETS WITH SPARSE SPONGE AND OCTOCORAL COVER The CCS is being adopted by industry, government and academia, with BIOTA: Sponge: SUBSTRATE: BIOTA: Fishes: Bony Massive forms: Consolidate (hard): several hundred copies of the fishes (37 990083) Simple (10 000904) Rock (82 001002) technical document and code file downloaded from the website. It has been used by the NERP Marine Biodiversity Hub, the Reef Life Survey, the New South Wales Marine Protected Areas monitoring program, the Australian Institute of Marine Science, and the Australian Centre for Field Robotics, and in two online annotation tools: CATAMI and

Squidle. Environmental consultants conservation values in marine the Commonwealth Protecting area to oil and gas companies (GeoOceans and Chevron Wheatstone Project) have also used the CCS. An illustrated CATAMI poster is publicly available.

TOP: A combination of coral functional groups, turf algae, and urchins at Middleton Reef in the Lord Howe CMR. Image: IMAS

LEFT: Taxonomic and morphological characteristics are combined in the CATAMI system to ensure standard annotation of marine imagery data. Image: CSIRO BIOTA: SUBSTRATE: BIOTA: Sponge: Cnidaria: Black Unconsolidated (soft): Hollow forms: Cups & Octocoral: Sand/mud: Coarse and alike: Cup/ CONTACT Branching 3D: sand (82 001014) goblet (10 000919) Luke Edwards Bushy (11 16898) [email protected] (08) 6304 6070

NERP MARINE BIODIVERSITY hub • FINAL REPORT 33 1 Protecting conservation values in marine the Commonwealth Protecting area

An illustrated poster highlights features of the CATAMI classification system.

34 NERP MARINE BIODIVERSITY hub • FINAL REPORT www.catami.org/classification Marine monitoring blueprint: meeting a monumental challenge

Australia’s Commonwealth waters support a range of marine of physical and biological indicators have been identified for 33 KEFs. biodiversity, ecological features and processes, and contribute to the economy through fishing, energy and tourism industries. KEFs represent areas of significant biodiversity or ecological functioning 1 Monitoring this environment is an enormous challenge, and the Department and integrity within Commonwealth of the Environment has been investing since 2008 in Australia’s capacity waters. The monitoring of KEFs to report on the health of the Commonwealth Marine Area (CMA). The therefore will provide an evidence investment is fostering new approaches to characterising and analysing base to support decision making marine areas – including environmental pressures, and monitoring change to conserve and protect the – by government agencies, research organisations and industries. Commonwealth marine environment. This project provided direction for the staged implementation of It will also strengthen the quality a monitoring program to meet the Department’s reporting needs. of environmental reporting on the Existing marine conservation values (Key Ecological Features, or KEFs) status and trends of marine health, identified by the Australian government were considered together with such as that undertaken for State the requirements, options and constraints associated with building a of the Environment reporting. national monitoring program. A central question was whether a sufficient Governance mechanisms that evidence base existed to support State of the Environment reporting on provide leadership, oversight and the health and trends of KEF habitat, features, processes and pressures. coordination for KEF monitoring have not been established. Approach Establishing an initial oversight Eight years of research on ecological indicators and monitoring for the and coordination group is an CMA were synthesised to begin clarifying the drivers and interests that important step in transitioning motivate the Department to seek information on marine ecosystem health. from KEF research to prioritised A search engine known as ARMARDA (see story on page 26) was built to operational KEF monitoring. assess the major marine databases in Australia. Existing data relevant to Existing data within KEF boundaries monitoring KEFs were summarised to identify opportunities for use in date back to the 1950s and determining status and trends, and information gaps. Finally, Australia’s mainly cover physical data used capacity (governance and functional) for monitoring KEFs was reviewed. to understand ocean circulation. Key findings Most scientific biological sampling has occurred for KEFs associated The Department seeks to improve the monitoring of marine ecosystem health with shelf reefs and areas of in the CMA through a focus on KEFs. Fifty-four KEFs have been identified across enhanced pelagic productivity. This Australia’s six bioregional marine planning areas (not including State waters or combined with satellite data is likely the Great Barrier Reef Marine Protected Area). Based on the existing scientific to initiate monitoring baselines understanding of marine ecosystems and their response to pressures, suites for some KEFs. Limited data have been collected for KEFs associated with seamounts, but further work is needed to gauge their value to monitoring. Relatively few biological datasets have been collected for KEFs associated with submarine conservation values in marine the Commonwealth Protecting area canyons, unique features of the deep sea, and shelf sediment basins. Australia’s marine observing community has the capability to deploy ocean observing equipment to generate new monitoring data for KEFs, including visual and video-based methods, acoustic and remote sensing methods and physical sampling. Methods with a relatively long history of deployment – such as diver visual census, active fishing gears, ABOVE: KEFs represent areas of significant biodiversity or ecological functioning and integrity within Commonwealth waters.

NERP MARINE BIODIVERSITY hub • FINAL REPORT 35 Streamlining marine monitoring indicators

Indicators for marine ecosystem national pelagic productivity analysis based on three productivity generating monitoring have proliferated in processes – upwelling areas (dominated by eddies), frontal density (thermal fronts) the past two decades, presenting and eddy kinetic energy – completed independently of the KEF-identification significant challenges integrating process. In this example, there is a high degree of similarity among the indicators and reporting indicator data at identified for each of these KEF systems: for example, nutrients and phytoplankton regional or national scales. To help indicators are common to the vast majority of KEFs in this group and upwelling overcome this problem, Marine and seabirds indicators are common to at least three of these KEFs. Biodiversity Hub scientists, in APPROXIMATE LOCATIONS OF KEY ECOLOGICAL collaboration with policy makers, FEATURES IN COMMONWEALTH WATERS 1 have grouped KEFs and identified suites of indicators for these groups. The six reporting groups are: ecosystems associated with canyons; deep seabeds; areas of enhanced pelagic productivity; seamounts; Meso-scale Tasman Front eddies shelf reefs and shelf seabeds. and eddy field This figure shows the approximate location of nine KEFs in Commonwealth waters that can be grouped to guide regional and national scale reporting on the status of and trends in areas of enhanced pelagic productivity. The location of the KEFs aligns closely with the results of a Kangaroo Island pool and Eyre Peninsula upwellings RIGHT: The KEF systems indicated here share a range Bonny Coast upwelling of common indicators. Bass Cascade and upwelling east of Eden East Tasmania subtropical convergence zone

and earth observing satellites – experience the least constraints (such as of enhanced pelagic productivity cost, ease of deployment, and maturity of data processing and analysis). (see story above), seamounts, shelf reefs and shelf seabeds. The Department will require data management arrangements for KEF monitoring and will need to clarity its role in managing KEF indicator data. Outputs and outcomes The Australian Ocean Data Network enables Australian government agencies This project has produced a blueprint and stakeholders to share and link KEF monitoring data. The Bureau of for improving the monitoring of Meteorology National Environmental Information Infrastructure provides marine ecosystem health in the reference architecture for enhancing the discovery, access and use of national

Protecting conservation values in marine the Commonwealth Protecting area CMA with tools including a KEF environmental information and should be used to configure data management atlas and KEF database identifying arrangements for KEF indicator data. Information products for KEF monitoring existing data, models and indicators. will need to be specified after monitoring priorities are identified. It has fostered a collective The marine monitoring blueprint identifies that Australia has the ecosystem understanding among policy makers understanding and practical capability necessary to begin KEF monitoring. and scientists of Australia’s marine Vision, governance and clear prioritisation will be important elements of monitoring capacity, and of how the establishment phase. this capacity can be improved through continued collaboration. New knowledge and opportunities A foundation has been laid for a more strategic approach to understanding CONTACT and monitoring marine ecosystem health that builds on past and present Paul Hedge research investment. The majority of the KEFs share common ecological [email protected] systems, and can be grouped to facilitate regional or national environmental (03) 6232 5023 reporting. Discussion between scientists and policy makers identified six reporting groups: for ecosystems associated with canyons, deep sea beds, areas

36 NERP MARINE BIODIVERSITY hub • FINAL REPORT Supporting the recovery of threatened, endangered and protected species 2 IMAGE: Russell Bradford, CSIRO

NERP MARINE BIODIVERSITY hub • FINAL REPORT 37 The need

Species that are listed as threatened, and New methods are needed to assist with species recovery plans, to support managers in decisions migratory species listed under international relating to new development and non-detriment agreements are protected as matter of findings for the export of CITES-listed species, and to 2 national environmental significance under support international obligations. Marine Biodiversity Hub scientists, building on recent developments to the Environment Protection and Biodiversity estimate the abundance of over-exploited commercial Conservation Act 1999 (EPBC Act). fish populations, developed new genetic approaches combined with acoustic telemetry to estimate The Australian Government seeks to develop targeted abundance and determine movement patterns and collaborative programs to coordinate species habitat use. These were applied to threatened river recovery and environmental protection efforts sharks in the Northern Territory, even when no adults across Commonwealth, State and Territory agencies could be directly sampled. The goal was to develop with responsibilities for the marine environment. an effective and affordable technique that could be It also seeks relevant, accessible and evidence- used for other rare and threatened mobile species. based information to support decision-making associated with development proposals. The task of Following the recent shark attacks in Western protecting listed species, however, is challenged by Australia attributed to White Sharks, the Australian the number of species involved, and the number for Government requested Hub scientists to apply these which insufficient data are available to develop or new methods to estimating the abundance of the measure progress against species recovery plans. White Shark (eastern and western populations) as well as the Grey Nurse Shark (eastern population). Marine species are listed under the EPBC Act in all categories from critically endangered to conservation dependent, and across most taxa including bony fish, cartilaginous fish, seasnakes, turtles, mammals, birds, and invertebrates. It is difficult to estimate the abundance of most of these species because they are typically both rare and widely distributed; for some species, such as the Largetooth Sawfish or Speartooth Shark, adults are rarely or never observed. Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery IMAGE: Michelle AIMS Jonker,

38 NERP MARINE BIODIVERSITY hub • FINAL REPORT Populations and habitat use of euryhaline sharks and rays

Populations of sawfishes and river sharks in the Northern Territory are thought to have declined dramatically in recent decades, raising concerns about their viability. 2 The Largetooth Sawfish, Pristis pristis, and the Dwarf Sawfish, P. clavata, are listed as Vulnerable under the Environmental Protection and Biodiversity Conservation Act 1999; the Speartooth Shark, Glyphis glyphis, is Critically Endangered, and the Northern River Shark, G. garricki, is Endangered. More information is needed about the distribution, ecology and population dynamics of these species to assist in their conservation, management and recovery. This project generated a better ecological understanding of the habitat use and habitat requirements, short and long- term movements, connectivity and spatial dynamics of these priority euryhaline elasmobranch species and collected tissue samples to enable abundance estimation with close-kin mark- recapture. The improved understanding has contributed to the multi-species Recovery Plan for Sawfish and River Sharks being developed by the Department of the Environment. Approach Fisheries-independent surveys in selected river systems were conducted using appropriate sampling gear (primarily gillnet and rod and line). Captured sharks were tagged and monitored with active and passive acoustic telemetry. Active tracking involves mounting a hydrophone to a tracking vessel to follow fish movement patterns and habitat use in real time (short-term telemetry). Passive tracking uses networks of moored acoustic receivers to detect tagged fish when they pass within range of a receiver (long-term telemetry). Extensive arrays of acoustic receivers (130 receivers) were deployed in seven Northern Territory and Queensland river systems to provide long-term monitoring of tagged animals (some 400 individuals from 10 species tagged).

ABOVE: A Largetooth Sawfish caught in the Adelaide River. Floodplain billabongs were found to be nursery areas for juvenile Largetooth Sawfish on the Daly River. The species Supporting endangered and threatened, of protected the recovery very low catch of animals aged one year and above suggests that few juveniles survive more than a year.

LEFT: Peter Kyne checks an acoustic receiver from the West Alligator River. Extensive arrays of acoustic receivers were deployed in seven Northern Territory and Queensland river systems to provide long-term monitoring of tagged animals. Images: Michael Lawrence-Taylor, Charles Darwin University

NERP MARINE BIODIVERSITY hub • FINAL REPORT 39 Mitochondrial genome sequencing of Speartooth Sharks and Largetooth existed from the NT). This species’ Sawfish was used to help profile their population structure. The mitogenome, distribution is still limited to less which is inherited through the mother, offers clues to how widely the than 10 rivers and estuaries, females are dispersing to breed (for example, between river systems). however, and uncertainty remains 2 Complete mitochondrial genome sequences have been published for over its abundance elsewhere in the four sawfish and river shark priority species (as well as for a suite of its range (such as the Kimberley other coastal and estuarine sharks and rays of northern Australia). region of Western Australia). The degree of population structuring Key findings between rivers and regions across Largetooth Sawfish, P. pristis its distribution is also unknown. Catch per unit effort (CPUE) was used to compare catches of fish species (such Movement data show highly seasonal as the number of sawfish caught per 100 m of gillnet per day) between surveyed distribution patterns within the rivers. Low catch rates were recorded throughout the NT, although the CPUE of South Alligator River (where 50 neonates (newborns) in the Adelaide River was comparable to the Fitzroy River sharks were acoustically tagged (WA) which is a key nursery area for P. pristis. (Fitzroy River data published by for long-term telemetry studies). Murdoch University.) Catches were dominated by sawfish less than one-year- In the dry season, animals were old (the 0+ age-class). The very low CPUE of animals aged one year and above is located mainly 40–80 km upstream; of concern, suggesting that few juveniles survive more than a year. Floodplain in the wet they remained around billabongs were found to be nursery areas for juvenile P. pristis on the Daly River. the river mouth, with limited movement to adjacent rivers. Analysis of mitochondrial DNA revealed strong population structuring of P. pristis across northern Australia: except for rivers flowing Speartooth Shark, G. glyphis into the Gulf of Carpentaria, all river drainages appeared to host a G. glyphis catches were highest in genetically distinct population. This means there is limited capacity the Adelaide River, with the South for the re-colonisation of localised populations that are depleted due Alligator River and Queensland’s to juvenile and adult mortality (at least for females at this stage). Wenlock River also supporting Dwarf Sawfish, P. clavata reasonable catches. Movement patterns were similar to G. garricki Limited numbers of P. clavata were recorded during the project, mainly due to with a downstream migration in the a lack of fishing effort in its core habitat of coastal and estuarine areas (most wet season and animals confined sampling for sawfish was undertaken in mid-upstream reaches of rivers to target to narrow (20–40 km) stretches P. pristis). All known records of P. clavata in the NT were reviewed and mapped, of river during the dry season. but the species remains poorly known in the NT. Records from mid-reaches of rivers demonstrate the use of this habitat as nursery areas for juvenile fish. Analysis of mitochondrial DNA revealed a strong catchment-level Northern River Shark, G. garricki separation of all known Australian Populations ofG. garricki were found in the Van Diemen Gulf area (in particular G. glyphis populations (Adelaide Kakadu National Park’s Alligator Rivers region), and in more rivers than River, Alligator Rivers, Wenlock had been documented previously. Catch rates were high in all rivers, with River) which has important more than 350 individuals recorded (before this project only eight records management implications. Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery

ABOVE: Little is known about Dwarf Sawfish in the Northern Territory. Image: Peter Kyne, Charles Darwin University

RIGHT: Fieldwork on the Adelaide River. Catches of Speartooth Shark were highest in the Adelaide River, with the South Alligator River and Queensland’s Wenlock River also supporting reasonable catches.Image: Mat Gillfedder

40 NERP MARINE BIODIVERSITY hub • FINAL REPORT Each population can be considered a separate management Outputs and outcomes unit, with limited capacity of adjacent populations to repopulate This project generated improved another population were significant declines to occur. understanding and knowledge New knowledge and opportunities to support the management 2 and recovery of threatened Research infrastructure and capabilities developed during this project sawfishes and river sharks. Expert will support ongoing monitoring and assessment, with acoustic receiver advice was regularly provided to arrays established in the Adelaide and South Alligator Rivers providing the Department. This included an opportunity for long-term monitoring of sawfishes and river contributing to assessments sharks. The existing G. garricki tissue sample collection provides the of proposed developments opportunity to assess population structuring across the range of this for their potential impact on species (when combined with required surveys of further key rivers). threatened species (referrals), and The occurrence and habitat of adult G. glyphis remains unknown. to developing a Recovery Plan There is a need to explore how advancing tagging technologies could for Sawfish and River Sharks. be applied to find adult populations. Large sub-adults (locatable Species information sheets were in key rivers at certain times of year) could be fitted with satellite developed and published for the tags, and larger fishing gear such as set longlines could be trialled to four species studied. A guide to catch (and then tag) adult females at pupping time. (Pupping period the sharks of Kakadu rivers, and has been determined based on the presence of pups in rivers.) protocols for surveying and tagging The project demonstrated the benefits of combining the disciplines sawfishes and river sharks were of field ecology and quantitative genetics. Recent developments in also published. More than 10 technologies for both disciplines have given rise to the quantitative scientific manuscripts have been information on population dynamics and habitat use that will produced, and a greater number guide management decisions affecting these rare species. are being prepared or planned.

CONTACT Number of samples collected for close-kin Peter Kyne [email protected] mark-recapture for NERP Marine Biodiversity Hub (08) 8946 7616

Speartooth Shark (NT rivers) 233

Speartooth Shark (Wenlock River, Qld) 102

Largetooth Sawfish 65 BELOW: A Northern River Shark White Shark 314 caught in the West Alligator River. This species was found in more Northern River Shark (for future application) 365 Northern Territory rivers than had been documented previously, but its abundance is uncertain elsewhere in its range. Image: Michael Lawrence-Taylor Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery

NERP MARINE BIODIVERSITY hub • FINAL REPORT 41 Partnering with indigenous communities

Largetooth Sawfish Pristis( pristis), Speartooth Sharks (Glyphis Traditional knowledge of sawfish habitat provided evidence for the glyphis) and Northern River Sharks (Glyphis garricki) are being previously-unrecognised importance studied in the Top End to learn more about their distribution, of off-stream floodplain billabongs 2 ecology and population status. for sawfishes in the Daly River region. Indigenous people are major land and sea custodians and managers in northern Access to the co-managed Australia where these species occur. Indigenous communities and rangers (Traditional Owners and Parks have been helping NERP Marine Biodiversity Hub scientists with their research, Australia) Kakadu National Park providing guidance, practical assistance and access to Indigenous lands, as well facilitated extensive research on as building skills and employment opportunities. The partnership is essential the river shark populations of the to furthering the understanding and management of threatened sawfishes Alligator River region. Indigenous and river sharks in the Northern Territory. Hub scientists aim to engage employment opportunities were further with Indigenous communities when projects are of mutual interest. provided to local communities in Kakadu, with participants Approach becoming key field personnel. The research team worked with Indigenous communities, Traditional New knowledge Owners and rangers to survey for sawfishes and river sharks in the Daly River region and the Alligator Rivers region of Kakadu National Park. The and opportunities collaboration provided employment and skill transfer opportunities to Indigenous communities and Indigenous communities participating in sawfish and river shark research. ranger groups in northern Australia are uniquely placed to partner in As well as fostering opportunities for Indigenous employment and research on threatened species capacity building, the project sought to jointly identify opportunities and many opportunities exist to to build on Indigenous knowledge, to ensure the effective and ethical undertake research on aquatic, communication of research outcomes to Indigenous communities, coastal and marine systems. Future and to provide opportunities for Indigenous participation in project surveys and genetic tissue sample development. These guiding principles were borrowed from the Indigenous collection of threatened sawfishes Engagement Strategy developed by the NERP Northern Australian Hub. and river sharks will benefit from Key findings partnerships with Indigenous communities and ranger groups. Partnering with the Malak Malak Traditional Owners and Ranger Group Of particular value is the exchange provided unique opportunities to access Indigenous lands to survey sawfish of knowledge between western habitat. This included the first application of environmental DNA (eDNA) scientific research and management survey techniques on threatened elasmobranchs, and on floodplains. priorities, and traditional knowledge (The eDNA technique use traces of DNA in water to detect the presence and management priorities. of species that occur there, through the collection and analysis of water Advancing technologies supporting samples and was a collaboration with the NERP Tropical Ecosystems Hub.) data collection on country will Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery

LEFT: Billabong sawfish gillnetting on Malak Malak country, Daly River. Image: Peter Kyne

42 NERP MARINE BIODIVERSITY hub • FINAL REPORT Saving sawfish in Darwin Malak Malak the Daly River Land Trust

Malak Malak Indigenous rangers and Traditional Owners have a unique understanding of sawfish habitats in the Daly River region, and have helped scientists to locate important floodplain areas that act as nursery areas for young sawfish. In September 2012, 2 as Top End floodplains were drying, the rangers raised the alert when Largetooth Sawfish Pristis( pristis) were stranded in a shallow waterhole near the Daly River. The team of researchers, rangers and Traditional Owners subsequently netted nine sawfish and two barramundi, and returned them to the river. Two weeks later the waterhole was dry. Largetooth Sawfish are born at the river assist future integration of mouth then move upstream, often spreading out into floodplain traditional knowledge (specifically, billabongs, but sometimes they can pick the wrong one. While the occurrence of critical habitat) and threatened species management. floodplains can be productive, fish can perish if the billabongs dry out before the following wet season, due to late rains or a hot, Outputs and outcomes dry season. Images: Amos Shields, Malak Malak Ranger Group Working with Indigenous communities in the Daly River region led scientists to discover the importance of off-stream floodplain billabongs for sawfishes, and drying floodplain billabongs were surveyed annually between 2012 and 2014 at the end of the dry season. The partnership also worked to save a group of juvenile sawfish that otherwise would have perished. Nine sawfish were relocated from a rapidly drying waterhole on the Malak Malak Land Trust to the main river channel in 2012, after scientists were alerted by Traditional Owners and Indigenous Rangers (see story at left). Employment was provided to several Indigenous community members during river shark and sawfish research in Kakadu National Park. Two publications were initiated that highlighted the natural values of Malak Malak country. The booklet Sawfish on Malak Malak Country is in preparation in partnership with the Malak Malak Ranger Group, and the brochure Migratory

Shorebirds of Tyumalagun, Malak species Supporting endangered and threatened, of protected the recovery Malak Land Trust was published in partnership with Malak Malak Traditional Owners and the NERP Northern Australian Hub.

CONTACT Peter Kyne [email protected] (08) 8946 7616

NERP MARINE BIODIVERSITY hub • FINAL REPORT 43 White Shark population and abundance trends

Evidence-based information is needed to address high- priority actions in the National Recovery Plan for the White Shark (Carcharodon carcharias) to underpin population and 2 risk assessments, and to support local-scale policies and management. This project developed, tested and applied tools for estimating the abundance and population status of White Sharks in Australian waters, including the first ever empirical estimate of adult White Shark abundance. Elements of this task included confirming population structure, identifying habitats, developing measures of key population attributes, and improving information on movement patterns. This built on research data gathered in the past decade. Approach Genetic data from individual sharks were analysed to identify sibling relationships, (sharks that share one or both parents), the most informative of which are half-sibling pairs from different birth-years. Genetic-based mark-recapture analysis provided the first empirical estimates of adult abundance and the basis for estimating reproductive frequency and adult survival. It also shed light on population structure see( story on page 46). Acoustic tags (5–10 year duration) and satellite tagging were used to trace movement patterns (including residency and depth-swimming behaviour), identify habitats, examine growth rates, and further explore ABOVE: Acoustic and satellite tagging were used to trace White Shark movement population structure. Aerial and vessel-based surveys at nursery patterns, identify habitats, examine areas were trialled to provide estimates of juvenile abundance. These growth rates and explore population data support a population model being developed to estimate total structure. Image: Justin Gilligan, NSW DPI population abundance and population trend for eastern Australia.

Key findings data also support the two-population Detections of acoustic-tagged juvenile sharks continue to provide movement structure across Australia, with data and, over time, will provide survival estimates. Juveniles were recorded on a low interchange rate between 273 acoustic receivers spanning the eastern Australian coast, from Lady Elliott populations. These data will provide Island in the southern Great Barrier Reef to Flinders Island off north-eastern the first empirically derived estimates Tasmania (more than 179,000 detections). A shark tagged in New South Wales of reproductive frequency and, was detected on receiver arrays in New Zealand and several sharks tagged by with further sample analysis, adult New Zealand colleagues were detected in eastern Australia. These data highlight mortality rates. These measures are the utility of broad-scale acoustic receiver arrays deployed under the Integrated needed for population models to Marine Observing System and data-sharing between partner institutions. estimate total population sizes for juveniles and adults, and to assess Tagging data continue to support a two-population model for White Sharks the relative and cumulative effects of in Australia, separated east and west by Bass Strait, and the migration mortalities over the whole life span. of juveniles along the eastern seaboard between eastern Tasmania/ south-eastern Victoria and the southern Great Barrier Reef. They provide The finding of half-sibling matches further evidence of shark movements between eastern Australia and New in a small number of sharks (51) Zealand, and multi-year return and occupancy of two known east coast analysed as a trial from the western Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery nursery areas (Port Stephens, NSW and 90 Mile Beach-Corner Inlet, Vic). population suggests the size of this population may also be estimated Tagging data predict a higher level of movement and potential for gene in future (with further sample flow (or transient movement of non-breeding sharks) between Australia analyses and refinements). and New Zealand than between the east and west of Bass Strait. Tagging of adults in South Australia Tissue samples were collated from 331 White Sharks (129 ‘eastern population’, combined with vessel-based and 185 ‘western population’ and 17 from New Zealand). Genetic analyses have aerial surveys of the southern identified half-sibling and full-sibling sharks in the relatively limited number of Australian coast are providing east coast samples. Adult population size for eastern Australia was estimated the first evidence for nursery at 750–1200 individuals; further analyses will improve this estimate. Genetic areas west of Bass Strait.

44 NERP MARINE BIODIVERSITY hub • FINAL REPORT New knowledge and opportunities Science-based advice was provided to support conservation actions, Tools developed in this project provide for the first empirical estimates of adult management of shark-based tourism, population size of a highly vagile threatened marine species. They provide the and policy regarding public safety. basis for effective monitoring that could be applied to assess other marine In the government sphere, advice 2 species for which population data are poor. Further refinements of the genetic has been provided to Federal and technique will enable estimates of single-generation abundance trends, without State agencies, departments and the need for long-term monitoring. This represents a paradigm shift in the ministers (including the Environment capacity to define conservation needs for this and similar threatened species. Protection Authority of Western Opportunities exist to improve knowledge of the western White Shark Australia, the Federal Department population (including identifying nursery areas), to continue tissue sampling of the Environment, New South tagged sharks, and to apply the integrated genetic analysis and modelling Wales Department of Primary approach to estimate population size and status. A similar approach is Industries and the South Australian now being applied to the Grey Nurse Shark and could be applied to other Department of Environment, species of concern such as the Mako Shark, the Dugong, and turtles. Water and Natural Resources). Outputs and outcomes Reports and journal papers have been generated on topics including This project has developed the first empirically-derived adult White novel genetic techniques for Shark population estimates (worldwide) and provides the basis for estimating population parameters, estimating measures of key population attributes (reproductive mark-recapture modelling, tagging frequency, survival rates) needed to estimate population trends. It has and tracking, movements and identified key habitats in eastern Australia and laid the groundwork for aggregations, habitat, and health. estimating total population size and status in Australian waters. Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery

ABOVE: Acoustic-tagged juvenile sharks continue CONTACT to provide management data and, over time, will Barry Bruce provide survival estimates to support a White Shark [email protected] population model. Image: Justin Gilligan, NSW DPI (03) 6232 5413

NERP MARINE BIODIVERSITY hub • FINAL REPORT 45 Estimating population size and

characteristics of rare and CONTACT Mark Bravington [email protected] endangered species (03) 6232 5118

Advanced genetic and statistical techniques have been combined to develop working. Dozens of full and half-siblings a reliable way of monitoring rare but wide-ranging species such as sharks and have been identified among hundreds sawfish and has the potential for extension to other species including dugongs of Speartooth Shark and White 2 and turtles. The method has evolved from a simpler version developed by Shark samples, and for these two CSIRO in 2012 that now underlies the management of Southern Bluefin Tuna. species sufficient data exist to make It is based on ‘mark-recapture’: the principle that if some animals in a given preliminary abundance estimates. area are caught and marked, the proportion of animals in a later, second round of captures that are caught twice can be used to estimate the total population. Besides adult abundance, other parameters that can be estimated The new monitoring technique extends the mark-recapture principle to from close-kin mark-recapture use natural genetic ‘marks’ to identify animals that are close-kin pairs include adult survival rates, breeding (full or half-siblings, or parent and offspring). These paired relationships frequency, female reproductive are identified from tissue samples taken from live or dead animals. parameters and stock structure. Importantly, because the mark is a natural piece of the inherited DNA, These parameters are important no first round of captures to place artificial marks is required. for evidence-based management, The ability to find half-siblings (that share the genetic mark from only one and have been impossible to parent) has only become possible in the past five years thanks to improved estimate for rare but wide-ranging genetic technology, and it means that juvenile samples can be used to study shark and sawfish species. the adult population. This is a breakthrough for many sharks and sawfish species for which adults cannot be caught in large numbers. Data from Ongoing challenges are to optimise other sources such as acoustic tagging provide additional information on the identification of close-kin pairs, factors including age-specific mortality rates and movement patterns. Where and to scope the potential of emerging feasible, these data can supplement the close-kin population estimate genetic tools. It also remains to to pinpoint when and where population-limiting mortality occurs. develop abundance and survival rate estimates for two shark species, and Key challenges tackled during this project have been to improve the reliability examples of how the outputs can of the genetic techniques and to devise a statistical and demographic provide evidence for the recovery of framework for close-kin mark-recapture that incorporates information from threatened and endangered species. additional sources. The good news is that the genetic techniques appear to be Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery

Speartooth Shark pup from the Adelaide River, NT. Image: Charlotte Klempin, Charles Darwin University

46 NERP MARINE BIODIVERSITY hub • FINAL REPORT 2

Conducting sawfish research in the South Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery Alligator River estuary, NT. Image: Charlotte Klempin

NERP MARINE BIODIVERSITY hub • FINAL REPORT 47 Supporting the IUCN Red List

The International Union for Conservation of Nature (IUCN) Shark Specialist Group (SSG) pictures a world in which sharks and rays are 2 valued and managed for sustainability. Its members conduct IUCN Red List assessments, contribute to conservation strategies and policies, identify research needs, and communicate to a range of audiences. In January 2014, the SSG published the first systematic, global assessment of shark status and conservation (including extinction-risk across 1041 species) to help guide responses to the issue of shark declines. Several NERP Marine Biodiversity Hub scientists participated in the SSG, including as the Co- Chair of Taxonomy and the Regional Vice- Chair for Australia and Oceania, thereby continuing more than a decade of involvement in the extinction risk study. Hub members also contributed to the global conservation strategy for sawfishes. ABOVE: A juvenile Largetooth Sawfish. The sawfishes were arguably the Approach most threatened family of marine fishes globally, with all five species The IUCN Red List of Threatened Species Categories and Criteria was applied globally Critically Endangered or to assess extinction risk. Thirteen workshops were held worldwide (over Endangered. Image: Peter Kyne the full period of the study) with the first in Queensland in 2003. Many Red List assessments for sharks and rays were authored or co-authored, and contributions were made to a global conservation strategy for sawfishes. Involvement with the IUCN process ‘provides an opportunity Key findings to complement species status The study found that, globally, 17.4% of all chondrichthyans were assessments and recovery threatened with extinction and 46.8% were Data Deficient (insufficient planning under Australia’s information available to accurately assess status). Taking into account the Environmental Protection and possible status of Data Deficient species, 23.9% of all chondrichthyans Biodiversity Conservation Act were predicted to be threatened with extinction: higher than for birds, 1999 and state legislation. and comparable to mammals. In Australia, 15.6% of chondrichthyans The high level of data deficiency were threatened with extinction and 23.3% were Data Deficient. reinforces the need for more The sawfishes were arguably the most threatened family of marine research that will reduce uncertainty fishes globally, with all five species globally Critically Endangered to acceptable levels and promote or Endangered. Northern Australia is a remaining population a better understanding of the stronghold for the four species occurring in the Indo-Pacific. status and sustainability of chondrichthyans in Australia. New knowledge and opportunities Many Australian chondrichthyan species are due for reassessment (species Outputs and outcomes should be reassessed every 10 years). In collaboration with a James Cook Additional scientific papers were

Supporting the recovery of threatened, endangered and protected species Supporting endangered and threatened, of protected the recovery University project (funded by the Fisheries Research and Development published on topics including Corporation) to review the status of Australia’s sharks, the IUCN Shark Specialist the global extinction risk and Group participated in an assessment workshop held in Townsville in February conservation of sawfishes, and 2015 to reassess the status of all Australian sharks and rays for the IUCN the conservation status of North Red List of Threatened Species. Australia’s shark experts, including several American, Central American and Marine Biodiversity Hub researchers, undertook updated assessments for Caribbean chondrichthyans. all 325 chondrichthyans (sharks, rays and chimaeras) occurring in Australian waters, with these to be published on the IUCN Red List later in 2015. CONTACT Peter Kyne [email protected] (08) 8946 7616

48 NERP MARINE BIODIVERSITY hub • FINAL REPORT Management of Commonwealth marine reserves and the Great Barrier Reef World Heritage Area 3 IMAGE: Matt Curnock

NERP MARINE BIODIVERSITY hub • FINAL REPORT 49 The need

Commonwealth marine reserves are areas established under the Environment Protection and Biodiversity Act 1999 (EPBC Act) 3 to help conserve Australia’s spectacular marine life. The establishment of Commonwealth marine In responding to the requirement for research to reserves in 2007 (South-east region) and 2012 meet the needs of CMR network managers, Hub (South-west, North-west, North and Temperate scientists have worked with the Department to: East regions and the Coral Sea) completed • break down higher level policy objectives to the Commonwealth waters component of the scientifically measureable operational objectives; National Representative System of Marine Protected Areas (NRSMPA), and met the • develop survey approaches to cost-effectively Government’s commitment at the United Nations monitor (or provide a baseline to monitor against) World Summit on Sustainable Development fine-scale changes in biodiversity that are statistically in 2002 to develop such a system by 2012. representative of the broader marine reserve; • conduct public surveys to determine how The CMR network was designed to meet the needs the public understands and values marine of a comprehensive, adequate and representative biodiversity and the CMR network; system (CAR) that also minimised impacts on other marine users. Scientific input from the • compare environmental conditions in areas closed Commonwealth Environment Research Facility to fishing compared with adjacent fished areas. (CERF) Marine Biodiversity Hub included assembling In the process of this research, Hub scientists have: all available data and predicting biodiversity distributions at medium to large scales (kms to • improved the knowledge and description of the thousands of kms) to meet the CAR objectives. marine environment within selected CMRs; While this scale of scientific data was appropriate • collated existing data to show the pressures for planning, it is of limited value for managing the facing the marine environment and their CMR network. Management requires more detailed potential for cumulative impactSection ( );1 knowledge at finer scales so that any changes in the • conducted an extensive review of existing environment inside the CMR can be compared with data for 54 CMRs (Section );1 and changes in similar areas outside the CMR network. • identified fish communities in all 14 reserves of the SECMR network. Monitoring the Great Barrier Reef World Heritage Area

At the request of the Australian Government, Hub researchers led a collaborative research project to establish an integrated monitoring framework for the Great Barrier Reef World Heritage Area, including social and economic aspects. The framework was designed to contribute to the strategic assessment of the Great Barrier Reef under the EPBC Act, as well as to the Long-Term Sustainability Plan for the World Heritage Area. Management marine Commonwealth of reserves and Heritage the Area GBR World IMAGE: Reef Life Survey

50 NERP MARINE BIODIVERSITY hub • FINAL REPORT Applying spatially balanced survey designs to monitor indicators in Commonwealth marine reserves

Australia’s Commonwealth Marine Reserve (CMR) network covers 2.76 million km2 of continental shelf, slope, and abyssal habitat. The shelf provides a mosaic of shallow water habitats (to about 200 metres deep) that support a diversity of marine species and species assemblages, but little is known about the extent of these habitats or the 3 status and trends of their associated assemblages. One way to address this important knowledge gap is to map the seafloor using multi-beam sonar (MBS) but in these water depths this would be a slow process. A survey vessel dedicated to mapping 24 hours a day, every day of the year, would take 3.5–17.5 years to cover the 306,627 km2 of CMR seafloor lying within the biologically diverse 40–200 m depth range. Even then, data would be available only for the seafloor habitats, not the resident species and assemblages. A more pragmatic approach is required to provide early and cost effective methods to gain insight about the extent of shelf habitats in CMRs and the status and trends of marine life. This project successfully implemented a new sampling approach that enables managers to acquire accurate baseline measurement of environmental assets in the CMR ABOVE: A hypothetical surface showing the network. Trends in these assets can also be collected in a cost-effective typical patchiness of a benthic biodiversity indicator in the South-east CMR network, manner during the prolonged period required to complete mapping. together with the features of 40 Simple Establishing the baseline status of the CMR network at an early stage, and Random Samples (blue dots) and 40 tracking trends in key indicators, are essential for management agencies spatially balanced GRTS samples (green to get timely information on the performance of the CMR network. dots). The clumping of the SRS samples is clearly evident, and in this instance the SRS samples fail to identify the Approach biodiversity hotspot in the bottom right of The alternative approach to continuous MBS acquisition termed a GRTS the sample frame. Both designs capture (Generalised Random Tessellation Stratified) design works by collecting the true mean value of the indicator but the confidence interval of the SRS samples at small scales across broad areas. Sampling inference methods estimator is 20% larger than that of the are then used to draw conclusions about the entire region of interest GRTS estimator because the variance of (such as a zone or reserve). This approach can complement continuous the indicator is higher. Image: CSIRO

MBS acquisition and allow monitoring of status and trends to start during BELOW LEFT: The GRTS design was used in the long lead-in time required to acquire continuous MBS data. surveys of the Tasman Fracture CMR to target reef habitat. Image: CSIRO/IMAS Theme 1 of the Marine Biodiversity Hub trialled the GRTS approach in the Flinders CMR, and subsequently employed it in the Geographe CMR and Houtman-Abrolhos Key Ecological Features (KEFs). The technique is endorsed means that the survey design can and used by the United States National Park Service, but has not previously accommodate unexpected loss been implemented in Australia nor adapted to the peculiarities of sampling of sampling effort due to poor from vessels in marine environments beyond the reach of divers. weather, equipment breakdowns, or the vagaries of the funding cycles, Key advantages without comprising statistical validity. The GRTS methodology ensures that sample sites in an area of interest, such as the shelf habitats of a CMR, Judgemental samples cannot be are distributed in a spatially balanced way. This used to infer the status of regions approach avoids problems experienced with that are not sampled. Simple random other sampling designs such as judgemental samples are undesirable because sampling, simple random sampling, they tend to clump in space (see or the placement of samples on a figure above). On average they are Management marine Commonwealth of reserves and Heritage the Area GBR World regular grid. The flexibility of less likely than spatially balanced the GRTS approach also samples to detect features of

NERP MARINE BIODIVERSITY hub • FINAL REPORT 51 LEFT: (A) Multibeam sonar habitat mapping and sample locations (1─40) of the GRTS design drop camera survey of shelf habitats of the Multiple Use Zone of the Flinders CMR showing the cluster 3 of mixed reef sample points discovered in the north-western corner of the reserve. MBS mapping of the drop camera locations (B), and of a continuous patch of seabed (C) shows the typical patchiness of the reef habitat. Image: GA/CSIRO/IMAS

survey teams to preferentially sample areas of particular interest if the location of these areas is known in advance. This facility was put to good use in the survey within the Tasman Fracture CMR to target reef habitats of rock lobster. It ensured a good sample size to test the effect of the exclusion of fishing within part of the CMR on the size-frequency distribution of rock lobster, and ensured that the data collected are representative of the CMR as a whole. interest, such as regions of high benthic biodiversity in the CMR network associated with distinct reef features that can be tens to thousands of Outputs and outcomes metres apart. The clumping also acts to inflate estimates of indicator Spatially balanced survey designs variance, (an essential factor in determining evidence for a trend). And have been successfully trialled at while regular grid sampling can allow the mean value of an indicator to be several CMRs and KEFs, facilitating assessed, it does not allow the variance of the indicator to be estimated. design and model-based inference of the extent and status of benthic New knowledge and opportunities habitats that would have not been By applying spatially balanced designs, Marine Biodiversity Hub project teams identified using judgmental, simple discovered what appears to be a cluster of mixed reef habitats in the north- random or regular survey designs. western corner of the Flinders CMR reserve (see figure at left), and seagrass beds and reefs in the Geographe CMR that are much more extensive than previously CONTACT thought (see stories on pages 54 and 57. Furthermore, the GRTS design allows Keith Hayes [email protected] (03) 6232 5260 Management marine Commonwealth of reserves and Heritage the Area GBR World

LEFT AND ABOVE: The GRTS design allows survey teams to preferentially sample areas of interest if the location is known in advance. This facility was used in surveys of the Flinders CMR, and to discover seagrass beds and reefs in the Geographe CMR. Images: CSIRO (left) and Curtin University

52 NERP MARINE BIODIVERSITY hub • FINAL REPORT Valuing the South-east Commonwealth Marine Reserves Network

Marine reserve networks are designed to protect biodiversity makers involved coastal zone and marine management used the and maintain the ecological integrity of marine ecosystems, Analytic Hierarchy Process to elicit however trade-offs are involved in their design and priorities the importance of different types of need to be identified for effective management. information used in decision making. 3 The costs and benefits of different designs, and priorities for stakeholders Key findings that have direct links to the ocean are relatively easy to quantify. Full public surveys are ongoing, Less so are the costs and benefits on the general public, who may but the results of the pilot surveys hold ‘existence values’ for assets protected by these networks. are informative. In the choice Identifying and quantifying these existence values may highlight a public experiment, respondents revealed desire for management, and provide management guidance. This research will positive values for protection, but provide information to managers about public attitudes, understanding and only if they had prior knowledge of effectiveness of communication in relation to marine reserve networks such the ecosystem attributes. This early as the South-east Commonwealth Marine Reserves (SECMR) Network. It will finding suggests that the preferences also develop an understanding of how coastal and marine decision makers revealed are not ‘constructed’ understand and apply the economic valuation of environmental services. during the survey, but may in fact reflect robust, pre-existing values. Approach Public education may extend those Decision makers and members of the public are being surveyed. In the latter values to a broader section of the case, large scale representative samples of the relevant population (from south- community. Ongoing work will eastern Australia) have been surveyed. The surveys include many attitudinal reveal the extent to which these questions about the respondents’ knowledge and perceptions of the SECMR values are affected by the way (such as threats, purpose, and level of protection). These are complemented information is provided in the survey. by valuation questions, using the choice experiment format. Respondents are The survey of decision makers found asked to choose between hypothetical management investments intended that biophysical criteria were used to protect different assets to differing degrees. This process reveals which in preference to economic values aspects of the SECMR the respondents’ value most. The effect of varying the (such as existence values derived form of presentation of from surveys) in decision making. information about the This partially reflected the academic reserve system (including background of most decision makers, videos and expert opinion) with relatively few having formal on values is also explored. economics training. The survey also found that, in most cases, Although a significant appropriate economic valuation amount of work on information was not available for use, identifying public values and decision-making processes had for environmental assets developed in the absence of such can potentially be used to information. Increased availability support management, it of economic valuation data may is not clear to what extent increase its use in decision making. such information is viewed as valuable by decision Outputs and outcomes makers. To address this This research is part of a large issue, in 2013, an Australia- program of valuation surveys that wide survey of decision will provide information on the values held by community members for several Australian marine ABOVE: A seastar among deepwater corals at 1115 m water depth in the Huon CMR, ecosystems. It is building knowledge part of the South-east Commonwealth about the perceptions of the

Marine Reserves Network. Image: CSIRO community towards marine reserve Management marine Commonwealth of reserves and Heritage the Area GBR World LEFT: A lobster forages on deep reef and marine assets, in terms of threats in the Huon CMR. Image: IMAS and current status. It also identifies the values held for assets protected CONTACT within marine reserves, and the Michael Burton way that the public is prepared [email protected] (08) 6488 2531 to trade-off different assets.

NERP MARINE BIODIVERSITY hub • FINAL REPORT 53 Surveys of Commonwealth marine reserves: Flinders

The Flinders Commonwealth Marine Reserve (CMR) east of sheltering invertebrates such as commercially important rock Tasmania’s Cape Barren Island stretches some 600 kilometres lobsters and fishes. Different and covers an area of 27,000 km2. seabed features such as low 3 profile, often sand-inundated Temperate reef systems in the CMR support many mobile and commercially- important species, but little has been known about biological communities reefs, and step features and beyond depths accessible to divers (below 25 m). This project trialled canyon heads, had quite different cost-effective survey techniques in the Flinders CMR, based on a novel assemblages, showing that application of a Generalised Random-Tessellation Stratified (GRTS) further sampling is needed to fully design (see story on page 51). It quantified and documented habitats and understand the diversity of the communities, mapped an important canyon head feature, and launched Flinders CMR shelf. Ultimately, a new, deep water Baited Remote Underwater Video (BRUV) system. The complete multibeam mapping with survey approach will facilitate biodiversity baseline inventories, monitoring, representative biological sampling and performance comparisons across Australia’s CMR network. is needed to fully inventory the extent and types of habitat and Approach the cover of key benthic species, but the GRTS approach provides a A flexible, two-phase survey design was implemented for the area of the statistically valid interim baseline Flinders CMR confined to the shelf. Phase one of the GRTS survey used a drop to improve knowledge and camera to characterise the seabed habitat at 40 sites. In phase two, further understanding of conservation habitat and biological samples were obtained from 12 of these sites using high- values in the Flinders CMR. resolution multibeam sonar, towed stereo video and shallow BRUV systems. Locations identified (during Phase 1) as low-profile reef supporting rich fish and invertebrate communities were preferentially sampled in this process. As a comparison to the GRTS-based approach, an area of approximately 30 km2 – within which shelf- incising canyon heads were known to be located – was continuously mapped using a high-resolution multibeam sonar. This mapping confirmed the presence of several low-profile reefs, some of which may be relict coastline features. Autonomous underwater vehicles were used to obtain further samples of habitats, fish and invertebrate communities on these reefs without the need for invasive sampling. In a first for Australian researchers, the survey team also deployed and retrieved three deep BRUV systems in water depths exceeding 500 m on the slope of the Flinders continental shelf. Key findings This project showed that cost-effective, quantitative baseline estimates of demersal habitat types and associated invertebrate communities can be developed for the shelf and upper slope regions of temperate CMRs (in this case Flinders CMR). Demersal fish communities in shelf regions can also be inventoried and characterised. Diverse reef systems revealed during the survey include steep, canyon-head structures with underwater cliffs, flat sedimentary rocks, and Management marine Commonwealth of reserves and Heritage the Area GBR World sandstone and mudstone stacks with ledges

RIGHT: Multibeam mapping completed at depth in the Flinders CMR. Stars mark the sites of BRUV drops and coloured dots indicate predominant substrate type: sand or mixed (reef sand). Image: CSIRO/IMAS/GA

54 NERP MARINE BIODIVERSITY hub • FINAL REPORT 3

New knowledge and opportunities ABOVE LEFT: Photographic inventories of deep-water fish communities at 500 m The survey approach used in this project was designed to meet the statistical depth were made for the first time in the requirements for establishing a long-term monitoring baseline. It aims to do Flinders CMR using Deep BRUVs: baited, this cost-effectively by maximising the information obtainable from a time- instrumented, camera systems deployed on limited survey, and providing a statistically coherent process for incorporating the seabed. Electronic controls initiate and synchronise the cameras, lights and bait information collected in future surveys. Seabed features and associated fauna delivery, enabling images to be collected are sampled in a way that enables their abundance throughout the CMR to for extended periods (weeks to months). be quantified, features of interest to be targeted, and biodiversity estimates Sensors measure environmental conditions. improved. This represents a significant advance on typical deep-water surveys. ABOVE CENTRE: Sponges and bryozoans growing on low-profile reef on the shelf A previously unknown cluster of mixed reef habitat was identified in the of the Flinders CMR. This image was north-western corner of the Flinders CMR shelf (now a candidate for taken with the CSIRO towed stereo subsequent continuous multibeam sonar). It has provided a basis for identifying camera system at 38 m depth. candidate indicator species that can be monitored for evidence of change. ABOVE RIGHT: Striped Trumpeter in The survey provided the first in-field experience with deep BRUVs and the Flinders CMR. Images: IMAS identified ways to improve equipment design and data analysis. With future hardware development, deep BRUVs have good potential for monitoring deep seabed ecosystems, and can be cost-effective because The spatially balanced design they can be deployed and retrieved by passing fishing vessels. approach developed for this CMR has subsequently been used for surveys Outputs and outcomes in the Oceanic Shoals, Geographe This project trialled a combination of techniques for long-term monitoring that and Tasman Fracture CMRs. are cost-effective, non-extractive, flexible, have a high power for extrapolation, and are transportable to the deep ocean (a large portion of CMRs). The A collaborative approach that techniques were used to produce quantitative estimates and high-resolution pooled the expertise and capacity maps of reef systems and associated diversity across the Flinders shelf. of diverse research partners was pivotal to the successful Quantitative baseline estimates and a comprehensive inventory of potential application of new and existing targets for sustained CMR monitoring strategy were demonstrated, sampling techniques within a novel (contingent on CMR operational objectives), providing valuable learning statistical design, and emphasised experiences that will improve the cost-effectiveness of future surveys. the value of collaboration. Standardised statistical survey design and methods are essential for Management marine Commonwealth of reserves and Heritage the Area GBR World establishing trends in key indicators within a CMR, and for cross-comparison CONTACT Keith Hayes between CMRs. These comparisons will assist in network management and [email protected] review, and can be designed to be adaptable to changing survey capacity. (03) 6232 5260

NERP MARINE BIODIVERSITY hub • FINAL REPORT 55 Southern Rock Lobster thrive in Tasman Fracture CMR

The Tasman Fracture Commonwealth Marine Reserve When depth-related differences in abundance were (CMR) is the southernmost CMR of the continental accounted for, however, the size structure reflected a Australian CMR network. It has been established strong effect of protection, with markedly larger male 3 for more than seven years, and protects previously- and female lobsters in the CMR. Model-based analysis fished shelf reef habitats in a ‘no-take’ Marine is under way to further examine these patterns. National Park Zone, one of few such zones on the An Autonomous Underwater Vehicle survey took a shelf within the South-east CMR network. This project photographic inventory of benthic habitats, to help evaluated the effects of this protection on target calibrate multibeam sonar estimates, and describe species (particularly for Southern Rock Lobster) and the dominant benthic biota. In March, a baited their ecosystem, and contrasted the changes with underwater video provided an initial inventory and adjacent habitats that remained open to fishing. size frequency of fish fauna to identify whether target Multibeam sonar mapping found most reef habitat in species such as Stripey Trumpeter and Jackass Morwong the north-west of the protected zone, continuing as have benefited from the no-take protection. coastal reef systems in adjacent state waters. The reefs When completed, this project will have provided an typically extended to about 100 m in depth, except inventory of the shelf reef habitat and associated for an isolated patch reef in the eastern sector that benthic fauna of the ‘no-take’ zone of the Tasman extended to 140 m depth and forms a unique feature Fracture CMR, an understanding of the benefits of this CMR, rising up to 20 m above the seabed. that no-take protection may offer exploited An intensive rock lobster potting survey on reef systems populations, an insight into the ecological processes in and adjacent to the CMR examined lobster abundances that structure deep reef populations in the CMR, and size structure in fished and protected locations. and a greater understanding of cross-shelf reefs. Initial findings indicate that overall abundances in the CMR protected zone are approximately 30% of nearby fished habitats (as the CMR contains significantly CONTACT Neville Barrett more deep reef than nearby fished locations, and [email protected] less of the shallower habitat that lobsters prefer). (03) 6227 7210

TOP: An intensive rock lobster potting survey on reef systems in and adjacent to the CMR examined lobster abundances and size structure in fished and protected locations.Image: IMOS/IMAS Management marine Commonwealth of reserves and Heritage the Area GBR World

ABOVE LEFT: The isolated patch reef that provides the most defining feature of the eastern sector of the no-take zone in the Tasman Fracture CMR. It is approximately 1 km in length and 300 m wide, and ranges from a depth of 95 m to 130 m. Image: IMAS/CSIRO

ABOVE RIGHT: An overview of knowledge of the Tasman Fracture CMR seabed features on the shelf and slope prior to the detailed NERP Hub survey of shelf reef habitats. The CMR is indicated by blue shading and the ‘no-take’ zone is delineated by a red-line in the eastern segment of the shelf. Image: IMAS/CSIRO

56 NERP MARINE BIODIVERSITY hub • FINAL REPORT Surveys of Commonwealth marine reserves: Geographe

The Geographe Commonwealth Marine Reserve (CMR) lies Key findings within and adjacent to Geographe Bay south of Perth, Preliminary analyses indicate that Western Australia, and has a depth range of 15–70 m. Geographe appears to contain one of the largest continuous seagrass beds 3 It is an area of high benthic productivity and high biodiversity that recorded. Fish assemblages differ by provides habitat for threatened and migratory seabirds, the humpback depth and habitat (seagrass, reef, whale and blue whale, and the Western rock lobster. More information sand). The complete project findings is needed in order to establish a monitoring program for this reserve, will be available in June 2015. which adjoins the Ngari Capes Marine Park (in state-managed waters). This project designed a statistically robust baseline survey of the Geographe New knowledge CMR to meet the research and monitoring needs of Parks Australia. and opportunities Approach The survey approach proved a cost-effective way to provide a Existing information was collated on the distribution and characteristics of key CMR baseline and a consistent habitat types (seagrasses, corals, rocky reefs and soft sediments) and associated monitoring approach that will benthic invertebrate and benthic vertebrate communities in the Geographe support future comparisons CMR. A statistically robust survey was designed to meet survey objectives between CMRs and regions. The defined with input from Parks Australia, building on and trialling survey GRTS design was supplemented methodologies developed for the Flinders CMR (see story on page 54). The with targeted reef monitoring survey was implemented during the period December 2014 to March 2015, and based on expert knowledge. the data analysis and final report will be completed by the end of June 2015. The survey consisted of 150 Baited Remote Underwater Video (BRUV) drops Outputs and outcomes across the CMR. The sampling sites were selected using the Generalised Existing information has been Random Tessellated Stratification survey designsee ( story on page collated and documented for 51). Additional habitat information was obtained by placing rear facing key habitat types and associated cameras on the BRUV units. The field crew were also able to deploy 50 communities in Geographe CMR. BRUVs at known reef and seagrass features, thereby augmenting existing Anticipated outcomes include a information on the fish communities on these features. Autonomous statistically robust baseline of habitat Underwater Video transects will be completed in late March 2015. extent – including a characterisation of habitat types and associated benthic communities – that will provide a basis for subsequent trend analysis to meet Parks Australia management objectives.

CONTACT Emma Lawrence [email protected] (07) 38335 538

TOP: A Prickly Leatherjacket (Chaetodermis penicilligera) camouflaged among macroalgal habitat at the Geographe CMR is photographed by a stereo baited remote camera system.

ABOVE LEFT: An Eagle Ray (Myliobatis tenuicaudatus) and two Pink Snapper (Pagrus auratus) on a mixture of macroalgal and sand habitat.

CENTRE LEFT: A Western Blue Grouper Management marine Commonwealth of reserves and Heritage the Area GBR World (Archerodus gouldii) swims past smaller reef fish feeding on the bait bag of a stereo-baited remote video system.

BOTTOM LEFT: A large Smooth Stingray (Dasyatis brevicaudata) swoops over the bait bag on a macroalgae substrate. Images: Curtin University

NERP MARINE BIODIVERSITY hub • FINAL REPORT 57 Sand and granite reef communities revealed at Freycinet CMR

Parts of the Freycinet Commonwealth Marine Reserve (CMR) east of Tasmania were opportunistically mapped by the Marine 3 Biodiversity Hub during transit voyages between Hobart and the Flinders CMR, a focus of Hub research. The transit mapping, plus additional, targeted transects, revealed relict coastline reefs in 80─100 m depths extending north of Bicheno. The reefs appear relatively continuous in the CMR, and provide important habitat for Stripey Trumpeter, an important species for commercial and recreational fishers. Further mapping detected reef features inshore of the relict coastline: complex granite reef systems supporting more substantial fish and invertebrate assemblages. Most notable was a 200 m long granite reef 7 km south-east of Bicheno that rose sharply from 80 m to 60 m. Benthic habitats and biodiversity have been photographed in repeated surveys with an autonomous underwater vehicle (AUV). (AUV surveys were begun at Freycinet CMR during the Commonwealth Environment Research Facility Marine Biodiversity Hub; later surveys have been supported by the Integrated Marine Observing System, the Institute for Marine and Antarctic

Studies and the Department of the Environment.) TOP: An isolated granite reef mapped 7 km to the south-east of Bicheno Preliminary examination of the AUV imagery at the Freycinet CMR. Tracks indicates that the relict reef systems are show the location of AUV surveys undertaken in 2011 and 2014 to generally very low profile and partially sand- provide an understanding of the inundated, with a sparse coverage of sponges biota and its temporal variability in and similar invertebrates, few benthic fish, and high-profile deep reef systems of the CMR network. Image: GA/IMAS with distinct brittlestar aggregations at the reef ABOVE: The AUV Sirius being deployed to sand interface. In stark contrast, the granite in the Flinders CMR from the reef has an extensive and complex sponge, Australian Maritime College Vessel Bluefin, on charter to the NERP Marine bryozoan and ascidian fauna and an abundant Biodiversity Hub. Image: IMAS fish assemblage, dominated by Butterfly Perch. UPPER RIGHT: An AUV-derived image Further work on the AUV imagery would provide of the benthos at the interface between sediments and relict reef a greater understanding of bioregional patterns, systems on the shelf in the Freycinet and year-to-year variability in biological indicators CMR. Features include bare sand to the right, an interface marked by of change. The acquired imagery and metadata is brittlestars, sponges, ascidians and Management marine Commonwealth of reserves and Heritage the Area GBR World available on the Australian Ocean Data Network. drift algae, and the sand inundated invertebrate turf matrix typical of the relict reef itself. Image: IMOS/IMAS

LOWER RIGHT: An AUV-derived image CONTACT from the granite bommie survey Neville Barrett shows large sponges (massive and [email protected] finger morphotypes), sea fans, and (03) 6227 7210 butterfly perch.Image: IMOS/IMAS

58 NERP MARINE BIODIVERSITY hub • FINAL REPORT Surveys of Commonwealth marine reserves: Coral Sea

Australia’a Coral Sea Commonwealth Marine Reserve (CMR) covers an area of 989,842 km2 and is one of the largest marine protected areas in the world. 3 Key Ecological Features identified for the Coral Sea include the Tasmantid seamount chain and the reefs, cays and herbivorous fishes of the Queensland and Marion plateaus. Despite the ecological value of emergent reefs in the Coral Sea, integrated surveys to characterise the distribution of reef communities have been lacking. This project analysed data from surveys covering most reefs in the Coral Sea CMR, helping to improve the scientific information base for reserve management. The results of recent fish, invertebrate and coral surveys by trained volunteer divers associated with Reef Life Survey (see story on page 65) at the majority of Coral Sea reef systems were analysed in this project. These data provide an ecological baseline of the state of shallow-reef biodiversity across the Coral Sea. Approach Data generated by volunteer Reef Life Survey divers were analysed following surveys of densities of fishes, invertebrates and macroalgae at 17 of 19 major reef systems across the Coral Sea. Dive teams surveyed 160 sites, primarily during May to July 2013. Of 160 sites analysed, 35 were in the former Coringa-Herald and Lihou Reef national nature reserves (declared in 1982) while all others were on reefs open to commercial and recreational fishing, albeit now included in the larger Coral Sea CMR. Key findings Coral Sea reef communities were found to be unique in Australian territory. They had different dominant fish and invertebrate species to those commonly observed on shallow reefs along the Great Barrier Reef (GBR), and a high similarity to reefs off oceanic Pacific islands over 1000 km distant, such as Tonga. Fish communities differed between northern (north of Marion Reef) and southern reefs. Areas closed to fishing since 1982 (the Coringa-Herald and Lihou reef systems) supported higher fish biomass than comparable sites. Abundance patterns were driven largely by planktivorous and benthos- associated damselfishes, schooling wrasses, and small-bodied surgeonfishes, while biomass patterns were typically driven by the few large-bodied individuals, such as sharks, groupers, coral trout and large grazers.

RIGHT, FROM TOP: Bird Island Reef in the Coral Sea; The olive sea snake (Aipysurus laevis) was extremely common on reefs in the southern Coral Sea, a global hotspot for seasnake diversity; Coral Sea reefs are inhabited by many species that are common among central Pacific Islands, but rare on the Great Barrier Reef, such as this ocellate damselfish Pomacentrus( vaiuli) at Cato Reef.

BELOW: Wreck Reef in the Coral Sea. Images: Reef Life Survey Management marine Commonwealth of reserves and Heritage the Area GBR World

NERP MARINE BIODIVERSITY hub • FINAL REPORT 59 3

Coral Sea reefs possess high densities of reef sharks and sea snakes, and are Outputs and outcomes a global hotspot for these groups. With declining numbers of sea snakes on The Coral Sea CMR provides a the GBR and off north-western Australia, the southern Coral Sea is a remnant reference yardstick for assessing stronghold for sea snake species. Sea snakes were ubiquitous and abundant changes in similar wave-exposed on all reefs from Marion Reef southwards, but were not observed on more coral reef environments with northern reefs. Higher numbers of reef sharks were sighted by divers in this greater human-related stresses, survey than present at most locations worldwide. The survey also provided including across the wider oceanic a first indication of sea turtle occurrence on many of the Coral Sea reefs. Pacific region. Ongoing monitoring Coral assemblages of most reefs were dominated by encrusting corals, of the same sites and reefs using with some exceptions. Coral cover is relatively high on southern reefs comparable methodology will such as Cato and Wreck Reefs (approximately 40%), where fragile contribute to long-term conservation branching corals are common, but tends to be much lower on central management of the Coral Sea CMR. and northern reefs, probably due to frequent cyclone disturbance. Data from the Coral Sea survey are New knowledge and opportunities being made available through the Australian Ocean Data Network Reef Life Survey provides a scientifically validated and cost-effective option for portal: data for fishes are partially consistent, long-term biodiversity monitoring of shallow marine biota, including available, and data for invertebrates for offshore locations that are expensive to visit, such as the Coral Sea. will become available later in 2015. The consistent, wide-ranging data collected by the surveys is establishing a global context that will enable trends over time in areas such as the Coral Sea to be compared on a regional, national and international scale.

CONTACT Graham Edgar [email protected] 0427 811 699 Management marine Commonwealth of reserves and Heritage the Area GBR World

ABOVE: A Queensland Groper (Epinephelus lanceolatus) at Bird Reef in the Coral Sea.

LEFT: A Reef Life Survey diver counts invertebrates at Holmes Reef in the Coral Sea. Images: Reef Life Survey

60 NERP MARINE BIODIVERSITY hub • FINAL REPORT Shaping integrated monitoring for the Great Barrier Reef World Heritage Area

The Great Barrier Reef (GBR) was inscribed on the GUIDANCE TO ESTABLISH AN INTEGRATED World Heritage list in 1981 in recognition of its MONITORING FRAMEWORK outstanding universal value. management principles of 3 In addition to its biophysical values, the GBR Region contains objectives governance integrated important elements of cultural and indigenous heritage, and from management monitoring supports many community and economic benefits such as plan or program fishing and tourism. As highlighted in the GBR Outlook Report 2014, cumulative pressures are diminishing the resilience of guidance for GBR ecosystems. Living coral is declining, with the average essential coral cover falling by half between 1985 and 2012. While monitoring the effects of cyclones, crown-of-thorns starfish and coral functions bleaching are the main causes of coral mortality, most long-term declines have occurred in central and southern regions, where human pressures are the most intense. STAGE 1 Monitoring in the GBR Region typically has responded establish an integrated monitoring framework to emerging issues (such as crown-of-thorns starfish), (IMF) long-term trends, or legislative requirements, rather than cumulative impacts or overall management needs. Furthermore, social and economic monitoring has not been STAGE 2 a high priority. This project has built the framework for a transitioning from an standardised and integrated ecological, social and economic IMF to an integrated monitoring program for the GBR World Heritage Area that monitoring program will be used to address these earlier shortcomings.

Approach ABOVE: An overview of the guidance An approach that learns from measurable outcomes was taken to required to establish an integrated establish an integrated monitoring framework to support adaptive monitoring framework (what management. The GBR Marine Park Authority reviewed information needs needs to be considered). for managing the GBR World Heritage Area, and the Australian Institute of Marine Science (AIMS) reviewed existing monitoring programs. Other The framework described in this collaborators included the NERP Marine Biodiversity Hub, the NERP report is based on the seven essential Environmental Decisions Hub, the NERP Tropical Ecosystems Hub and the monitoring steps identified by the Queensland Department of Environment and Heritage Protection. United States National Park Services. Conceptual models are central The integrated monitoring framework was established using practical guidance to capturing and communicating developed specifically for this project. The guidance was developed using interactions between ecosystems, knowledge and advice from a broad range of experts in the fields of policy society and the economy to furnish all development, natural resource management, science and data management. stakeholders a similar understanding of how the system functions. BELOW: Living coral is declining in Great Barrier Reef ecosystems. Image: Reef Life Survey Management marine Commonwealth of reserves and Heritage the Area GBR World

NERP MARINE BIODIVERSITY hub • FINAL REPORT 61 Tourism is one of many community benefits bestowed by the GBR region. Image: Matt Curnock

3 Key findings APPLYING THE GUIDANCE FOR ESSENTIAL The integrated monitoring framework established by this project provides MONITORING FUNCTIONS the foundation for developing an integrated program for the GBR World Heritage Area. The program would monitor, evaluate and report on 1: clearly defining purpose of the condition of and trends in values underpinning relevant matters monitoring program and of national environmental significance and the associated drivers and monitoring objectives pressures. This includes Outstanding Universal Value recognised under the World Heritage listing, as well as benefits to the community. 2: compiling and analysing relevant information on Governance is critical to the leadership and coordination required for existing monitoring programs integrated monitoring, to articulate clear responsibilities for prioritisation, A B C D and to effective implementation. Governance arrangements for the Reef Water Quality Protection Plan 2013 may provide a useful model for 3: develop conceptual models guiding the development of the governance arrangements necessary to coordinate a monitoring program for the World Heritage Area. 4: developing overall sampling Fifty-two high-priority values, processes, pressures and drivers design for integrated monitoring (reduced from hundreds) have been identified for monitoring. 4a: selecting indicators 4b: selecting monitoring programs Further refinement is needed to reduce the number of priorities and E 4c: developing samping designs to improve the specificity of the priorities and their objectives. Sixty-five existing monitoring programs were candidates for inclusion 5: developing monitoring in an integrated monitoring program. This existing network, while protocols relatively extensive, is insufficient to monitor the identified priorities.

Multi-stakeholder workshops identified the following monitoring 6: managing data programs as fundamental building blocks: the AIMS Long Term Monitoring 7: analysing data Program, the Eye on the Reef monitoring program, the Integrated Marine 8: reporting and communication Observing System, the Paddock to Reef Monitoring Program, commercial 9: reviewing and auditing

fisheries monitoring, seagrass monitoring, the Social and Economic A–existing conceptual models and known gaps. B–existing monitoring Long Term Monitoring Program and threatened species monitoring. programs and known gaps. C–existing monitoring protocols and known gaps. D–existing infrastructure processes or protocols and known gaps. E–iteration will be required as sampling design informs and is informed Integrated monitoring for the World Heritage Area will require broader by selection of monitoring programs. use of conceptual models, development and promotion of standard monitoring protocols, and improved coordination and collaboration ABOVE: Essential monitoring functions between end-users and existing data management systems. Existing to be considered in developing an monitoring programs will need to better serve managers, and an integrated monitoring framework. overarching data analysis and reporting group or unit will be needed. The framework contributed to New knowledge and opportunities a strategic assessment of the The integrated monitoring framework provides the basis for effective World Heritage Area and is guiding monitoring of the World Heritage Area. It articulates monitoring priorities, the development of a reef-wide provides the first assessment of the capacity of existing monitoring programs integrated monitoring and reporting to address these priorities, and provides direction for integrating long-term program to review the success of the monitoring with short-term and compliance monitoring programs. The Reef 2050 Long-Term Sustainability framework can be used more broadly in Australia. For example, it built on Plan (draft released for public knowledge developed for monitoring marine ecosystem health (the monitoring comment in September 2014). It will blueprint) and will contribute to monitoring for future strategic assessments. build upon and coordinate existing monitoring and reporting activities Management marine Commonwealth of reserves and Heritage the Area GBR World Outputs and outcomes and will be linked to the outcomes and targets identified in the Plan. Guidance has been provided for establishing an integrated monitoring framework to support adaptive management of the GBR World CONTACT Heritage Area, and an integrated monitoring framework has been Reef Life Survey established. Information needs for management, and existing Paul Hedge monitoring programs, have been reviewed during this process. [email protected] (03) 6232 5023 IMAGE:

62 NERP MARINE BIODIVERSITY hub • FINAL REPORT International extension 4 Reef Life Survey IMAGE:

NERP MARINE BIODIVERSITY hub • FINAL REPORT 63 The need

4 International extension International

The Australian Government has regional partnerships and international responsibilities that can benefit from scientific exchange.

These include marine bioregional planning, While international scientific research establishment of the Commonwealth and extension are not directly supported Marine Reserve network, and fisheries by the NERP Program, the benefits management. Communicating these are significant. This section provides developments assists countries in the examples of how Marine Biodiversity Hub region and beyond, and profiles Australia’s research has been showcased, thereby capabilities. supporting the Australian Government’s broader international agendas.

64 NERP MARINE BIODIVERSITY hub • FINAL REPORT IMAGES: Reef Life Survey increase in MPAs was used as a proxy for conservation effectiveness. conservation for as aproxy MPAs in used was increase Total biomass fish blocks. mby5transect 50 along underwater sighted sizes and allfishes of numbers to survey methodology aconsistent used Divers data. quantitative standardised with investigation worldwide largest the countries: in87 MPAs 40 and obtained data Survey Life Reef of years five of analysis involved project This interact. factors these how determine to required of was tens tofrom hundreds of data MPAs analysis Statistical watertemperature. and compliance, of level pressure, fishing regulations, local include: They of MPA size,MPAs. declaration age,the following populations of species recovery the of ratemagnitude and the influence Many factors Approach areas (MPAs).protected marine effective of typical features management to identify dataset RLS global the analysed project This species. of recovery the affect areas protected how marine of analysis global a for foundation the providing worldwide, sites than 2400 more and inAustralia sites 1500 and species than 3000 more cover now surveys change. for Standardised indicators of identification the support These data. baseline biodiversity marine coastal quantitative Australia’s comprehensive, most provides Survey Life Reef monitoring. coastal in participation community improves and environment, inshore the of health the about awareness public raises divers, recreational and managers scientists, marine links also It trained to ascientific level of data collection. habitats which are carried out by volunteer recreational divers Reef Life Survey (RLS) long-term conducts monitoring of coastal of marine protectedof marine areas Reef Life analysis Survey global LOCATIONS AND NUMBERS OF REEF LIFE SURVEY SITES WORDWIDE SITES SURVEY LIFE REEF OF NUMBERS AND LOCATIONS 29 17 76 40 26 11 22 43 9 20 7 15 52 16 28 143 136 34 91 21 3 16 16 14 11 20 5 22 3 141 28 27 32 22 14 5 10 16 13 5 9 13 NERP MARINE BIODIVERSITY BIODIVERSITY MARINE NERP 12 86 52

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12 8 16 16 573 396 266 hub hub 10 1640 100 5 480 • FINAL REPORT 65 REPORT • FINAL 2 1 ), and geographic ), geographic and 42 23 2 232 4 International extension 4 International extension areas for up to 20 years due to interactions within the food web. food the within to interactions due upto 20areas for years fished nearby and conditions baseline to MPAs in to change relative continue populations macroalgal and that fish,show invertebrate Tasmania of program MPAUniversity (IMAS) long-term monitoring the from data Comparative tool. monitoring ongoing as an potential has further It environment. adjacent the MPAs, with and between both of MPAs:status the comparing and evaluating for data providing and baselines establishing in value its has demonstrated Survey Life Reef broadened. has been divers RLS trained of network the and surveyed, have been blocks transect 14,000 and sites than 2400 More average. on sites 100 atabout each assessed, have been invertebrates and turtles, sea snakes, mammals, fishes, of species Globally, than 4500 more New knowledge and opportunities ( proximity in differences vast despite reefs, Queensland than to mainland reefs to related Polynesian closely more were communities Seareef Coral Overall, GBR. the of typical invertebrates and fewerof fishes presence the and islands, offshore with associated species of predominance Reef (GBR). Barrier the to was due ThisGreat the of those from different distinctly animals to be reef Sea Coral Hubfound Biodiversity Marine the for Reserve Marine Commonwealth Sea Coral the in expedition Survey Life A Reef findings Additional 66 NERP MARINE BIODIVERSITY BIODIVERSITY MARINE NERP 66 hub hub • FINAL REPORT • FINAL see story on page 59 page on story see ). ABOVE: www.reeflifesurvey.com Survey. Life Reef through boosted been has also conservation marine in engagement Public species. marine threatened of and ecosystems, to marine threats of goals, conservation achieve effectively MPAs for to necessary conditions management the of understanding animproved have facilitated data Survey Life Reef biodiversity. marine of distribution the mapping for tools improved has delivered project This outcomes and Outputs Image: Reef Life Survey Life Reef Image: areas. fished than sharks more times 39 have project this in identified features key five the with areas protected Marine CMR. obesus the Environment reporting. Environment the to of State contribute would that condition reef shallow of monitoring Australia-wide long-term consistent, for approach effective cost- yet rigorous scientifically a provides Survey Life Reef 0427 811 699 0427 [email protected] Edgar Graham CONTACT A Whitetip Reef Shark ( Shark Reef A Whitetip ) at West Islet in the Coral Sea Sea Coral the in Islet West ) at

Triaenodon management acrossmanagement globe the biodiversity Supporting provided impetus to international discussions of area-based management in management of area-based discussions to international impetus provided have workshops The EBSAs. for definition internationally-agreed the that meet areas200 thanmore identified and ocean, global the of than two-thirds more bodies. international Together, or regional 79 and considered they countries 92 from specialists involved workshops CBD regional of series global The ABNJ. areas, in protected marine including management tools, spatial implementing consider they if community international bythe upon drawn be can that and information products produced has identification scientific Their their surroundings. than standpoint, ascientific from significant, biologically more relatively areas considered are EBSAs EBSAs. of description scientific the that facilitated workshops CBD Hemisphere Southern of to aseries support technical provided scientists Hub Areas region. the in (EBSAs) Marine Significant Biologically or Ecologically describing for CBD bythe established criteria scientific the meeting areas identify to nations Hemisphere Southern helping been have Hubscientists Biodiversity Marine In this context, ABNJ. in biodiversity of use sustainable and conservation to the related issues consider community international the to help program technical and scientific a (CBD) is undertaking Diversity Biological on Convention the Group, UN the by made Working recommendation the Notwithstanding jurisdiction. national beyond diversity biological marine of use sustainable and (under UNCLOS), instrument, conservation the binding on (UNGA)legally- a negotiate Assembly UN thatGeneral the recommended 2015 in early Group Working Jurisdiction National Beyond Biodiversity the UN of meeting final The used. sustainably or managed, conserved be (ABNJ)should jurisdiction national areas in beyond biodiversity how on exists agreement international comprehensive global, no At present, ocean resources. provides the international legal framework for using the world’s The United NationsConvention on the Law of the Sea (UNCLOS) AREAS OF THE GLOBAL OCEAN GLOBAL THE OF AREAS SIGNIFICANT BIOLOGICALLY AND ECOLOGICALLY Image: Marine Geospatial Ecology Lab, Duke University Duke Lab, Ecology Geospatial Marine Image: NERP MARINE BIODIVERSITY BIODIVERSITY MARINE NERP

discussion beyond the use of EBSAs. of use the beyond discussion the moves areas, and protected marine developing for ideas and options with nations has provided This ABNJ. in biodiversity marine on Group Working Assembly General Nations United to the and CBD the to presented have and been ABNJ, for as options suggested have been inAustralia planning bioregional marine Hubto support Biodiversity Marine bythe Tools developed UN. the including conventions and agencies to international referred been and haveCBD the to Parties of Conference atthe community international the by accepted areas have been these of majority teams, great the Duke University and CBD the with collaboration (or seas ABNJ). regional the in In and waters own intheir EBSAs to identify supported have been countries Hemisphere Southern outcomes and Outputs and information-rich structures. structures. information-rich and complex to more progress gradual the supports governance, and and knowledge scientific available using management ecosystem-based and planning spatial marine of implementation early encourages process hierarchical adaptive The ABNJ. and in jurisdictions, national within both application, their demonstrates and frameworks existing from keythat takes elements approach an adaptive, hierarchical byproposing EBSAs of use ongoing the supported has also project This inABNJ. resources marine of use sustainable and conservation management, the regarding fora UN relevant in decision-making support might information EBSA how is to investigate step next The science. marine global to essential networks international and capacity to building contributed and ABNJ, (03) 6232 5382 (03) 6232 [email protected] Piers Dunstan CONTACT

hub hub • FINAL REPORT 67 REPORT • FINAL

4 International extension 4 International extension access and use the information to support local marine spatial planning. planning. spatial marine local to support information the use and access (such as Kiribati) countries individual to help (now way) under aprocess and system sharing information aregional of development the include These planning. to marine fundamental processes on agreement rapid to reach Secretariat Forum Islands Pacific the and Programme Environment Regional Pacific the of Secretariat the scientists, Australian has allowed experience The management. and monitoring asprioritising ameans of Features Key of Ecological anunderstanding facilitated and drivers, policy on advice provided Department, the for information prepared have Scientists contributions. hubs havesignificant made NERP biodiversity and marine NERP) of (the forerunner Facility Research Environmental Commonwealth the under developed Tools expertise and project. EPOG the of as part countries individual and agencies regional with working are Hub researchers Sydney. of University the and CSIRO Environment, the of Department and Department the Attorney-General’s Australia, Geoscience include Participants Governance (EPOG) Ocean project. Pacific Enhancing funded Australian-aid the through framework Oceanscape the in identified actions several is supporting Australia to act. that has authority the framework governance for a communicated effectively knowledge, new requires framework the Implementing security. food and livelihoods regional to support designed Pacific Oceanscape Pacific In 2010, twenty-three Pacific Island leaders endorsed the the endorsed leaders Island Pacific In 2010, twenty-three PacificEnhancing Ocean Governance outcomes. sustainable to achieve required experience governance and scientific the both is providing Government Australian the and Hub Biodiversity Marine the between Collaboration 10–20 years. after come only this will Realistically, needed. where governance new of implementation and development the support and capacity, local and regional enduring provide must however, projects aid regional threats.and effective, values be To communicating and identifying for techniques bytranslating region inthe planners marine have helped They international interests in marine sustainable development. marine bioregional planning process to the support nation’s and experience gained during their guiding role in Australia’s Marine Biodiversity Hub scientists are applying knowledge Coral Triangle the and Pacificislands to Australian aid Supporting 68 NERP MARINE BIODIVERSITY BIODIVERSITY MARINE NERP 68 Image: Piers Dunstan Piers Image: Kiribati. in fisheries community-based existing support to governance regional developing for options provide to Wollongong of University the and Community Pacific the of Secretariat the Government, Australian the with working are researchers Hub Biodiversity Marine , a conservation and sustainable management framework framework management sustainable and , aconservation hub hub • FINAL REPORT • FINAL Framework for a a for Framework integrated into national policy. into national integrated be could scale local ata activities bywhich means the and assets biological of distribution the to understand governments helping by management marine improved support will project ongoing This consideration. under issues are mining sea deep and management climate, resource livelihoods, Coastal managed’. effectively and designated seascapes ‘Priority Plan Action: of Regional the 1of Goal to Regional relating those particularly issues, transboundary and regional-scale key of understanding an improved linked to foster being are datasets socio-economic and ecological new and Existing Timor-Leste. and Islands Solomon Guinea, the New Papua Malaysia, Philippines, the Indonesia, countries: six across management and protection reef coral supports Triangle which Initiative, Coral the with engagement its in Department the assisting also are Hubscientists Biodiversity Marine Coral Triangle Initiative ABOVE: where needed Image: Piers Dunstan. Piers Image: needed where governance new support and capacity, local and regional enduring provide (03) 6232 5382 (03) 6232 [email protected] Piers Dunstan CONTACT Regional aid projects must must projects aid Regional

the method is appropriate for monitoring marine protected areas. protected marine monitoring for is appropriate method the technique, anon-destructive As size and structure. abundance diversity, species as such assemblages fish and shark pelagic of characteristics quantify effectively can systems camera video stereo Mid-water Key findings partners. international from support with Polynesia, French in Palau, islands Tonga, Gambier and Caledonia, Rapa/Marotiri, and New In 2012–2014,Archipelago, Chagos to made were expeditions wildlife. other and fishes and sharks pelagic for surveys international in involvement to further led systems new the of success The fish assemblages. and shark pelagic of size and structure abundance diversity, inthe changes monitoring for used are data These animals. individual of length as abundance, well as the and richness species determine to software custom using is analysed imagery Video arm. byahorizontal is held canister abait and stability and buoyancy maintains floats of system A housings. infixed mounted are cameras two which on bar horizontal asupported, of consist rigs camera mid-water The grounds. testing ideal CMR) provided Canyon Perth and CMR Shoals CMRs (Oceanic new in baselines pelagic establish to conducted surveys field Hub Biodiversity NERP Marine andtested. developed were data quantitative collecting for systems camera video stereo mid-water non-destructive and reviewed were fish assemblages and shark pelagic to sampling Approaches Approach pageon story 70). (see Seas initiative Pristine Geographic National by the supported expeditions pelagic during used have been inthis project developed systems camera Mid-water community. international to the areas interest of (CMRs), as other as in well Reserves Marine Commonwealth in fish assemblages and shark pelagic for baselines of development the to contributed It fishes. and pelagic sharks for monitoring techniques non-destructive developed This project fisheriescatch data are unavailable. fishes, particularly in marine reserves and other areas where quantitative data on the population status of pelagic sharks and sampling Non-destructive methods are needed to provide Australia to Austral the Islands from fish: Monitoring pelagic NERP MARINE BIODIVERSITY BIODIVERSITY MARINE NERP

San San Felix, NationalSociety Geographic Manu Image: system. camera video stereo mid-water the of canister galapagensis ( Shark A Galapagos video stereo mid-water of use expanding MPAs. The international and network CMR of Australia’s effectiveness the to assessing contribute that can species pelagic on data baseline to collect used be can systems camera video stereo Mid-water opportunities and New knowledge as tunas, oceanic sharks, and orcas. orcas. and sharks, as tunas, oceanic animals such marine to large phase pre-recruitment their in fishes reef juvenile animals of from range wide a include and diverse, are systems, camera video stereo by mid-water as unveiled assemblages, Pelagic assessments. impact environmental as such applications other and MPA for baselines monitoring to establishing contribute also estimates The hotspots. pelagic MPAs of byidentifying design the support systems camera video stereo bymid-water generated abundance and richness of species Estimates requirements. monitoring on depending as acoustics, such techniques complementary with combined and (moored, drifting), configurations vessels), varying in oceanographic (small to large tenders platforms of avariety from deployed be can that technique versatile highly acost-effective, are systems camera video stereo Mid-water

) bumps the bait bait the ) bumps hub hub Carcharhinus • FINAL REPORT 69 REPORT • FINAL 4 International extension 4 International extension based ecological research on endangered Australian vertebrates. Australian endangered on research ecological based field- Fund Award for Middleton Margaret its through Science of Academy Australian the from byagrant online, supported is available CMR Canyon the Perth from footage video of high-quality A compilation • • • • • • • • • at: data and imagery shark and fish pelagic have collected systems camera video Stereo CMRs. of performance inassessing useful may be This information reserves. in fish marine pelagic of richness species and abundance the to estimate techniques new developed project This outcomes and Outputs context. inaninternational evaluated to be assemblages Australia’s of pelagic status the enable will systems camera 70 NERP MARINE BIODIVERSITY BIODIVERSITY MARINE 70 NERP 0400 024 999 0400 [email protected] Meeuwig Jessica CONTACT Tonga, central Pacific. Tonga, Pacific. central and Pacific; central Polynesia, French Pacific; western Rapa/Marotiri, Pacific; western Caledonia, New Pacific; Palau, western Ocean; Indian central Archipelago, Chagos Sea; Timor CMR, Shoals Oceanic WA; CMR, Canyon Perth Bay,Shark WA;

hub hub • FINAL REPORT • FINAL enhanced. and developed are reserves managers in these locations as marine marine as locations these in managers The National Geographic Pristine Seas Seas Pristine Geographic National The and media project to find, survey, and and survey, find, to project media and scientists joined the final two Pristine Pristine two final the joined scientists initiative is an exploration, research, research, exploration, an is initiative dominated by large apex predators. predators. apex large by dominated the ocean. Marine Biodiversity Hub Hub Biodiversity Marine ocean. the Marotiri, the southernmost islands islands southernmost the Marotiri, help protect the last wild places in in places wild last the protect help cameras to survey ocean habitats habitats ocean survey to cameras of French Polynesia in the Austral Austral the in Polynesia French of Seas expeditions of 2014 to Palau 2014Palau to of expeditions Seas (western Pacific) and Rapa Iti and Iti Rapa and Pacific) (western The surveys will be used to assist assist to used be will surveys The Archipelago of the South the of Archipelago Image: Manu San Felix, National National Felix, Image: San Manu They used pelagic stereo video video stereo pelagic used They pristine seas pristine Exploring Exploring Geographic Society Pacific. Pacific.

IMAGE: Reef Life Survey Science leader reflections •

NERP MARINE BIODIVERSITY hub • FINAL REPORT 71 Theme 1 • Keith Hayes National monitoring • evaluation and reporting Existing information, methods and capabilities were harnessed trends in marine imagery data. This was achieved through a highly in this research theme to develop a blueprint for a sustained collaborative approach that made national monitoring strategy targeting Key Ecological Features use of the individual capabilities of (KEFs) in Australia’s Commonwealth waters. Hub partners and collaborators. New methods were devised for survey design, and for analysing data from Impact non-extractive sampling techniques: part of the toolkit required for a national This research theme has developed monitoring program. A novel marine application of the Generalised Random a scientific perspective on how to Tessellation Stratified survey design was successfully trialled in Commonwealth proceed with a national marine marine reserves (CMRs) and KEFs in Commonwealth waters east of the monitoring program, as well as Abrolhos Islands were mapped. Shelf rocky reef systems, demersal fish and practical tools to support its benthic invertebrate communities were identified in the Flinders CMR, the implementation. Resource managers Abrolhos KEF, the Solitary Islands KEF and the Geographe CMR. More than will require further information 110 km² of additional high-resolution multibeam sonar data were acquired

Science leader reflections and guidance as they work to in the Solitary Islands KEF, Flinders CMR and Tasman Fracture CMR. incorporate this scientific foundation Research in this theme examined how marine reserves affect the in an enduring national program marine environment, how to use drop cameras in combination with for monitoring the performance baited remote underwater video systems to simultaneously assess fish of the CMR network and marine communities and habitat distribution, and how management activities ecosystem health more generally. are affecting habitats and fish communities. Existing data were used Outputs from this theme contributed to identify productivity trends in enhanced-pelagic-productivity KEFs, to an integrated monitoring and to test qualitative model predictions for rock lobster, urchin and framework for the Great Barrier kelp communities in Tasmania’s Maria Island marine reserves. Reef World Heritage Area. A national nomenclature standard was developed for labelling habitat features and organisms in marine imagery and a national data catalogue, Research partners ARMARDA, was built to visualise biological and oceanographic datasets collected at KEFs and CMRs. This facility was developed to identify any Australian Centre for Field Robotics, consistently collected data useful for monitoring KEFs and CMRs. The University of Sydney End-user engagement Australian Institute of Marine Science Scientists engaged with the Department of the Environment to help CSIRO articulate priority management questions relating to the health of the Department of Fisheries Australia’s Commonwealth waters (subsequently progressed in the Western Australia national monitoring blueprint). A shared understanding was reached of the need for robust survey designs and flexible monitoring programs Geoscience Australia to accommodate variability in funding and research capacity. Integrated Marine Observing System Building capacity New South Wales Office of Environment and Heritage Experience has been gained in designing and implementing surveys in waters beyond depths accessible to divers, with the built-in flexibility necessary for New South Wales Department of a long-term monitoring program. Additional expertise and novel analytical Primary Industries methods have been developed to analyse spatial correlation and temporal University of Tasmania

University of Western Australia An example of sedimentary rock-type features found across the shelf in the Flinders CONTACT CMR. Image: IMAS/GA Keith Hayes [email protected] (03) 6232 5260

72 NERP MARINE BIODIVERSITY hub • FINAL REPORT Theme 2 • Tony Smith Supporting management of marine biodiversity • This theme explored methods and tools for valuing marine Issues associated with the design and implementation of marine biodiversity, identifying threats, and evaluating approaches to biodiversity offsets were explored. conservation management. These included the performance Tools and analyses were designed to support the implementation of marine of offsetting strategies in the bioregional plans, monitoring the South-east Commonwealth Marine Reserves presence of cumulative impacts, (SECMR) Network, and assessment and management of listed species under and community preferences the Environment Protection and Biodiversity Conservation Act 1999. for aspects of offset design. End-user engagement Impact Research in this theme focused on stated needs of the Department of the Specific advice on protected species Environment. Scientists and departmental representatives engaged through and biodiversity management has workshops, briefing sessions, seminars, and one-on-one meetings to shape been used by the Department, individual projects. In some cases, however, changes in the policy environment such as to support non-detriment findings for sawfish in northern led to Departmental priorities changing and this complicated the definition Science leader reflections of relevant projects. The result was that while some projects appear to have Australia. The longer term impact satisfied Departmental needs, others experienced delays and frustration, and of the close-kin methods applied this affected the potential uptake of research findings. For example, trying to to river sharks and White Sharks is finalise objectives for the research focussed on integrating social, economic and likely to be large when applied to a environmental values was difficult, and progress has been delayed as a result. range of threatened marine species. Nevertheless, given the focus and Building capacity aims of this theme, the overall Regional scale quantitative analysis of pressures and cumulative impacts level of impact has been less than on seabed fauna led to the first quantitative evaluation of conservation anticipated. Difficulty in specifying management strategies and trade-offs for this area. This capacity to evaluate needs and objectives, and changing existing and potential alternative biodiversity management options on priorities, has led to delays and and off reserves, as well as the relative impact of alternative pressures frustrations. This experience points including marine industries, can be used to support evidence-based to the need for early dialogue and decision making in these difficult-to-observe offshore environments. continuing communication so that there is shared understanding Landscape approaches to managing high-priority conservation values of how projects will meet focussed on the SECMR and shark species of temperate Australia. the Department’s needs. Extensive data integration led to improved knowledge and understanding of demersal shark distribution and of important areas where several species overlap. Research infrastructure and capabilities developed Research partners during this project will support ongoing monitoring and assessment of sawfishes and river sharks in the Northern Territory, and of species such Charles Darwin University as White Sharks around Australia. New close kin mark-recapture methods CSIRO provide a quantum leap in the capability to assess threatened species. Northern Territory Department of Largetooth Sawfish.Image: Peter Kyne Primary Industry and Fisheries University of Tasmania

University of Western Australia

CONTACT Tony Smith [email protected] (03) 6232 5372

NERP MARINE BIODIVERSITY hub • FINAL REPORT 73 Project profile • Peter Kyne • Barry Bruce

Supporting management and • recovery of threatened species

Threatened species research started as a relatively small Research partners development project on euryhaline elasmobranchs under Australia Zoo Theme 2, but early promising results led to the addition of emerging priority research on White Sharks. Department of Fisheries Western Australia The project investigated the distribution, movements, habitat use and status of threatened sawfishes, river sharks and White Sharks, including Flinders University options to effectively assess and monitor the status of threatened Griffith University species. It provided world-first abundance estimates for White Sharks and Speartooth Sharks, and developed novel molecular and statistical tools for Integrated Marine Observing System estimating demographic parameters, abundance and population status. Kakadu National Park

End-user engagement Malak Malak Traditional Owners Working through the NERP Marine Biodiversity Hub gave us an unprecedented and Ranger Group Science leader reflections level of collaboration and communication, both between research partners, and Melbourne Aquarium with the Department of the Environment. A team of scientists with ecological, technical, and resource management expertise provided diverse research Murdoch University capacity, and regular communication made a strong contribution to policy New South Wales Department of making and management. For example, expert advice was provided on updating Primary Industries species recovery plans, assessments of proposed developments for their effect on threatened species, and on Australian submissions to the International NERP Northern Australia Hub Union for Conservation of Nature (IUCN) Red List of Threatened Species. Northern Territory Department of Building capacity Primary Industry and Fisheries Research tools developed during this work ranged from the molecular to the South Australian Research and landscape scale and included species-level ecological and technical expertise Development Institute essential for designing future monitoring programs. Cutting-edge genetic and statistical techniques (close-kin mark-recapture) were developed and applied Tag For Life to key management questions. Extensive arrays of acoustic receivers (130 Territory Wildlife Park receivers) were deployed in seven Northern Territory and Queensland river systems to monitor tagged animals (10 species and some 400 individuals). University of Queensland These arrays and tagged individuals will provide data for up to five more years. Tagged juvenile White Sharks will also provide ongoing movement data for population modelling, via acoustic receivers spanning Australia’s east coast.

Impact CONTACT This research provided up-to-date information to assist in mapping, monitoring, Peter Kyne assessments and referrals. It also identified for the first time practical options [email protected] for monitoring and assessing ‘difficult to assess’ aquatic threatened species. (08) 8946 7616

Peter Kyne conducts field work on the Adelaide River, NT. Image: Mat Gilfedder

74 NERP MARINE BIODIVERSITY hub • FINAL REPORT Theme 3 • Scott Nichol National ecosystems knowledge • This theme delivered new datasets and models that Building capacity characterise large-scale processes influencing marine High performance computing and satellite data analysis was biodiversity patterns on a national scale. It focused on areas developed and applied to modelling prioritised by the Department of the Environment through connectivity and sea-surface marine bioregional planning, such as the Commonwealth dynamics, and gene sequencing and machine learning methods Marine Reserve network. were applied to understanding A larval dispersal model was developed to help understand connectivity biogeographic structure and across the marine estate, with a focus on Key Ecological Features and benthic biodiversity prediction. marine protected areas. The theme also produced new genetic data on the taxonomy of brittle stars and squat lobsters to better understand Impact biogeographic patterns of benthic biodiversity, nationally and globally. Continuing engagement with the Department has ensured the

Thirty-six national marine datasets (new and updated) were compiled Science leader reflections accessibility and utility of research and published. These included descriptions of sea floor topography outputs. Further improvements are and sediments, submarine canyons, sea-surface water quality and possible by increasing the direct seabed exposure to waves and currents, as well as national catalogues links between departmental and of marine biota, including rare and threatened species. research data systems. Models and New insights into seafloor processes associated with physical features on datasets produced in this theme have the continental shelf (reefs, bank, pinnacles, canyon heads) were gleaned been used by researchers inside and from field research undertaken in themes 1 and 4, particularly the expedition outside the Marine Biodiversity Hub. to Oceanic Shoals Commonwealth Marine Reserve, where hard-ground reefs influenced seafloor biological communities and fish aggregations. Research partners

End-user engagement Australian Institute of Marine Science Representatives from the Department were engaged in meetings and discussions to share progress reports and highlights. The engagement built trust CSIRO and understanding, and facilitated the collaborative development of summary Dalhousie University, Canada documents and provision of data through the Australian Ocean Data Network. Geoscience Australia

Integrated Marine Observing System

Museé National d’Histoire Naturelle du Luxembourg

Museum Victoria

National Computational Infrastructure at the Australian National University

Oceans Institute, University of Western Australia

University of Melbourne

CONTACT Scott Nichol [email protected] (02) 6249 9346

ABOVE: High resolution multibeam sonar image of the seabed in the Oceanic Shoals Commonwealth Marine Reserve. Image: Geoscience Australia

NERP MARINE BIODIVERSITY hub • FINAL REPORT 75 Theme 4 • Julian Caley Regional biodiversity • discovery to support marine bioregional plans

Strong, national, multidisciplinary collaboration in marine that was used to develop the first qualitative model of the KEFs in science was exercised and developed in this theme to better the area, a departmental goal for understand Australia’s north and north-west marine regions. all the KEFs identified across the Sparse data are available to support effective management of these vast CMR network and a prerequisite to areas, which face increasing cumulative pressures from environmental their inclusion in national marine change and extractive industries, including fisheries and oil and gas. ecosystem health monitoring. High-resolution bathymetry, geochemical and geophysical data, and biological www.nerpmarine.edu.au/rv-solander-blog collections and observations contributed to a qualitative model of the Key Ecological Features (KEFs) of the Oceanic Shoals Commonwealth Marine Reserve that confirmed their biodiversity value and regional significance. Research partners Science leader reflections End-user engagement Australian Institute of Marine Science Consultation with the Department of the Environment helped to prioritise CSIRO theme priorities to support management needs to understand the value Geoscience Australia of KEFs in a regional context and to explore unsurveyed areas of a recently declared Commonwealth Marine Reserve. Visual outputs from surveys, Museum and Art Gallery of the including pictures and videos, proved useful for communicating with the Northern Territory Department and a broader audience. A video developed by the Marine Museum Victoria Biodiversity Hub that featured research footage and modelling to highlight the values of a Commonwealth Marine Reserve was used by the Department University of Western Australia at the IUCN World Parks Congress (Sydney 2014). Pelagic camera highlights and a brochure about the Oceanic Shoals voyage were also produced. CONTACT Building capacity Julian Caley [email protected] Research partners combined unique expertise to survey some 600 km² of (07) 4753 4138 seabed containing KEF (banks, pinnacles and shoals) and non-KEF habitats. Multibeam sonar and other acoustic tools were used to create high-resolution seabed maps and biological material was sampled with epibenthic sleds. Seabed habitats and fish communities were observed with towed cameras BELOW: Mid-water stereo video camera and benthic and pelagic baited video systems. The survey, processing systems were among a suite non-destructive and analysis provided training for doctoral and post-doctoral students, sampling methodologies developed to survey established new sample and data collections, and successfully trialled new, marine habitats and fish communities. non-destructive, sampling methodologies such as Image: University of Western Australia pelagic baited cameras. It also discovered more than 150 km2 of new KEF habitat in the Oceanic Shoals CMR. Impact Research in this theme designed and delivered information products to support priority needs identified by the Department. The field expedition supported the roll-out of standardised survey and monitoring protocols including the Generalised Random Tessellated Stratified technique for selecting survey sites, and the application of standardised and new methods for environmental and biodiversity sampling. It also provided new information

76 NERP MARINE BIODIVERSITY hub • FINAL REPORT People and publications • IMAGE: William Gladstone, University of Technology, Sydney

NERP MARINE BIODIVERSITY hub • FINAL REPORT 77 Researchers and staff, past and present

Australian Institute of CSIRO continued Northern Territory Marine Science (AIMS) Peter Last Fisheries (NT Fisheries) • Julian Caley Emma Lawrence Mark Grubert Glenn De’ath Rhys Leeming Grant Johnson Sean Pascoe Andrew Heyward Thor Saunders Toby Patterson Hugh Sweatman David Peel Richard Pillans People Roland Pitcher University of Tasmania Charles Darwin Wendy Proctor (UTAS) University (CDU) Melody Puckridge Sarah Jennings Wayne Rochester Pierre Feutry Satoshi Yamazaki Peter Kyne Tony Smith Olivier Thebaud Dave Watts Institute for Marine and Antarctic Studies Commonwealth Helen Webb William White Neville Barrett Scientific and Industrial Alan Williams Nic Bax Research Organisation Just Berkhout (CSIRO) Colin Buxton Graham Edgar Franzis Althaus Geoscience Justin Hulls Russ Babcock Australia (GA) Vanessa Lucieer Bruce Barker Brendan Brooke Russell Bradford Peter Harris Mark Bravington Floyd Howard Barry Bruce Jin Li University of Western Ross Daley Scott Nichol Australia (UWA) Jeff Dambacher Kim Picard Michael Burton Piers Dunstan Rachel Przeslawski Euan Harvey Nick Ellis Lynda Radke Gary Kendrick Jessica Ford Justy Siwabessy Jessica Meeuwig Scott Foster Maggie Tran David Pannell Mike Fuller Kimberly van Niel Daniel Gledhill Anya Waite Mark Green Museum Peter Grewe Rasanthi Gunasekera Victoria (MV) Keith Hayes Adnan Moussalli Richard Hillary Tim O’Hara Danny Holdsworth Toy, Ben Geoff Hosack Robin Wilson James Innes Gary Poore Penny Johnson Gordon Keith Rudy Kloser

78 NERP MARINE BIODIVERSITY hub • FINAL REPORT Skipton Woolley Woolley Skipton Luke Thomas Perkins Nicholas Every Sharon Buckley Kate Bouchet Philippe Jean Baptiste-Marre Camille Mellin Mellin Camille McCallum Anna Tom Letessier Bech Peter Kyne Kool Johnathan Hugall Andrew Huang Zhi Hill Nicole Hovey Renae Feutry Pierre Nikos Andreakis Russell Thomson Thomson Russell Stuart-Smith Rick Rogers Abbie Monk Jacquomo PhD Scholarships researchers Postdoctoral

MV UWA UTAS CDU CDU UWA QUT MV UWA CDU GA MV GA UTAS UWA CDU AIMS UTAS UTAS UWA UTAS AIMS Kay Alex Tomas Badura Ludovic Fragnol Richert Claire Lewis Ben Emma Flannery Klempin Charlotte Baut le Mathilde Brame Alexandre Evans Rhian Fuessel Adriana Paredes Samantha (Dalhousie) Devitt CDU Karen CDU Baust (Oxford) Sebastian Summer scholar Summer Masters Interns

UWA UWA UWA UWA GA GA CDU CDU CDU CDU UTAS QUT NERP MARINE BIODIVERSITY BIODIVERSITY MARINE NERP Jemina Stuart-Smith –image database Stuart-SmithJemina –image officer –executive Randell Vicki –communication Ozimec Annabel –editor Nelson Vicki broker –knowledge Paul Hedge designer –graphic Crosswell Lea communication – Bennett Bryony designer –graphic Bell Louise Administration support support officer support manager project officer, editor, report editor, report Images: William Gladstone, UTS Gladstone, William Images: hub hub • FINAL REPORT 79 REPORT • FINAL • People Research collaborators

Australian Institute of James Cook University Queensland University of • Marine Science Tom Bridge, Alistair Harry, Tansyn Technology Jamie Colquhoun, Ben Radford, Noble, Colin Simpfendorfer Kerrie Mengersen, Louisa Coglan Christine Schönberg, Marcus Stowar Kakadu National Park RMIT Australia Zoo Anne O’Dea, Khan Spokes, Dan Rod Conroy Wilkins, Steve Winderlich Charles Darwin University Secretariat of the Pacific People Karen Gibb Malak Malak Traditional Owners Regional Environmental and Ranger Group Programme Convention on Biological Rob Lindsay, Francis Miljat, Rita Tim Carruthers Diversity Purack, Amos Shields, Aaron Green, Jihyun Lee South Australian Research and Albert Myoung, Anthony and Chris Development Institute Commonwealth Scientific and McGregor, Lindsay Parsons, Matthew Charlie Huveneers, Paul Rogers Industrial Research Organisation Shields Tag for Life Sharon Appleyard, Thor Carter, Melbourne Aquarium Denise Hardesty, Ming Feng, Mike Territory Wildlife Park Fuller, Alistair Graham, Karen Miyazaki University Dion Wedd Gowlett-Holmes, Ian McLeod, Tara Yukio Iwatsuki Martin, Ido Nevat, Toby Patterson, University of Adelaide Murdoch University Corey Bradshaw John Pogonoski, Tony Rees, Andrew David Morgan, Nicole Phillips Revill, Sharon Tickell University of Melbourne NERP Northern Australia Hub Prue Addison, Bastien Rochowski, Department of Fisheries, David Williams (AIMS); Duncan Terry Walshe Western Australia Buckle, David Crook, Michael Douglas Lynda Bellchambers, Mattias Bracini (CDU); Tim Jardine, Mark Kennard, University of New South Wales Department of Parks and Brad Pusey, Dominic Valdez, Renata Ferrari, Gareth Peters, Wildlife, Western Australia Francisco Villamarin (Griffith Uni) Gordana Popovic Kim Friedman NSW Department of Primary University of Queensland Flinders University Industries Hamish Campbell, Craig Franklin, Alan Jordan, Hamish Malcolm Jennifer Ovenden Fox Shark Research Foundation Andrew Fox NSW Office of Environment University of Sydney, Australian and Heritage Centre for Field Robotics Geoscience Australia Peter Davies, Tim Ingleton, Stefan Williams Ian Atkinson Tim Pritchard University of Tasmania (Institute Great Barrier Reef Marine Park Northern Territory Fisheries for Marine and Antarctic Authority Quentin Allsop, Chris Errity, Studies) Julia Chandler, Fergus Molloy Andrew Gould, Poncie Kurnoth Cynthia Awruch, Adam Barnett, Justin Bell, Marie-Jeanne Buscot, Guangxi Academy of Sciences Northern Territory Museum Xiao Chen, Renjie Sun Melody Puckridge, Michelle Treloar, Belinda Glasby Carolina Zagal, Jayson Semmons Indo-Pacific Environmental Ocean and Coast Research University of Western Australia Pty Ltd Johnathan Werry Dean Thorburn Jason Kennington, Ana Sequeira, Ohio State University/Charles Michael Stat, Thomas Wernberg Integrated Marine Observing Darwin University University of Wollongong System Tim Berra Tim Moltmann Colin Woodroffe Pawsey Supercomputing Centre Wildlife Marine IUCN Shark Specialist Group/ Luke Edwards Simon Fraser University Will Robbins Nick Dulvy, Lucy Harrison Xiamen University Min Liu

80 NERP MARINE BIODIVERSITY hub • FINAL REPORT IMAGE: William Gladstone, UTS NERP MARINE BIODIVERSITY BIODIVERSITY MARINE NERP hub hub • FINAL REPORT 81 REPORT • FINAL • Publications Publications Funded by the National Environmental Research Program (includes peer reviewed articles – submitted, in review, accepted, in press, published)

N1. Addison, P. F. E, de Bie, K., N8. Bird, T. J., Bates, A. E., Lefcheck, N16. Cameron M.J., Lucieer V.L., and Rumpff, L. (in review). A novel J. S., Hill, N. A., Thomson, R. J., Edgar, G. Barrett N., Johnson C.R., Edgar G.J. (2014). participatory modelling approach J., Rick D Stuart-Smith, Wotherspoon, Understanding community-habitat to set conservation management S., Krkosek, M., Stuart-Smith, J. F., associations of temperate reef fishes using • thresholds. Conservation Biology. Pecl, G. T., Barrett, N. S., and Frusher, fine-resolution bathymetric measures S. (2014). Statistical solutions for of physical structure. Marine Ecology N2. Addison, P. F. E., Flander, L. error and bias in global citizen science Progress Series. doi: 10.3354/meps10788 B., and Cook, C. N. (2015). Are we datasets. Biological Conservation. missing the boat? Current uses of doi:10.1016/j.biocon.2013.07.037 N17. Ceccarelli, D. M., A. McKinnon, long-term biological monitoring data D., Andréfouët, S., Allain, V., Young, J. W., in the evaluation and management N9. Bouchet, P. J., Meeuwig, J. J., Kent, Gledhill, D. C., Flynn, A., Bax, N. J., Beaman, of marine protected areas. Journal of C. P. Salgado, Letessier, T. B., and Jenner, R., Borsa, P., Brinkman, R., Bustamante, Environmental Management 149, 148–156. C. K. (2014). Topographic determinants R. H., Campbell, R., Cappo, M., Cravatte, doi:10.1016/j.jenvman.2014.10.023 of mobile predator hotspots: Current S., D’Agata, S., Dichmont, C. M., Dunstan, knowledge and future directions. Biological P. K., Dupouy, Cecile, Edgar, G. J., Farman, Publications N3. Althaus, F., Hill, N. A., Edwards, Reviews. doi:10.1111/brv.12130 R., Furnas, M., Garrigue, C., Hutton, T., L., and Ferrari, R. (2013). CATAMI Kulbicki, M., Letourneur, Y., Lindsay, D., Classification Scheme for scoring marine N10. Bouchet, P., Meeuwig, J., Huang, Menkes, C., Mouillot, D., Parravicini, biota and substrata in underwater Z., Letessier, T., Nichol, S., Watson, R. V., Payri, C., Pelletier, B., de Forges, B. imagery – A pictorial guide to the (in review). Continental-scale models Richer, Ridgway, K., Rodier, M., Samadi, Collaborative and Annotation Tools for of pelagic fish hotspots: can geoscience S., Schoeman, D., Skewes, T., Swearer, Analysis of Marine Imagery and Video guide the conservation of mobile S., Vigliola, L., Wantiez, L., Williams, A., (CATAMI) classification scheme. oceanic predators? Ecology Letters. Williams, A., and Richardson, A. J. (2013). The Coral Sea: Physical Environment, N4. Althaus, F., Hill, N. A., Ferrari, R., N11. Bouchet, P. J. and Meeuwig J. Ecosystem Status and Biodiversity Assets. Edwards, L., Przeslawski, R., Schonberg, C. J. (in review). Drifting baited stereo- Advances in Marine Biology. doi:10.1016/ H. L., Stuart-Smith, R., Barrett, N., Edgar, videography: A novel sampling tool for B978-0-12-408096-6.00004-3 G., Colquhoun, J., Tran, M., Jordan, A., surveying pelagic wildlife in offshore and Rees, T. (submitted). Standardized marine reserves. Ecosphere. N18. Chen, X., Kyne, P. M., Pillans, classification of benthic biota and substrata R. D., and Feutry, P. (2015). Complete N12. Bridge, T. C. L., Ferrari, R., Bryson, from underwater imagery: the CATAMI mitochondrial genome of the Endangered M., Hovey, R., Figueira, W. F., Williams, Classification Scheme. PLoS ONE. Narrow Sawfish S. B., Pizarro, O., Harborne, A. R., and Anoxypristis cuspidata (Rajiformes: Pristidae). Mitochondrial DNA, N5. Anderson, A., Cook, G., and Byrne, M. (2014). Variable responses of 1–2. doi:10.3109/19401736.2014.1003898 Bax, N. J. (2014). Mining and biodiversity benthic communities to anomalously IN Biodiversity – Science and Solutions warm sea temperatures on a high- N19. Chen, X., Liu, M., Grewe, P. for Australia. In Biodiversity – Science latitude coral reef. PLoS ONE 9, e113079. M., Kyne, P. M., and Feutry, P. (2013). and Solutions for Australia. Biodiversity doi:10.1371/journal.pone.0113079 Complete mitochondrial genome of the – Science and Solutions for Australia. Critically Endangered speartooth shark N13. Bruce, B. D. and Bradford, pp. 167–178. (CSIRO Publishing.) (Carcharhiniformes: R. W. (submitted). Segregation or Glyphis glyphis Carcharhinidae). Mitochondrial DNA, 1–2. N6. Ban, N. C., Bax, N. J., Gjerde, K. M., aggregation? Sex-specific patterns doi:10.3109/19401736.2013.809443 Devillers, R., Dunn, D. C., Dunstan, P. K., in the seasonal occurrence of white Hobday, A. J., Maxwell, S. M., Kaplan, D. M., sharks at the Neptune Islands, South N20. Chen, X., Wiley, T., Kyne, P. M. and Pressey, R. L., Ardron, J. A., Game, E. T., and Australia. Journal of Fish Biology. Feutry, P. (in press). Complete mitochondrial Halpin, P. N. (2013). Systematic conservation genome of the Critically Endangered N14. Burgess, G. H., Bruce, B. D., planning: A better recipe for managing the Smalltooth Sawfish Cailliet, G. M., Goldman, K. J., R. Grubbs, Pristis pectinata high seas for biodiversity conservation (Rajiformes: Pristidae). Mitochondrial DNA. and sustainable use. Conservation D., Lowe, C. G., MacNeil, A. M., Mollet, H. Letters. doi:10.1111/conl.12010 F., Weng, K. C., and O’Sullivan, J. B. (2014). N21. Coleman M. A., Bates A. E., A re-evaluation of the size of the white Stuart-Smith R. D., Malcolm H. A., Harasti N7. Ban, N. C., Maxwell, S. M., Dunn, shark (Carcharodon carcharias) population D., Jordan A., Knott N. A., Edgar G. J. D. C., Hobday, A. J., Bax, N. J., Ardron, J. off California, USA. PLoS ONE 9, e98078. and Kelaher B. P. (in press). Functional A., Gjerde, K. M., Game, E. T., Devillers, R., doi: 10.1371/journal.pone.0098078 traits reveal early responses in marine Kaplan, D. M., Dunstan, P. K., Halpin, P. 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Williams, A., Althaus, F., Althaus, A., Williams, Williams, A., Althaus, F., Althaus, Clark, A., Williams, Williams, S. B., Pizarro, O., Pizarro, B., S. Williams, Wilcox, C., and Donlan, J. Donlan, and C., Wilcox, Williams, S. B., Pizarro, O., Jakuba, O., Jakuba, Pizarro, B., S. Williams, Wilcox, C., and Donlan, J. Donlan, and C., Wilcox, Williams, A., Schlacher, T. Schlacher, A., Williams, hub hub • FINAL REPORT 91 REPORT • FINAL • Publications 92 NERP MARINE BIODIVERSITY hub • FINAL REPORT Bird Island Reef. Image: Reef Life Survey IMAGE: Reef Life Survey

Contact Director, NERP Marine Biodiversity Hub Prof Nic J Bax [email protected] (03) 6232 5341

The NERP Marine Biodiversity Hub is supported through funding from the Australian Government’s National Environmental Research Program, administered by the Department of the Environment (DoE). Our goal is to support marine stakeholders in evidence-based decision making for marine biodiversity management. Stakeholders include DoE, the Australian Fisheries Management Authority (AFMA), the Australian Petroleum Production and Exploration Association (APPEA) and the Integrated Marine Observing System (IMOS). June 2015

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