annual report 2010 - murdoch university · well as the completion of the phd thesis by claire...

Centre for Fish, Fisheries and Aquatic Ecosystems Research

ANNUAL REPORT 2010

Cover Page: Broke Inlet - photo by Bryn Farmer Inside Cover Page: Snapper – photo by Simon Allen Credits: Editor: Neil Loneragan Layout and Design: Nathalie Kennedy / Murdoch Design Data Collection and Preparation: Neil Loneragan and Irene Abraham All written material may be used without permission provided correct reference to persons quoted and the University is included. August 2013

CONTENTS

Page 1 Centre for Fish, Fisheries and Aquatic Ecosystems Research - Annual Research Report 2010

1. MANAGEMENT BOARD .........................................................................................3 2. ADMINISTRATIVE DETAILS...................................................................................3

Centre members as at December 2010....................................................................3 Director’s report...................................................................................................5 Committee membership/ Community service ...........................................................7

3. RESEARCH ACTIVITIES........................................................................................9 3.1 Ecosystems and Community Ecology ............................................................... 10

3.1 a) Estuaries and Catchments......................................................................... 10 3.1 b) Freshwater.............................................................................................. 13 3.1 c) Marine (including biological oceanography) ................................................. 14 3.1 d) Resource partitioning and trophic interactions ............................................. 15 3.1 d) Fisheries dynamics and modelling.............................................................. 16 3.1 d) Marine Protected Areas ............................................................................. 17 3.1 f) Biodiversity and Conservation.................................................................... 18

3.2 Biological and evolutionary processes and evolution ......................................... 23 3.2 a) Fish and invertebrate population biology..................................................... 23

3.3 Specialist Research areas.............................................................................. 24 3.3 a) Freshwater Fish and Fish health................................................................. 24 3.3 b) Social and economic assessment ............................................................... 25 3.3 c) Stock enhancement and restocking ............................................................ 26

4. PUBLICATIONS for 2010 .................................................................................... 27 5. POSTGRADUATE STUDENTS AND THEIR RESEARCH TOPICS ................................... 34 6. HONOURS STUDENTS AND THEIR RESEARCH TOPICS............................................ 38 7. SUMMARY OF RESEARCH FUNDING ..................................................................... 39

7.1 List of projects and research income for 2010 ................................................... 39 8. ACKNOWLEDGEMENTS ...................................................................................... 45

Centre for Fish, Fisheries and Aquatic Ecosystems Research - Annual Research Report 2010

ADMINISTRATIVE DETAILS


1. MANAGEMENT BOARD Chair Professor Stuart Bradley Director Professor Neil Loneragan Centre member Professor Norm Hall Centre member Professor Ian Potter Centre member Dr Howard Gill Centre member Dr Jennie Chaplin Centre member Professor Lynnath Beckley Centre member Associate Professor Alan Lymbery Head of school Associate Professor Carolyn Jones External representative Associate Professor Rod Lenanton Postdoctoral representative Dr David Morgan Postgraduate student representatives Mr Peter Coulson Mr Chris Hallett

2. ADMINISTRATIVE DETAILS

Centre members as at December 2010 Director Neil Loneragan PhD (SELS) Academic staff

Lynnath Beckley PhD (SELS) Stuart Bradley PhD (SELS) Kate Bryant PhD (SELS) Max Cake PhD (SELS) Jennie Chaplin PhD (SELS) Stan Fenwick PhD (HS) Howard Gill PhD (SELS) John Huisman PhD (SELS) Carolyn Jones (SELS)

Halina Kobryn PhD (SELS) Alan Lymbery PhD (HS) Philip Nicholls PhD (HS) Ken Pollock PhD (SELS) Ian Potter PhD (SELS) Peter Rogers DSc (SELS) Malcolm Tull PhD (LB) Fiona Valesini PhD (SELS) Mike Van Keulen PhD (SELS) Graham Wilcox PhD (HS)

Adjunct/Emeritus appointments

Zaven Arzoumanian PhD Bob Clarke PhD Jeffrey Dambacher PhD Rob Doupé PhD Nick Dunlop PhD David Fairclough PhD Daniel Gaughan PhD Norm Hall PhD Greg Jenkins BSc David Johnston PhD Rod Lenanton PhD

Michael Krützen PhD Hector Lozano-Montes PhD Peter Madsen PhD Stephen Newman PhD Brad Norman MPhil Gavin Partridge PhD Margaret Platell PhD Jeremy Prince PhD Magnus Wahlberg PhD Richard Warwick PhD

Research Fellows Simon Allen MSc (SELS)

Stephen Beatty PhD (SELS) Lars Bejder PhD (SELS) Belinda Cannell PhD (SELS) Joseph Christensen PhD (LB)

Hugh Finn PhD (SELS) Alex Hesp PhD (SELS) Amanda Hodgson PhD (SELS) Steeg Hoeksema PhD (SELS) David Morgan PhD (SELS) David Holliday (SELS)

Research staff Florian Mayer (SELS) Claire Smallwood (SELS)

Gordon Thomson (SELS) Kristin Wouters (SELS)

ADMINISTRATIVE DETAILS cont…


PhD students

Jo Marie Acebes (AE*) Mark Allen (SELS) Farhan Bokhari (HS) Samantha Bridgwood (SELS/UWA) Amanda Buckland (SELS) Janja Ceh (SELS/AIMS) Warren Chisholm (SELS) Ben Chuwen (SELS) Natasha Coen (SELS) Alan Cottingham (SELS) Rainbo Dixon (SELS/UAdel) Emily Fisher (SELS) Ben French (SELS) Sarah Fretzer (SELS/CSIRO/DoF) Michelle Gardner (SELS) Susan Gibson–Kueh (HS) Chris Hallett (SELS) David Holliday (SELS/CSIRO) Mathew Hourston (SELS) Michelle Ingram (HS) Ashlee Jones (SELS) Michael Klunzinger (HS/SELS) Mark Langdon (SELS) Elaine Lek (SELS) Thea Linke (SELS)

Anne Lif Lund Jacobson (UTAS/LB) Karen Marshall (SELS) Fiona McAleer (SELS) Shannon McCluskey (SELS/UW) Frazer McGregor (SELS/AIMS/UWA)) Heather McLetchie (HS) Glenn Moore (SELS) Owen O’Shea (SELS/AIMS) Nicole Phillips (SELS) Mahmoud Rashnavadi (HS/SELS) Rebecca Roberts (SELS/LB) Andrew Rowland (SELS) Claire Smallwood (SELS) Holly Smith (SELS/DEC) Calais Tink (SELS) Joanna Tonge (SELS) Natalie Toon (SELS) Mike Travers (SELS/DoF) James Tweedley (SELS) Julien Tyne (SELS) Lauren Veale (SELS) Kristel Wenziker (SELS/DEC) Sharon Yeo (SELS/CSIRO)

MPhil/MSc students

Valissa Buchanan (SELS) Krista Nicholson (SELS)

Simon Wee (SELS) Jeff Whitty (SELS/JCU)

Honours students Nicholas Breheny (SELS/DoF)

Rowena Burch (SELS) Amy Griffiths (SELS) Felicity Hart (SELS) Adrian Hordyk (SELS) Broderic Hosie (SELS/DoF) Vanessa Jaiteh (SELS)

James Keleher (HS/SELS) Nicholas Konzewitsch (SELS) Michelle Lo (SELS) Jonathan Murphy (HS/SELS) Alicia Sutton (SELS) Jessica Williams (SELS)

AE Faculty of Arts and Education (* through Asia Research Centre) AIMS Australian Institute of Marine Science CSIRO Commonwealth Scientific and Industrial Research Organisation DEC Department of Environment and Conservation DoF Department of Fisheries HS Faculty of Health Sciences JCU James Cook University LB Faculty of Law and Business SELS Faculty of Sustainability, Environmental and Life Sciences UAdel University of Adelaide UTAS University of Tasmania UW University of Washington UWA University of Western Australia

DIRECTOR’S REPORT


Director’s report The research areas of staff and students in the Centre for Fish, Fisheries and Aquatic Ecosystems Research (CFFAER) incorporate the activities of people across four Schools in the University (Biological Sciences and Biotechnology, Environmental Sciences, Veterinary and Biomedical Sciences and the School of Business). The areas of research covered by Centre members include population and community biology, biological oceanography, systematics, fisheries and ecosystem modelling, recreational fishing, biology of wildlife species, conservation biology, marine protected areas, restocking, aquaculture, genetics and fish health. The breadth and scope of the research activities by Centre members in 2010 is illustrated by their participation in a total of 53 funded research projects, with a total research income of $2.7 million, including $1.46 million of nationally competitive Category 1 research projects. In 2010, the staff and students of the Centre have continued to publish a substantial number of papers in international journals (57 in 2010), books (2), book chapters (1), technical reports and/or popular articles in 2010 (11). This included publication of the third edition of the very successful book Two Oceans: A guide to the marine life of Southern Africa (Branch, Griffiths, Branch and Beckley). The activities of research students continue to be a vital part of the Centre’s success, with 45 Postgraduate (41 PhDs, four Masters) and 13 Honours students enrolled during the year. A highlight was the completion of the research programs of seven PhD and seven Honours students in 2010. We welcomed Dr Amanda Hodgson as the winner of the inaugural Bill Dawbin Postdoctoral fellowship funded by the Australian Marine Mammal Centre and Dr David Johnston, from Duke University as an adjunct Associate Professor. Some of the research highlights in marine fisheries and ecosystem research include: the development of approaches to classify marine habitats using hyperspectral data and completing the Final Report for the detailed spatial patterns of reef use at Ningaloo for marine conservation and development planning as part of the CSIRO Ningaloo Cluster (as well as the completion of the PhD Thesis by Claire Smallwood on this project); completing the Final Report for the development of ecosystem models for the central west coast (Jurien Bay region) to evaluate the effects of spatial closures on food webs; the completion of sampling and publications on the fish species and assemblages in estuaries on the south and west coast of Western Australia. These latter studies, funded by FRDC, WA Marine Science Institution (WAMSI) and the Department of Fisheries WA, Department of Environment and Conservation (DEC), Department of Water, provide valuable information on the current status of these systems and how the fish and benthic macro-invertebrate faunas in two of these estuaries (the Swan and Peel-Harvey) have changed over the last three decades. Three research voyages were completed on the National Vessel RV Southern Surveyor by Professor Lynnath Beckley and her team: they included a voyage to understand the productivity of the Kimberley shelf, which was the first comprehensive multi-disciplinary biological oceanography study in this remote part of Australia; and one to provide insight into the biological oceanography of the phyllosoma stage of the western rock lobster. Professor Ken Pollock initiated a series of training workshops as part of his FRDC project on quantitative methodologies for fisheries and conservation sciences. These involved presentations from a number of international experts in the fields of estimating fisheries mortality (Dr John Hoenig, Virginian Institute of Marine Sciences), estimating population size using mark-recapture (Prof. Ken Pollock) and qualitative modelling (Dr Jeffrey Dambacher, CSIRO). Detailed biological research continued on the Black Bream (Acanthopagrus butcheri) in the Swan-Canning and Blackwood estuaries and on the wrasses (Labridae) in the central west coast region. These studies provide rigorous, detailed information on growth and

DIRECTOR’S REPORT cont…


mortality, size and age at maturity and maximum size and age that is fundamental for developing informed management plans for these species. Staff and students in the CFFAER have continued to be very active in undertaking research on species of conservation significance, such as the dolphin populations of the Bunbury region and the Swan River, Freshwater Sawfish in the Kimberley, and on Fairy Penguins in Cockburn Sound. Remote sensing and tagging technology have been used to understand the movement and home ranges of Whale Sharks, Fairy Penguins and Freshwater Sawfish. Monitoring of Australia’s only critically endangered (EPBC Act 1999) freshwater fish species, the Western Trout Minnow, has continued in conjunction with studies on the vulnerable Balston’s Pygmy Perch and assessments of the effectiveness of fishways for protecting native fish. In freshwater, the impacts of invasive species, such as Eastern Mosquitofish and Goldfish, on biodiversity and system function have also been an important focus of activity, with a number of control programs in place.

Research on fish health includes studies of the health of cultured and wild aquatic species and of the environments in which they are found. Current research projects in this area are addressing the causes and consequences of stream salinisation, the role of invasive species in disrupting food webs and transmitting diseases, the development of sustainable inland saline aquaculture and understanding parasitic diseases of wild and cultured aquatic species.

Centre members identified three major areas for strategic development at a research planning day: estuarine research; quantitative methodologies for marine fisheries and wildlife, and marine wildlife research. Discussion papers were developed for each area for consideration by Centre members and senior members of the University administration. One of the outcomes from the investigation of marine wildlife was the decision to host a meeting on identifying knowledge gaps and research priorities for marine wildlife in north-western Australia. This meeting, which was held in December, involved participants from government, industry and researchers from Murdoch, University of Western Australia and Curtin University.

Centre members have been involved in the organisation of the 4th International Symposium of Stock Enhancement and Sea Ranching, planned for Shanghai in 2011. Professor Lynnath Beckley started her two-year term as President of the Australian Marine Sciences Association. We have also hosted a number of international visitors (Dr John Hoenig – Virginian Institute of Marine Science, Dr Michael Krüetzen – University of Zurich, Dr Pilar Olivar – Institute of Marine Science, Barcelona, Professors Bob Clarke and Richard Warwick – Plymouth Marine Laboratories, Professor Rory Wilson, University of Swansea, Dr Dina Zilberg - Ben Gurion University) and national visitors (Associate Professor Greg Skilleter – University of Queensland, and Dr Margaret Platell – University of Newcastle). We gratefully acknowledge the support that we have received for our research from FRDC, WAMSI, Department of Fisheries and many other government and industry partners and collaborators.

Neil Loneragan, Director

AWARDS/COMMITTEE MEMBERSHIP

Page 7 Centre for Fish and Fisheries Research - Annual Research Report 2010

Committee membership/ Community service Stephen Beatty • Australian Society for Fish Biology

(Executive Council) • Australian Society for Fish Biology (Alien

Fishes Committee, State Representative) • Margaret River Hairy Marron Recovery

Team • Bennett Brook Cichlid Taskforce Lynnath Beckley School of Environmental Science: • Honours Committee • School Advisory Committee (Industry) • Editor – School Annual Report Faculty of Science and Engineering: • Board member, Centre for Fish, Fisheries

and Aquatic Ecosystems Research Other Organisations: • African Journal of Marine Science (Editorial

Board) • Australian Marine Sciences Association

(President National Council) • Australian Marine Sciences Association

(WA Branch Committee member) • Rottnest Island Authority (Environmental

Advisory Committee member) • Australian Society for Fish Biology

(Recreational fishing research committee member)

• Sustained Indian Ocean Biogeochemical and Ecological Research (International Scientific Committee member)

• Monitoring Recreational Fisheries -Victoria DPI and FRDC (Technical Advisory Committee member)

• Integrated Marine Observing System (WA Node), Scientific Reference Group (Murdoch representative)

Lars Bejder • Board member of the Society for Marine

Mammalogy • Chair of the Education Committee for the

Society of Marine Mammalogy • Member of the Scientific Committee of the

International Whaling Commission • Member of the steering-committee for the

International Whaling Commission’s Large-scale whale-watching research initiative (LaWE)

• Board of Management for the Bunbury Dolphin Discovery Centre, Bunbury, Western Australia

Belinda Cannell • Member of Shoalwater Islands Marine Park

focus group

• Invited speaker for Shoalwater Islands Marine Park Discovery Series

• Department of Environment and Conservation - advice on effect of different management activities on Little Penguins

Jennifer Chaplin • University Appeals Committee Joseph Christensen • Secretary of the Australian Association for

Maritime History

Howard Gill • Board, Biological Sciences and

Biotechnology • Academic Chair, Biological Sciences Major • Academic Chair, Conservation and Wildlife

Biology Major • Recfishwest Committee and Executive • Murdoch University Animal Ethics Norm Hall • Editorial Advisory Committee of Marine

and Freshwater Research • Northern Prawn Fishery Resource

Assessment Group • Department of Fisheries - Advice on

matters relating to the stock assessment and management of fisheries

Matt Harvey • WA Branch Committee member of

Australian Marine Sciences Association Alex Hesp • Executive Committee member of

Australian Society for Fish Biology (ASFB) • Education Committee member of

Australian Society for Fish Biology (ASFB) • Board member of West Australian Fish

Foundation David Holliday • Australian Marine Sciences Association

(WA Branch Committee member) Halina Kobryn • Board and Standing Committee member of

Western Australian Satellite Technology and Applications Consortium (WASTAC)

• Member of Murdoch University Academic Council

Neil Loneragan • Biological Sciences and Biotechnology,

Research Committee • Board, Biological Sciences and

Biotechnology • WA Fisheries Research Advisory Board

RESEARCH ACTIVITIES cont…


• WA Rock Lobster Ecosystem Effects of Fishing Scientific Reference Group

• Research Subcommittee, Rock Lobster Industry Advisory Council

• Western Australian Marine Science Institute Steering Committee for Ecosystem Based Fisheries Management (Node 4)

• Ningaloo Research Coordinating Committee

• Chair, International Scientific Committee, 4th International Symposium on Stock Enhancement and Sea Ranching

• International Advisory Board for RESCOPAR research program, University of Wageningen

Alan Lymbery • Zoological Parks Authority Research Board • Managing Editor, Pacific Conservation

Biology • Editor, Biodiversitas • Chair, School of Veterinary and Biomedical

Sciences, Honours Committee • Chair, Scientific Program committee, 24th

International Conference of the World Association for the Advancement of Veterinary Parasitology

David Morgan • Executive Council of the Australian Society

of Fish Biology - WA representative • Threatened Species Committee (Australian

Society for Fish Biology) – WA State representative

• Alien Fishes Committee (Australian Society for Fish Biology) – WA State representative

• Recreational Freshwater Fisheries Stakeholder Sub-committee – Committee member

• Fitzroy River Fishway Steering Committee • Sawfish Expert Review Panel • Bennett Brook Cichlid Taskforce • Member – Australian New Guinea Fish

Association Ian Potter • Editorial Board of Environmental Biology

of Fishes • Western Australian Fish Foundation

Peter Rogers • Chair, Western Australian Marine Science

Institution • Member of Advisory Board of Integrated

Marine Observation Systems Claire Smallwood • Australian Marine Sciences Association

(WA Branch Committee member)

Malcolm Tull • Vice-President, International Council for

Maritime History • President, Economic Society of Australia,

Western Australian Branch • Treasurer, Australian Association for

Maritime History • Appointment by Minister for Fisheries in a

three-person panel – Development of management strategies for the pearling industry.

Fiona Valesini • Deputy Chair of the Coastal and Marine

Reference Group for Perth Region NRM Mike van Keulen University Administration: • Deputy Academic Chair Marine

Science • Director of the Coral Bay Research

Station • University Dive Officer General Community Service • President: North West Research

Association • Member: Council of the Royal Society of

WA • Member: WA State Marine Policy

Stakeholder Group • Member: Marine Reserve Council of WA • Maintain and coordinate two high-profile

international e-mail research discussion lists: Seagrass Forum and Mangrove

• Managing Editor: Pacific Conservation Biology

RESEARCH ACTIVITIES


3. RESEARCH ACTIVITIES Research objectives The main ongoing objectives of the Centre for Fish, Fisheries and Aquatic Ecosystems are to: 1. Undertake high quality research that addresses questions fundamental to the understanding of biological, ecological and evolutionary processes in aquatic ecosystems. 2. Communicate the results of our pure and applied studies to the wider scientific community through publishing in international journals and presentations at relevant national and international conferences. 3. Provide research students with rigorous and intellectually-stimulating training in contemporary biological, ecological and genetic approaches to fish biology, fisheries and conservation science, with particular emphasis on developing their quantitative skills. 4. Maintain strong research collaboration with scientists both within and outside Australia. 5. Undertake the research required to provide managers with sound quantitative data that can be used to develop policies for conserving fish resources and the environment, and also marine conservation planning. 6. Communicate, through peer reviewed technical reports, papers, seminars and discussions, the implications of the results of the above studies to scientists, managers and stakeholders. 7. Continue to attract the funding required to undertake the high quality research that is essential for this group to remain at the forefront of fisheries science and to provide the data required by fisheries, conservation and environmental managers to develop appropriate management plans. The wide range of studies undertaken by the staff in the Centre are aimed at enhancing our knowledge of particular fundamental biological processes in fishes and of aquatic ecosystem functioning in general, as well as addressing urgent management issues. These studies have been planned to involve postgraduate students and thereby ensure that the Centre produces fish biologists, fishery scientists, ecologists and conservation biologists with the relevant and high quality research training required to help fulfil the future needs of resource management and scientific agencies. The research activities in the Centre have been organised into three inter-related and overlapping themes to better reflect the role of our research in providing knowledge for Ecosystem Based Fisheries Management and marine and freshwater conservation planning. These areas are: 1. Ecosystems and Community Ecology; 2. Biological Processes and Evolution (including population biology and genetics), 3. Specialist Research Areas (e.g., freshwater fish and fish health, stock enhancement and remote sensing) The research activities of the Centre are reported under these themes below.



3.1 Ecosystems and Community Ecology 3.1 a) Estuaries and Catchments

Estuarine Health Index

Chris Hallett has been awarded his PhD for a thesis entitled ‘The development and validation of an estuarine health index using fish community characteristics’. This work, which was supervised by Dr Fiona Valesini, Dr Steeg Hoeksema and Prof. Ian Potter and funded by the Swan River Trust, Department of Water, Department of Fisheries and Murdoch University, has developed a multi-metric, biotic index of estuarine health for the Swan Estuary. This index integrates information from a suite of metrics, each of which quantifies a different aspect of the fish community, e.g. species diversity and composition, use of the estuary as a nursery habitat, and the trophic structure of the estuarine fish community. The study utilized fish community data collected between 1976 and 2009 to establish appropriate reference conditions for each metric, against which the current and future status of the estuary may be assessed. Chris’s PhD study, for which he was also awarded a Western Australian Marine Science Institution top-up scholarship, represents the first attempt within Western Australia to develop a multi-metric index of estuarine health based on fish assemblage characteristics. The work formed part of a broader Murdoch University project funded by the Department of Water, Department of Fisheries and the Swan River Trust, to develop a range of biotic indices for establishing and monitoring estuarine health. It is envisaged that the index developed from this work will provide a reliable, practical and cost-effective method for assessing the health of the Swan Estuary and potentially other estuaries across Western Australia. Chris is currently engaged in a follow-up project which aims to validate the spatial and temporal variability of this health index and which will conclude with the design of an appropriate sampling regime for future annual monitoring of the health of the Swan Estuary. He is also currently engaged in a project, funded by the Swan River Trust, which aims to examine the effects on benthic macroinvertebrate communities of two artificial oxygenation stations located on the Swan River.

RESEARCH ACTIVITIES


Flow diagram of process for evaluating fish as indices of estuary ecosystem health. (Chris Hallett).

Faunal Assemblages and Habitat

James Tweedley has submitted his PhD thesis for review entitled “Relationships between faunal assemblages and habitat types in Broke Inlet, Western Australia”. James’ research was supervised by Dr Fiona Valesini, Dr Steeg Hoeksema and Prof. Ian Potter and funded by the Fisheries Research and Development Corporation, Department of Environment and Conservation and Murdoch University. James employed a quantitative classification



scheme, using enduring environmental variables, to identify statistically the various habitat types present in the nearshore and offshore waters of the “near-pristine” and seasonally-open Broke Inlet on the south coast of Western Australia. This was the first time this novel approach had been applied to identify habitats in the deeper, offshore waters of an estuary. Hierarchical agglomerative clustering with a similarity profiles test identified 11 statistically different habitat types in nearshore waters and three in offshore waters. This rigorous classification scheme then provided the basis for determining whether the compositions of the fish and benthic macroinvertebrate fauna were related to habitat type in Broke Inlet and, if so, to what extent. The fish faunas of Broke Inlet were sampled at all habitat types using seine and gill nets seasonally for two years, while the benthic macroinvertebrates of this system were sampled using a corer seasonally for a year. The effectiveness of the habitat classification procedure was evaluated by determining, using multivariate statistical techniques, whether the spatial patterns exhibited by the compositions of the fish and benthic macroinvertebrate faunas matched those of the habitat types, as defined by enduring environmental variables. While such matching did occur with the fish faunas in nearshore habitats and, to a lesser extent, in offshore waters, it was not successful with the benthic macroinvertebrate faunas in either nearshore or offshore waters. The lack of matching between the invertebrate faunas and habitat types largely reflects the ubiquitous nature of the majority of the abundant species representing those faunas, i.e. they are adapted to a wide range of environmental conditions and thus habitat type. James presented an account of various aspects of his work at the Australian Marine Science Association Student workshop in Perth and gave a talk and presented a poster on different topics of his work to the Royal Society of Western Australia, the details of which were included in the Proceedings of the Royal Society.

The bar at the mouth of Broke Inlet in winter 2009

Estuarine Ecology – Nematodes

During 2010, Mat Hourston, Ian Potter and Fiona Valesini, together with Richard Warwick of the Plymouth Marine Laboratory in the U.K., decided to compare the data Mat had collected for the nematode fauna of the nearshore waters of the microtidal Swan-Canning Estuary with those obtained for corresponding habitats in nearshore coastal marine waters outside that estuary. The results, which were considered in the context of traditional paradigms, demonstrated the following. On the basis of species composition, the nematode fauna of the Swan-Canning Estuary could be considered to comprise one suite of species that were located downstream of the narrow channel between the main basins and another which was located upstream of that

RESEARCH ACTIVITIES


channel, where salinity varied more markedly throughout the year, and declined to lower levels. The number of nematodes species and species diversity were greater in the two estuarine regions than in the marine sites, when considered on the basis of comparisons between the fauna in individual cores (α-diversity), but not when comparisons were made between the estuarine and the coastal marine area as a whole (β-diversity). This reflects the fact that more species are present overall in the marine than estuarine environments, but that they occur in lower densities and have patchy distributions. In contrast to the trends exhibited by species richness and diversity derived from cores, the densities of macroinvertebrates in cores were far greater in the estuary than marine environment, presumably reflecting the greater productivity in estuarine than local coastal marine ecosystems. Although studies elsewhere have found that the densities of nematodes were greater outside the estuary, our results reveal that this was due to the sampling sites in those studies being located immediately outside the mouth, where they would benefit directly from the discharge of nutrients from the estuary. The species composition in even the downstream estuarine area differed markedly from that in the marine environment even though salinities in that area were at or close to that of full strength seawater for most of the year. Indeed, only one of the five most abundant species from the marine environment was found in either of the other two estuarine regions, and even then it was present in only low numbers. The differences in composition between the coastal marine waters and the estuary were so pronounced that they were still evident at the genus and family levels. 3.1 b) Freshwater Research by the Freshwater Fish and Fish Health group is reported separately under specialist areas in Section 3.3 below.

Lampreys

Ian Potter and Howard Gill, together with Claude Renaud of the Museum of Nature, Canada, have completed a comprehensive review of the biology of lampreys for a three-volume treatise on the freshwater fishes of North America. This facilitated the production of broad-based generalisations regarding this agnathan (jawless) group, which took into account the marked divergence between certain characteristics of the sole family of northern hemisphere lampreys (Petromyzontidae) and those of their southern hemisphere counterparts, the Mordacidae and Geotriidae. During the course of preparing data for the above review, it became increasingly obvious that the taxonomic status of certain lampreys, at both the species and generic levels, were conspicuously different, depending on whether morphological or molecular data were employed for cladistic analyses. Consequently, Ian, Howard and Claude carefully documented and highlighted the extent of these differences for a review of lamprey systematics, which they had

The suctorial disc and dentition of a) a fully metamorphosed Mordacia mordax and of early upstream migrants of b) Geotria australis, c) Petromyzon marinus and d) Lampetra fluviatilis.



been invited to write for a new book on “Lampreys: Biology, Conservation and Control”. This book is being edited by Margaret Docker of the University of Manitoba and is to be published by Springer. The production of this chapter was a particularly useful exercise as it stimulated Howard and Ian to obtain the DNA samples for virtually the full suite of living lampreys, which had been obtained during a previous study with Nick Lang of the Field Museum, Chicago. They are confident that the resultant DNA analyses, which will be undertaken in collaboration with Dave Berryman and Frances Brigg, will enable a greatly improved scheme to be developed for the phylogeny of this important early vertebrate group. The material will also be used to obtain estimates of the time of divergence of northern and southern hemisphere lampreys and to then consider that timing in the context of past geological events. Karen Paton has shown great perseverance in continuing, while having a full-time position in Canberra, to analyse and write up the data, which she had obtained earlier for aspects of the bioenergetics of the southern hemisphere lamprey Geotria australis. These data form part of Karen’s Ph.D., which is being supervised by Max Cake and Ian Potter. Geotria australis is characterised by having an exceptionally long spawning run of 12-15 months. As this species does not feed during this upstream migration, it has to rely for energy on stores accumulated during the preceding marine trophic phase, which accounts for lipid comprising 21% of its wet body weight when it migrates from the sea into rivers. Karen subjected, to an exercise and recovery regime, batches of individuals of G. australis from the beginning of their migration and at sexual maturation at the end of that migration. The measurement of various metabolites during that regime showed that vigorous activity by these non-trophic adults is fuelled by anaerobic metabolism of glycogen early in the spawning run and also later by mature females, but by aerobic metabolism of its energy reserves by mature males. Shaun Collin, David Hunt and Nathan Hart of the University of Western Australia and Trevor Lamb of the Australian National University are continuing their collaboration with Ian Potter and Howard Gill to develop an explicit hypothesis for the sequence of events that led to the evolution of the vertebrate eye. This study is drawing on data obtained from disparate fields, such as molecular genetics, anatomy, developmental biology, electrophysiology and palaeontology. Shaun and his colleagues have been fortunate in being awarded an Australian Research Council Discovery grant, which commences in January 2011 and thereby enables continuity to be maintained with their previous ARC grant. 3.1 c) Marine Biological oceanography Research on biological oceanography by the Marine Management group focussed on the Leeuwin Current, the remote region offshore of the Kimberley and on the ecology of rock lobster larvae, krill and larval fishes. The Leeuwin Current studies were based on an extensive voyage with the RV Southern Surveyor in 2007 which covered the full western seaboard of the continent (22o-34oS) and offshore into oceanic waters. Dr David Holliday and Prof. Lynnath Beckley prepared publications on the physical oceanography and the larval fish assemblages from this voyage. The larval fishes showed considerable cross-shelf connectivity and this was illustrated by using particle back-tracking in the BRAN model. Further work on samples collected during this voyage is underway, with focus now on elucidating diversity and distribution patterns for krill and chaetognaths. A multi-institutional, CSIRO-led research voyage off the remote Kimberley coast was undertaken with the RV Southern Surveyor in April 2010. With five transects extending from inshore waters (King Sound) out to oceanic waters (2000 m depth). The physical, chemical and biological oceanography of this macro-tidal region were examined. Professor Lynnath Beckley and post-doctoral fellow Dr David Holliday sampled the macro-

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zooplankton and larval fishes of the region and elucidated clear patterns in the larval fish assemblages and interesting responses to tide. There is high diversity with many larvae of species important in demersal fisheries, such as snappers and groupers, and pelagic fisheries such as tuna. Larval fish assemblages in areas such as King Sound and the Lacepede Islands were quite distinct from other shelf regions. Dr Pilar Olivar from the Institute of Marine Science in Barcelona made another visit to Murdoch to work with us on the identification of larval lantern fishes from northern Australia. The FRDC-funded joint research project between UWA, Murdoch, CSIRO and WA Department of Fisheries investigating the planktonic larval stage (phyllosoma) of the WA rock lobster undertook a research voyage with the RV Southern Surveyor in 2010in the waters between Fremantle and the Abrolhos islands and out to 400 km offshore. The phyllosoma drift in oceanic waters for nearly a year before metamorphosing into the puerulus stage and recruiting back to coastal reefs and seagrass beds. After several years of unexplained recruitment failure, the WA rock lobster fishery is under severe pressure with catch quotas implemented for the first time. Experiments were carried out on the ship to investigate the feeding preferences of the lobster larvae and these studies revealed that the phyllosoma preferred chaetognaths. An extensive survey of the prey field in the south-eastern Indian Ocean from 28o-32oS was also carried out and this research established an apparent mismatch in the distribution of the phyllosoma with their preferred prey. Several students including Nick Breheny, Alicia Sutton and Jonathon Saville accompanied Prof. Beckley on these voyages and made substantial contributions to the success of the scientific endeavours. In addition, in 2010, Prof. Lynnath Beckley and Nick Breheny assisted a team of UWA scientists on the RV Southern Surveyor with their oceanographic research off the Ningaloo coast. This voyage enabled the collection of higher resolution data than previously available for this region and also provided insights into the complicated headwaters of the Leeuwin Current. Nick Breheny completed his Honours thesis on the larval fish assemblages which occur in association with the known spawning aggregations of pink snapper in Cockburn and Warnbro Sounds. Alicia Sutton started her Honours thesis on the krill assemblage off the Rottnest Canyon – a bathymetric feature that attracts a seasonal aggregation of blue whales. 3.1 d) Resource partitioning and trophic interactions Research on trophic interactions and food web structure and function is being carried out in the upper Swan estuary and the Perth metropolitan waters, both supported by WAMSI. The research in the Swan forms part of the PhD studies of Thea Linke, supervised by Dr Fiona Valesini, Prof. Ian Potter and Dr Luke Twomey (Oceanica Consulting), and involves using dietary analyses and tracer studies (stable isotopes and fatty acid analyses) to identify the prey and primary sources of food for three species in this region. The research in the Perth metropolitan waters (funded by WAMSI and FRDC) is led by Prof. Ian Potter and Dr Margaret Platell, and will synthesise dietary information from previously funded FRDC studies and collect new information on the diets of Pink Snapper and Trevally, to develop an understanding of the demersal food web and trophic flows in this region. This research forms the basis of the PhD studies by Ben French who commenced his studies in June 2009. The information from this research will provide the basis for assessing how the depletion of key demersal species, such as Dhufish and Pink Snapper, is impacting ecosystem structure and function. In her PhD studies, Thea Linke, is investigating the trophic relationships between three species of fish and their prey in two south-western Australian estuaries (the Swan River Estuary and Wilson Inlet). The three species include an omnivore (Black Bream Acanthopagrus butcheri), a benthivore (Bluespot Goby Pseudogobius olorum) and a planktivore (Western Hardyhead Leptatherina wallacei), all of which constitute important



parts of the food chain in the two estuarine systems. Thea has received additional support for her studies from the WAMSI. Thea is using three different approaches to fish dietary studies, which will enable her to gain a very sound understanding of the pathways of material transfer (including sources of primary production) in the two estuaries. The resultant data from the three approaches, i.e. stomach content analyses, carbon and nitrogen stable isotope analyses (of fish and their prey) and fatty acid analyses (of fish and their prey), will be integrated to construct detailed food webs for the two ecosystems. Thea has maintained strong links with researchers at Hamburg University, where she has completed her fatty acid analyses. 3.1 d) Fisheries dynamics and modelling Fisheries modelling PhD student Emily Fisher with Alex Hesp and Norm Hall recently completed a 2.5 year FRDC-funded study in which they developed a management strategy evaluation model. The study explored a range of questions, including the effectiveness of computer model interface designs for communicating stock assessment information, the accuracy and precision of mortality estimates derived from different catch curve analyses, and the effectiveness of commonly-used management measures in recreational fisheries for regulating fishing mortality. A copy of the final report is available from the FRDC. Emily Fisher, Masters student, Elena Sulin, Alex Hesp and Norm Hall recently commenced another 2.5 year FRDC-funded study to develop a stock assessment model for estimating growth, mortality and migration parameters for fish species, such as King George Whiting and Silver Trevally, which exhibit offshore size-related movements. The project involves fish sampling to enable current assessments of the stock status of these species. Thanks are extended to Kim Smith, Josh Brown and Chris Dowling (DoF) for their kind assistance in collecting King George Whiting. PhD student Calais Tink, and Alex Hesp and Norm Hall are continuing their agent-based modelling studies of recreational fisher behaviours. Surveys of recreational fishers were undertaken at angling clubs to gather data on how fishers target demersal fish species, such as West Australian Dhufish. Plans are now underway to also undertake a phone diary survey, linking in with a major phone diary survey being carried out by the Department of Fisheries, WA. The computer model was developed under a grant provided by FRDC. Alex Hesp, James Tweedly, Calais Tink, Norm Hall, together with Richard Campbell (DEC/ECU) and Rory McAuley (DoF), are developing an agent based model to estimate rates of encounter between Australian sea lions and gillnets used by WA commercial demersal gillnet fisheries. The model simulates movements of sea lions using information derived from satellite-tracking data. The activities of commercial gillnet fisheries in each of three financial years will be “replayed” in the model, using data recorded in fishers’ log books. The project, which is due to be completed in August, 2011 is being funded by FRDC and by WAFIC. PhD student Alan Cottingham, Norm Hall and Alex Hesp, are developing a new growth model for Black Bream. Growth rates of this species in the Swan River, in particular, have changed markedly in recent years, but traditional growth models are not well suited to tracking changes in growth over time. The new model will also be applied to this species in the Blackwood River Estuary, where growth rates of wild black bream have also changed in recent years, following restocking of this species nearly 9 years ago. Behavioural studies of rock lobster Panulirus cygnus Natalie Toon, supervised by Neil Loneragan, is completing a PhD on investigating environmental, biological and fishery effects on the behaviour of the Western Rock Lobster

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(Panulirus cygnus). The behaviour of lobster affects their catchability (‘q’), which is an important component of any wild caught fishery and is a parameter that is utilised in stock assessments for the Western Rock Lobster fishery. She has completed video studies in both the laboratory and field of lobster behaviour within and around commercial fishing pots. In the laboratory, she examined how behaviour is influenced by water temperature, moon phase (light intensity), lobster size and pot neck type (stick and plastic neck). Video observations have been used in both a controlled aquarium environment and in situ field environment to observe the behaviour of the Western Rock Lobster around commercial fishing pots. Ecosystem modelling Ecosystem modelling work has focused on developing both qualitative and quantitative ecosystem models for marine and estuarine systems in Western Australia. The final report for the qualitative modelling work has been guided and lead by Dr Jeffrey Dambacher (CSIRO) to develop conceptual understanding and test hypotheses about the Jurien Bay ecosystem. This work, funded by the FRDC, is examining the impact of spatial closures on the food webs of the region, and has been progressing well. Dr Hector Lozano-Montes, in collaboration with Neil Loneragan and Russ Babcock (CSIRO), has developed an Ecopath model for 2005, based largely on data gathered by the CSIRO Jurien Bay collaborative study, and the model has been used to evaluate different management options e.g. increasing fishing effort, reducing commercial fishing on rock lobster. A spatial model has been developed (Ecopath) and used to evaluate the implications for catches and biomass of selected species in increasing the size of sanctuary zones from 4 % to 30%. Interviews were completed with people in the region to develop an understanding of the state of the system in the early 1980s. Qualitative and quantitative models are being developed for the Peel-Harvey estuary through the PhD studies of Sarah Fretzer, supervised by Norm Hall and Hector Lozano (CSIRO). These studies are supported by WAMSI. Excellent progress is being made on the management strategy evaluation (MSE) and agent-based modelling studies, which are being funded by FRDC and being supervised by Alex Hesp and Norm Hall. These studies are aimed at providing training in quantitative skills for Honours and PhD students and at developing tools for exploring certain fisheries management questions. 3.1 d) Marine Protected Areas Based on earlier extensive field work by the Marine Management group, research continued on the two Ningaloo Collaborative Cluster projects, namely, human use of the reef and mapping of the benthic habitats using an extensive hyper-spectral data set. The Final report for the reef use project has been completed and several publications have been completed based on the Ningaloo aerial, coastal and interview surveys. Spatial and temporal patterns in human use have been elucidated and, in addition, the extent of recreational fishing, travel networks, the influence of marine park zoning on recreational activities and the influence of coastal tenure on human use have all been examined. Claire Smallwood graduated with a PhD based on this work. Dr Mandy Lombard visited from South Africa in March 2010 and conducted a workshop on systematic conservation planning which was extremely useful to the group. In addition, she worked with Prof. Beckley to finalise a manuscript on a systematic evaluation of the incremental protection of broad-scale habitats at Ningaloo Reef. Following on from the Ningaloo human use project, which indicated very high repeat visitation, Joanna Tonge developed a PhD which examined the concept of place attachment amongst campers along the southern Ningaloo coast, in particular, how it related to support for conservation and management actions. Rebecca Roberts has also been working



on her PhD thesis on the economics of coastal hazards in the north west of Australia, using a hedonic pricing model to determine whether the threat of cyclonic storm-surge inundation affects house prices in Exmouth. This study is relevant in view of revision of the Western Australian Coastal Planning Policy, expanding industry along the coast of northern Australia and the predicted effects of climate change on sea levels and increased extreme weather events. The comprehensive final report on the outcomes of using high resolution, remotely-sensed hyperspectral imagery to map the benthic habitats and bathymetry over the 300 km long fringing reef in Ningaloo Marine Park and the Muiron Islands is also in development. This represents one of the largest coral reef areas mapped using hyperspectral imagery in the world and provides remarkable thematic resolution and a benchmark of reef habitats which will aid managers, planners and ecologists for many years. Dr Halina Kobryn and colleagues are busy completing several publications based on this work. 3.1 e) Biodiversity and Conservation

Marine Mammal Research

The members of Murdoch University’s Cetacean Research Unit (MUCRU) work on both applied and empirical conservation-based research projects. MUCRU has five core research areas: assessments of anthropogenic impacts on cetaceans; cetacean population biology and behavioural ecology; interactions between cetaceans and their ecosystems; marine mammal health; and development of novel methodological approaches. These research areas reflect the diversity and breadth of experience and expertise held by MUCRU personnel. Above all, MUCRU members seek to conduct research that improves the scientific basis for the conservation of Australian cetaceans and for decision-making by industry, government, and the community. In 2010, we further expanded our research program and collaborations, and strengthened existing partnerships with industry and government agencies. Below, we outline key highlights from 2010. Workshop: Building long-term research capacity and partnerships for marine wildlife research in Western Australia with special emphasis on marine mammals. In December 2010, MUCRU hosted a marine mammal workshop entitled: Building long-term research capacity and partnerships for marine wildlife research in Western Australia with special emphasis on marine mammals. The workshop was chaired by Dr Nick Gales (Australian Antarctic Division) and Prof. Neil Loneragan (Murdoch University) and brought together approximately 45 participants representing Australian Federal and Western Australian State Government organisations (Department of Sustainability Environment Water Populations and Community, WA Department of Environment and Conservation, WA Department of Fisheries, Environmental Protection Authority, WA Museum), Industry (Australian Petroleum Production and Exploration Association, Dampier Port Authority, Woodside, Chevron), environmental consultants (Oceanica, RPS, Worley Parsons) and research organisations (Curtin University, Edith Cowan University, Murdoch University, University of Western Australia, Australian Institute of Marine Science, Australian Marine Mammal Centre, Centre for Whale Research). The long-term aim of the workshop is to develop a coherent and integrated strategy for marine mammal and marine wildlife research and, in particular, to facilitate strategic research partnerships across institutions and research areas. The specific aims of the workshop were to:

1. understand management and industry needs and priorities for research; 2. gain a better understanding of the current research and research capacity in

Western Australia for marine mammals and marine wildlife in general; and 3. to identify research gaps and opportunities for collaboration.

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The key themes and issues identified during the workshop were: 1) The numerous large scale developments in north western Australia highlight the need for a long-term coordinated, multidisciplinary approach to research for assessing the cumulative impacts of developments on marine mammal populations; 2) Impact assessments of marine developments would benefit greatly from strategic research on study design, survey methodologies and data analyses, which would lead to the development of standardised protocols. 3) The workshop highlighted the value and need to synthesise research priorities for government and industry and develop an overall research strategy that addresses these priorities; 4) Organisations and researchers should be encouraged strongly to make metadata and data on marine mammals readily available, as soon as possible after completion of the work; and 5) Researchers need to engage managers, industry and indigenous communities through all stages of the research i.e. planning, development, implementation and completion of research, not just the communication of project results after projects have been completed.

Participants of the marine wildlife workshop. Development of Unmanned Aerial Vehicle technology for marine mammal surveys: 2010 saw the arrival of Dr Amanda Hodgson who was awarded the prestigious Bill Dawbin Postdoctoral Research Fellowship from the Australian Federal government through the Australian Marine Mammal Centre. The objective of the three-year Fellowship is to develop Unmanned Aerial Vehicles (UAVs or drones) methodology and technology to replace standard manned aerial surveys of marine mammals. Dr Hodgson chose to bring the Fellowship to Murdoch University to work with the Cetacean Research Unit and collaborate with Prof. Ken Pollock. Amanda is working closely with Insitu Pacific - the largest UAV company in Australia.



The team from Insitu Pacific and Amanda Hodgson with the ScanEagle UAV in Shark Bay, 2010 Investigation of the genetic structure and abundance of fishery-impacted dolphin populations of the Pilbara region, North-Western Australia. Research Associate Simon Allen together with colleagues (Bejder, Bryant, Krutzen, Loneragan and Pollock) were awarded a two and half year category 1 grant from the Australian Federal government, through the Australian Marine Mammal Centre, to investigate the abundance and genetic structure of fisheries impacted bottlenose dolphins in the north west, WA. Specifically, between 150 and 350 bottlenose dolphins have been caught in the Pilbara Trawl Fishery since late 2003. Little data on dolphin stock identity or abundance exists and whether recent declines in dolphin catch reflect better bycatch reduction devices or a declining dolphin population remains unknown. To assess the level of impact that dolphin bycatch is having on this undetermined stock, the project aims to: identify population genetic structure across fishery-impacted areas; conduct photo-identification to determine the number of dolphins interacting with trawlers; and, carry out an aerial survey to estimate dolphin abundance. The research has national application in reducing negative delphinid-fisheries interactions. Marine Mammal Health research The Marine Mammal Health research program spearheaded Drs Carly Holyoake and Nahiid Stephens from Conservation Medicine Program, School of Veterinary and Biomedical Sciences developed further collaborations with Murdoch University Cetacean Research Unit. A major milestone in 2010 was the submission of a Technical Report on the 2009 unusual mortality event of bottlenose dolphins that occurred within the Swan Canning Riverpark. The report reviews findings from the investigation into the mortalities of six bottlenose dolphins in the Swan Canning Riverpark in 2009. The report: (a) describes the epidemiology and pathology of these mortalities; (b) presents background information on the ecology of dolphins in the Swan Canning Riverpark and factors known to affect dolphin health; and (c) discusses the potential role of chemical contaminants in the mortalities. These mortalities were investigated in context of dolphin deaths in the Swan Canning Riverpark prior to 2009 and a series of mortalities of dolphins in the Bunbury area between 2008-10, as well as marine mammal mortality events in other locations.

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Quantifying the effects of human interactions on spinner dolphins in resting bays in Hawaii and assessing the effectiveness of time area closures as a proposed mitigation approach Drs Bejder and Johnston (Duke University) were awarded funding from both the US National Oceanographic and Atmospheric Administration and the US Marine Mammal Commission to commence a three-year study to quantify the effects of human interactions on spinner dolphins in Hawaii, and to assess the effectiveness of time area closures as a proposed mitigation approach. This collaborate research project between Murdoch University and Duke University is forming the basis for Julian’s Tynes PhD research at Murdoch. Specifically, Julian will be spending five months every year over the next two-three years in Hawaii aimed at: 1) quantifying spinner dolphin daytime habitat use and resting behaviour in a proposed time area closures; 2) determining residency and fidelity patterns of spinner dolphins during day time in near shore habitats in the proposed time area closures and surrounding waters; 3) producing quantitative measures of spinner dolphin exposure to human activities within resting bays; and 4) producing quantitative measures of spinner dolphin exposure to human activities in near shore shallow water environments outside resting bays.

Spinner dolphin (Stenella longirostris) mother, calf and remora

South West Marine Research Program

Cetacean research in the south-west in 20010 focused on bottlenose dolphins (Tursiops sp.) through the South West Marine Research Program (SWMRP). Founded in 2007 on an initial partnership between the Bunbury Dolphin Discovery Centre and Murdoch University, with support from the South West Development Commission, the SWMRP is composed of partners from industry, government, research and the community. Partners include Bemax Cable Sands, BHP Billiton Worsley Alumina Pty Ltd, Bunbury Dolphin Discovery Centre, Bunbury Port Authority, the City of Bunbury, Cristal Global, Department of Environment and Conservation, Iluka, Millard Marine, Naturaliste Charters, South West Development Commission and WA Plantation Resources. The overall aim of the SWMRP is to assess the long-term viability of dolphin populations by building an understanding of their biology and ecology, including gene flow with other geographic areas and interactions with the environment, food resources and human activities (tourism, port activities and port development). Three synergistic research projects targeting the Bunbury region are contributing to achieving this overall aim: 1) Document abundance and habitat use of bottlenose dolphins (PhD candidate Ms Holly Smith). This work includes mark-recapture techniques to estimate dolphin population size. Ms Smith has also been analyzing the social structure of the local dolphin population by comparing association data between individuals of varying age and sex classes. She is also calculating dolphin home range patterns using minimum convex polygon estimates and



kernel density estimates. Lastly, she is creating a habitat model that will be used as a tool to predict dolphin distribution according to environmental factors such as water depth, water temperature and benthic substrate type. Ms. Smith completed her field work in 2010 and will now concentrate on data analyses for her PhD dissertation. 2) Investigate the factors affecting the distribution of dolphin prey species (PhD candidate Ms Shannon McCluskey). Ms. McCluskey’s research into the food habits and foraging behaviour of the Bunbury bottlenose dolphin population is progressing with her final field season planned for winter 2010. Shannon is using variety of methods to help decipher bottlenose dolphin diet and foraging preferences. These include: prey sampling (gillnets, seining and fish traps), estimation of prey calorific value, dolphin stomach content analyses, stable isotope analysis, and spatial modelling of the marine environment to develop models of dolphin foraging patterns. Prey are being sampled from sites within three regions (Leschenault Estuary, Koombana Bay, and along Back Beach). Sampling is taking place in summer months when dolphins are present in the highest numbers, and winter months, when dolphins are observed in lower numbers. Ms. McCluskey completed her field work in 2010 and will now concentrate on data analyses for her PhD dissertation. 3) Investigate the population and conservation genetics of dolphins in Albany, Augusta, Busselton, Bunbury and Cockburn Sound (PhD candidate Claire Daniels; UNSW), Specifically, this research aims to provide 1) a species identification of the dolphins in Bunbury and wider south-west Western Australia and 2) an estimation of the level of gene flow between dolphin populations along the coast of south-west Western Australia.

Study of the effect of a boat ramp at Becher Point on the food resources of Little Penguins on Penguin Island

Western Australia’s largest colony of Little Penguins, Eudyptula minor, breeds on Penguin Island, within the Shoalwater Islands Marine Park, near Rockingham. Previous research in the 1980s and 1990s have shown that Sandy sprat, Hyperlophus vittatus, compose up to 80% of the penguins’ diet and that the Sandy sprat originate mainly from a nursery site at Becher Point, 7 km south of Penguin Island. This small, schooling baitfish typically spawns in the inshore marine waters along the lower west coast of Australia from May to September, and the new recruits (juveniles) then make their way into the shallow waters along the coast, and also into estuaries, which they use as “nurseries” until they are mature. Juvenile Sandy sprat (from ~20 mm in length) have been caught in large numbers (up to 44505 individuals in any one month) around the Becher Point area between August to December, with the greatest and most consistent catches often occurring in October and November. The recent construction of a boat ramp in May 2010 at Becher Point and the associated projected increase in boating traffic, adjacent to this major Sandy sprat nursery, may impact the viability of this nursery thereby affecting Sandy sprat abundance in the local area. This may then, in turn, affect the breeding success of the Little Penguins and the long-term viability of the penguin colony.

This study will re-assess the diet of Little Penguins during breeding and correlate diet with various breeding parameters monitored by DEC. Diet will be determined by analysing DNA in penguin faecal samples. Diet composition and breeding success will also be correlated with Sandy sprat abundance at the Becher Point nursery site following

Little Penguins coming ashore are kept in a holding pen until weighed, scanned and marked with a subcutaneous transponder.

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the construction of the boat ramp. The abundance of the penguins may be impacted in the long-term through the loss of a major prey resource. The abundance of the population was estimated by a ‘mark and recapture’ method in 2007 and 2008. As the current adult stock of Sandy sprat is unlikely to be affected by the construction of the boat ramp, further annual population estimates of the Penguin Island colony will be obtained to provide a more robust baseline dataset of abundance. It will then be possible to determine any trend in the population prior to a potential impact on the Sandy sprat stocks from the boat ramp, providing that there is not a marked increase in penguin mortality from boating activities associated with the boat ramp. As DEC is continuing to monitor various breeding parameters, it may also be possible to correlate annual estimates with various breeding parameters as well as penguin diet composition.

The study will also analyse historical Sandy sprat abundance data recorded in beach seine net samples collected at Becher Point by the Department of Fisheries since the 1990s to determine whether temporal trends in this fish species are significantly correlated with those in a suite of (a) relevant environmental variables (where data are available) and (b) Little Penguin reproduction and survival parameters. Monthly sampling of the nearshore fish fauna will be undertaken between August and December in 2011-2013 at and surrounding the site of the newly constructed boat ramp at Becher Point to determine, primarily, whether there is any evidence to suggest that this construction is related to any significant changes in juvenile Sandy sprat abundance and distribution in the area. Finally, a cost-effective and robust monitoring regime will be designed to enable the abundance of Sandy sprat in the Becher Point area to be reliably measured into the future.

To date, the penguin population was estimated in 2010 using mark-recapture, and 32 volunteers. These volunteers were mostly Murdoch University veterinary and biology students. The estimated population was much lower than estimates obtained for 2007 and 2008. This most likely reflects a lower breeding population at the time of the study, rather than an absolute reduction in the population. Fifty-two faecal samples were collected and were analysed under the supervision of Drs Mike Bunce and James Haile. They were analysed using high throughput sequencing and quantitative PCR. From these samples the penguins were feeding on Sandy sprat, but pilchard (Sardinops sagax) also composed a large proportion of the diet.

3.2 Biological and evolutionary processes and evolution 3.2 a) Fish and invertebrate population biology

The biology of labrids

Elaine Lek has made very good progress on her PhD, which has involved studying the biological characteristics of three co-occurring species of wrasse (Labridae) over reefs in the Jurien Bay Marine Park (JBMP) at 30°S and in the waters off Perth at 32°S. This study is supervised by Dr David Fairclough and Prof. Ian Potter, with invaluable assistance being provided by Prof. Norm Hall and Dr Alex Hesp with the age, growth and reproductive studies and by Dr Margaret Platell and Prof. Bob Clarke (Plymouth Marine Laboratory) with the diet studies.

Elaine’s results demonstrated that the maximum length, weight and age of Coris auricularis, Notolabrus parilus and Ophthalmolepis lineolatus were almost invariably greater at the higher latitude and thus cooler waters than at the lower and therefore warmer waters. These results are consistent with the predictions of the Metabolic Theory of Ecology (MTE), which is based around the fact that the metabolism of ectotherms is related to temperature. However, the early growth rate of each species is also greater in the cooler latitude, which runs counter to the predictions of MTE. This implies that these species



contain a range of evolutionary modifications that render reaction rate relatively independent of the temperature at which an organism is adapted to live (see Hochachka & Somero, 2002; Clarke, 2004; Clarke and Fraser, 2004).

The diets of each of the three labrid species were found by Elaine to comprise a wide range of prey, which included large and small crustaceans, bivalve molluscs, echinoids, annelids and gastropods. However, the dietary compositions of those species as recorded in terms of the percentage contributions of the various prey components, were significantly different from each other at each latitude, which would reduce the potential for competition for food resources when these species co-occur. The dietary composition of each species also differed between the JBMP and waters off Perth, presumably reflecting differences in the relative abundances of the various prey taxa at those two different localities.

Elaine’s work on the reproductive biology of the three labrid species is well advanced and she is thus well positioned to submit her thesis in the middle of 2011.

3.3 Specialist Research areas 3.3 a) Freshwater Fish and Fish health The research focus of the Freshwater Fish Group and Fish Health Unit is the conservation of native freshwater fishes. We currently have research projects addressing the biology and genetics of native fish species, mitigating threats such as salinisation, river regulation and invasive species, and the development of sustainable inland saline aquaculture. Further information about the work of the group is available at http://www.freshwaterfishgroup.com. Biology and genetics Dr David Morgan and Dr Stephen Beatty have continued to work on the biology of freshwater fish fauna of south-west river systems, including the Warren, Donnelly, Harvey, Murray, Angove, Hay, Denmark, Margaret and Blackwood Rivers. One of the highlights of this work was the discovery of a putative new species of pygmy perch; this is currently being investigated with detailed genetic and morphological analyses. A major focus of recent work, involving Jeff Whitty’s masters project, has been the acoustic tracking of freshwater sawfish (Pristis spp.) in the Fitzroy River and other systems of the Kimberley region. These exciting studies are uncovering much new information about the movement patterns, habitat utilisation and general biology of these iconic freshwater fish species. Jon Murphy undertook an Honours project on the population genetics of two of the most widespread species of freshwater fish in the south west of Western Australia; western minnow (Galaxias occidentalis) and western pygmy perch (Nannoperca vittata). John found a genetic disjunction between south coast and west coast populations of these two species, suggesting that fish communities in these regions may need to be managed separately for conservation purposes. He also found substantially greater genetic variation among populations of western pygmy perch than among populations of western minnow, which is likely to reflect the larger size and greater dispersal ability of minnows. Michael Klunzinger has continued a PhD on the ecology of the freshwater mussel, Westalunio carteri. This species, the only freshwater mussel in the south west of Western Australia, is listed as Vulnerable on the IUCN Red List. It is thought to be threatened by secondary salinisation, but almost nothing is known of its current distribution, life history and biology. To date, Michael has mapped the current range of the species and determined

RESEARCH ACTIVITIES


that the range is contracting from historical distribution records, identified a large number of host fish species for the parasitic first stage of the mussel life cycle and measured the salinity tolerance of the species. This work will be extremely important in understanding the conservation status of this little known freshwater species. Mitigating threats Michelle Ingram and Farhan Bokhari continued their PhD projects on the effect of salinisation in the Collie River on the diversity and resilience of riparian plant and associated invertebrate communities. These two projects, with funding assistance from the Australian Flora Foundation, have found dramatic effects of stream salinity on species diversity at several trophic levels (producers, first-order consumers, second-order consumers). Mahmoud Rashnavadi is examining the effect of salinity on fish biology and parasitism in the Blackwood River, in a PhD project supported by the Australia and Pacific Science Foundation. Mahmoud has found evidence of differences in growth rates, reproductive activity, diets and parasitism in populations of a number of fish species exposed to different salinity regimes James Keleher completed an Honours project on the swimming ability of native and exotic freshwater fishes in the south west of Western Australia. This was the first ever study of the swimming performance of native fishes in Western Australia and will provide valuable data for the construction of fishways, designed to allow fish to pass over in-stream barriers to dispersal. Inland saline aquaculture We completed a project, funded by RIRDC, on using a cultivated form of the halophyte Distichlis spicata (NyPa Forage) to remove nutrients from inland saline aquaculture effluent. In vitro laboratory tests have demonstrated the efficacy of the plant in nutrient removal and suggested that irrigation with aquaculture effluent markedly improves nutrient value of the plant as a livestock feed. The ability of irrigated NyPa Forage to maintain sheep liveweight over the summer/autumn period was confirmed in small scale paddock trials. 3.3 b) Social and economic assessment The WAMSI Node 4.5 project ‘Socio-Economic Implications Associated with Implementing EBFM’, directed by Prof. Malcolm Tull, reached an advanced stage during 2010. Investigations into the financial impact of recent changes to the management of the inshore demersal species suite in the West Coast Bioregion on the West Coast Demersal Fishery (commercial fishers) and the Western Australian Fishing Tour Operator sector (charter boat operators) were conducted by Dr Joseph Christensen and Dr Seamus McElroy (UWA) during a series of interviews, with field-work for the project supported by the use of CFFAER vehicles. With Associate Prof. Paul McLeod (UWA), a telephone survey of boat-based recreational fishers was also conducted during April-May 2010, to assist with the Node 4.5 sub-project concerned with the modelling of recreational fisher behaviour.

In November 2010, Malcolm Tull and Joseph Christensen participated in the conference ‘Oceans Past III: stories from the sea - history of marine animal populations and their exploitation’ at Trinity College, Dublin. Both presented papers arising out of research undertaken as part of the Asia sub-project of HMAP (History of Marine Animal Populations)- Joseph on the historiography of recreational fishing in Western Australia, and Malcolm on the broad historical development of the fisheries of the Indo-Pacific region. At the conclusion of the conference, Malcolm was invited to host the next HMAP conference in



Perth. Planning for the ‘Oceans Past IV’ conference, scheduled to be held in Fremantle on 7-9 November 2012, will continue throughout 2011.

3.3 c) Stock enhancement and restocking Biological performance and genetics of restocked Black Bream in the Blackwood River Estuary In 2001 and 2002, the Black Bream Acanthopagrus butcheri was cultured from broodstock collected from the Blackwood River Estuary, in which it completes its life cycle but had become depleted in abundance. Prior to releasing these cultured fish into the estuary, their otoliths were stained with alizarin complexone. The retention of this stain by otoliths for the 3.5 years after the fish had been released thus enabled the biological performance of those cultured fish to be tracked during that period (Potter et al., 2008). As the stain was still present in the otoliths of cultured fish in 2010, the biological characteristics of cultured fish could be studied over a further five-year period. In this more recent study, we also restricted comparisons with wild fish to the same year classes as the cultured fish and therefore to fish that had been exposed to the same environmental conditions.

Alan Cottingham and Michelle Gardner undertook the biological and genetic studies as part of PhD and Honours theses, respectively, with Dr Alex Hesp, Dr Jennie Chaplin and Prof. Ian Potter, as their supervisors. Nicole Phillips kindly assisted with the genetic studies and Trevor Price generously provided us with samples of the fish he caught, while Greg Jenkins (Aquaculture Development Unit, Maritime W.A. Training Centre) was responsible for culturing the Black Bream. Financial support was provided by the Department of Fisheries, WA, the West Australian Fish Foundation, the Australian Fisheries Research and Development Corporation and Murdoch University.

Recent analyses of our data for the full period during which cultured fish had been present in the Blackwood River Estuary demonstrate that the 2002 cohort, introduced at ~4 months old in autumn, survived far better than the 2001 cohort, introduced at ~7 months old in winter when conditions were more severe. Our results also demonstrated that restocked fish had grown nearly as fast as wild fish and that all restocked fish that survived to six years of age reached maturity. The introduction of restocked fish was accompanied by a reduced growth of wild fish, presumably reflecting the influence of the substantial increase in the density of Black Bream brought about by restocking.

Genetic comparisons, using data from 7 microsatellite loci, demonstrated that the expected heterozygosity (HE) and relatedness (r) of restocked and wild fish, which is naturally characterised by low levels of genetic polymorphism, were similar. Although culturing did not lead to an obvious increase in the level of inbreeding, it did result in the loss of some rare alleles. However, the combined biological and genetic results, together with the contribution of restocked A. butcheri to the commercial catch for this species in this estuary having risen to 62-74% by 2007-10, imply that restocking, if carried out appropriately, is a useful tool for replenishing depleted stocks of Black Bream in estuaries.

Fourth International Symposium on Stock Enhancement and Sea Ranching (4ISSESR)

Planning continued for the fourth ISSESR to be held in association with the 9th Asian Fisheries and Aquaculture Forum in Shanghai in April 2011. Professor Neil Loneragan is Chair of the International Scientific Committee for this Symposium and Mr Greg Jenkins, The Director of Aquaculture Research at Challenger Institute and an adjunct Senior Lecturer at Murdoch, is also a member of the International Scientific Committee.

PUBLICATIONS


4. PUBLICATIONS for 2010 Books Branch, G.M., Griffiths, C.L., Branch, M.L. &

Beckley, L.E. 2010. Two Oceans - A guide to marine life in southern Africa. Struik Nature, Cape Town. 456pp.

Morgan, D, Beatty, S, Allen, M, Klunzinger, M, Kuiter, R 2011, A field guide to the freshwater fishes, crayfishes and mussels of south-western Australia, SERCUL, Perth

Book chapters Hallegraeff,, G, Bolch, C, Huisman, JH, de

Salas, 2010, Planktonic dinoflagellates, Algae of Australia: Phytoplankton of Temperate Coastal Waters, ABRS, Canberra, CSIRO Publishing, Melbourne, 145-212

Refereed publications in 2010 Bacher, K, Allen, S, Lindholm, A, Bejder, L,

Krutzen, M 2010, Genes or Culture: Are mitochondrial genes associated with tool use in bottlenose dolphins (Tursiops sp.)?, Behavior Genetics: 40(5), 706-714

Alberts, S, Altmann, J, Bejder, L, Connor, R, Daher, M, Engleby, L, Flaherty, C, Premack, D, Read, A, Ridgway, S, Silk, J, Spradlin, T, Tyack, P 2010, Memories, Marine Mammal Science, 26(2), 501-507

Beatty, S, Morgan, D 2010, Teleosts, agnathans and macroinvertebrates as bioindicators of ecological health in a south-western Australian River, Royal Society of Western Australia. Journal, 93(2), 65-79

Beatty, S, Morgan, D, McAleer, F, Ramsay, A 2010, Groundwater contribution to baseflow maintains habitat connectivity for Tandanus bostocki (Teleostei: Plotosidae) in a south-western Australian river, Ecology of Freshwater Fish, 19(3), 595-608

Beckley, L 2010, Profile of recreational anglers visiting rottnest island, southwestern Australia, Tourism in Marine Environments, 6(1), 1-10

Calado, A, Huisman, JH 2010, Commentary: Gmez, F., Moreira, D., and Lpez-Garca, P. (2010). Neoceratium gen. nov., a New Genus for All Marine Species Currently Assigned to Ceratium (Dinophyceae).

Protist 161: 35-54, Protist, 161(4), 517-519

Calver, M, Wardell-Johnson, G, Bradley, SB, Taplin, R 2010, What makes a journal international? A case study using conservation biology journals, Scientometrics: an international journal for all quantitative aspects of the science of science, communication in science and science policy, 85(2), 387-400

Ceh, J, Van Keulen, M, Bourne, D 2010, Coral-associated bacterial communities on Ningaloo Reef, Western Australia, F E M S Microbiology Ecology, 75(1), 134-144

Cooch, E. V., Conn, P. B., Ellner, S. P., Dobson, A. P. and K. H. Pollock (2010). Disease dynamics in wild populations: modeling and estimation a review. Journal of Ornithology. Online.

Cossington, SC, Hesp, S, Hall, N, Potter, I 2010, Growth and reproductive biology of the foxfish Bodianus frenchii, a very long-lived and monandric protogynous hermaphroditic labrid, Journal of Fish Biology, 77(3), 600-626

Coulson, PC, Hesp, S, Potter, I, Hall, N 2010, Life cycle characteristics of the Blue Morwong Nemadactylus valenciennesi, compared with those of other species of Cheilodactylidae, Marine & Freshwater Research, 61(1), 104-118

Davies, C, Beckley, L 2010, Zooplankton from the inshore waters of Christmas Island (Indian Ocean) with reference to larvae of the red land crab, Gecarcoidea natalis, Royal Society of Western Australia. Journal, 93(1), 43-50

Davis, A, Pusey, B, Thorburn, D, Dowe, J, Morgan, D, Burrows, D 2010, Riparian contributions to the diet of terapontid grunters (Pisces: Terapontidae) in wet-dry tropical rivers, Journal of Fish Biology, 76(4), 862-879

Donaldson, RD, Finn, HF, Calver, M 2010, Illegal feeding increases risk of boat-strike and entanglement in Bottlenose Dolphins in Perth, Western Australia, Pacific Conservation Biology, 16(3), 157-161

Doupe, R, Knott, M, Schaffer, J, Burrows, D, Lymbery, A 2010, Experimental herbivory of native Australian macrophytes by the introduced Mozambique tilapia Oreochromis

PUBLICATIONS cont…


mossambicus, Austral Ecology: 35(1), 24-30

Doupe, R, Mitchell, J, Knott, M, Davis, A, Lymbery, A 2010, Efficacy of exclusion fencing to protect ephemeral floodplain lagoon habitats from feral pigs (Sus scrofa), Wetlands Ecology and Management, 18(1), 69-78

Feng, M, Slawinski, D, Beckley, L, Keesing, J 2010, Retention and dispersal of shelf waters influenced by interactions of ocean boundary current and coastal geography, Marine & Freshwater Research: 61(11), 1259-1267

Fletcher, W, Shaw, J, Metcalf, S, Gaughan, D 2010, An Ecosystem Based Fisheries Management framework: the efficient, regional-level planning tool for management agencies, Marine Policy, 34(6), 1226-1238

Frere, C, Krutzen, M, Mann, J, Connor, R, Bejder, L, Sherwin, W 2010, Social and genetic interactions drive fitness variation in a free-living dolphin population, Proceedings of the National Academy of Sciences, 107(46), 19949-19954

Frere, C, Krutzen, M, Mann, J, Watson-Capps, J, Tsai, Y, Patterson, E, Connor, R, Bejder, L, Sherwin, W 2010, Home range overlap, matrilineal and biparental kinship drive female associations in bottlenose dolphins, Animal Behaviour, 80(3), 481-486

Game, ET, Grantham, HS, Hobday, AJ, Pressey, RL, Lombard, AT, Beckley, LE, Gjerde, K, Bustamante, R, Possingham, HP, Richardson, AJ, 2010, Pelagic MPAs: The devil you know, Trends in Ecology & Evolution, 25(2), 63-64

Griffiths, S, Pollock, K. H., Lyle, J, Pepperell, J, Tonks, M, Sawynok, W 2010, Following the chain to elusive anglers, Fish and Fisheries, 11(2), 220-228

Hallett, C S, Daley, R 2010, Feeding ecology of the southern lanternshark (Etmopterus baxteri) and the brown lanternshark (E. unicolor) off southeastern Australia, ICES Journal of Marine Science: 68(1), 157-165

Huisman, JH 2010, (Common) Seaweeds of India, Journal of Applied Phycology, 22(3), 381-383

Jackson, G, Norriss, , Mackie, M, Hall, N 2010, Spatial variation in life history characteristics of snapper (Pagrus auratus)

within Shark Bay, Western Australia, New Zealand Journal of Marine and Freshwater Research: 44(1), 1-15

Jensen, F., Beedholm, K., Wahlberg, M., Bejder, L. and Madsen, P.T. (2010) Bottlenose dolphin short-range communication in a shallow, noisy environment. The Journal of the Acoustical Society of America, 128 (4). p. 2467.

Jones, AJ, Hall, N, Potter, I 2010, Species compositions of elasmobranchs caught by three different commercial fishing methods off southwestern Australia, and biological data for four abundant bycatch species, Fishery Bulletin, 108(4), 365-381

Klunzinger, M, Morgan, D, Lymbery, A, Ebner, B, Beatty, S, Thomson, GT 2010, Discovery of a host fish for glochidia of Velesunio angasi (Sowerby, 1867) (Bivalvia:Unionoida:Hyriidae) from the Fortescue River, Pilbara, Western Australia, Australian Journal of Zoology, 58(4), 263-266

Link, W.A., Yoshizaki, J., Pollock, K.H., and Bailey, L. L. (2010). Uncovering a latent multinomial: analysis of mark-recapture data with misidentification. Biometrics 66: 178-185

Lymbery, A, Hassan, M, Morgan, D, Beatty, S, Doupe, RD 2010, Parasites of native and exotic freshwater fishes in south-western Australia, Journal of Fish Biology, 76(7), 1770-1785

Marr, S, Marchetti, M, Olden, J, García-Berthou, E, Morgan, D, Arismendi, I, Day, J, Griffiths, C, Skelton, P 2010, Freshwater fish introductions in mediterranean-climate regions: Are there commonalities in the conservation problem?, Diversity and Distributions: 16(4), 606-619

Metcalf, S, Moyle, K, Gaughan, D 2010, Qualitative analysis of recreational fisher response and the ecosystem impacts of management strategies in a data-limited situation, Fisheries Research, 106(3), 289-297

Morgan, D 2010, Fishes of the King Edward River in the Kimberley region, Western Australia, Western Australian Museum. Records. Supplement, 25, 351-368

Morgan, D, Tang, D, Peverell, S 2010, Critically endangered Pristis microdon (Elasmobranchii), as a host for the Indian


parasitic copepod, Caligus furcisetifer Redkar, Rangnekar et Murti, 1949 (Siphonostomatoida): New records from northern Australia, Acta Parasitologica, 55(4), 419-423

Ochwada-Doyle, F, Gray, C, Loneragan, N, Taylor, M 2010, Using experimental ecology to understand stock enhancement: Comparisons of habitat-related predation on wild and hatchery-reared Penaeus plebejus Hess, Journal of Experimental Marine Biology and Ecology, 390(1), 65-71

Parnell, J, Womersley, H, Sinkora, D, Vaughan, A, Huisman, JH 2010, W.H. Harvey's Australian travelling sets of algae at the Herbarium of Trinity College Dublin (TCD) and the National Herbarium of Victoria (MEL), Australia, Biology and Environment. Proceedings of the Royal Irish Academy, 110(2), 119-161

Platell, M, Hesp, S, Cossington, SC, Lek, E, Moore, S, Potter, I 2010, Influence of selected factors on the dietary compositions of three targeted and co-occurring temperate species of reef fishes: implications for food partitioning, Journal of Fish Biology, 76, 1255-1276

Pledger, S., Pollock, K.H. ,and Norris, J.L. (2010). Open capture-recapture models with heterogeneity: II. Jolly-Seber model, Biometrics, 66, 883-890.

Polacheck, T, Eveson, J, Laslett, G, Pollock, K. H., Hearn, W 2010, Erratum: Integrating catch-at-age and multiyear tagging data: A combined Brownie and Petersen estimation approach in a fishery context, Canadian Journal of Fisheries and Aquatic Sciences (2006) 63, (534-548)), Canadian Journal of Fisheries and Aquatic Sciences, 65(6), 1244

Potter, I 2010, On the origin: environmental biology of fishes, Environmental Biology of Fishes, 87, 275-276

Potter, I, Chuwen, BC, Hoeksema, SH, Elliott, M 2010, The concept of an estuary: A definition that incorporates systems which can become closed to the ocean and hypersaline, Estuarine, Coastal and Shelf Science, 87, 497-500

Pueschel, C, Huisman, JH 2010, Observations of Pihiella liagoraciphila (Pihiellales, Rhodophyta), Phycologia, 49(1), 42-47

Reid, A, Lymbery, A, Ng, JN, Tweedle, S, Ryan, U 2010, Identification of novel and zoonotic Cryptosporidium species in marine fish, Veterinary Parasitology, 168(3-4), 190-195

Riddle, J.D., R.S. K.H. Pollock, and T.R. Simons. (2010). An unreconciled double observer method for estimating detection probability and abundance, Auk 127:841-849.

Riddle, J.D., R.S. Mordecai, K.H. Pollock, and T.R. Simons. (2010). Effects of prior detections on estimates of detection probability, abundance, and occupancy, Auk 127:194-99.

Riddle, J.D., S.J. Stanislav, K.H.Pollock, C.E. Moorman, and F.S. Perkins. (2010). Separating components of the detection process with combined methods: an example with northern bobwhite. Journal of Wildlife Management 74:1319-1325.

Stanislav, S., Pollock, K.H., Simons, T. R. and M.W. Alldredge. (2010). Separation of availability and perception processes for aural detection in avian point counts: a combined multiple observer and time-of-detection approach, Avian Ecology and Conservation. 5 Online.

Tarr, N. M., T. R. Simons and K. H. Pollock (2010). An experimental assessment of vehicle disturbance effects on migratory shorebirds, Journal of Wildlife Management 74: 1776-1783.

Thompson, R.C.A, Lymbery, A, Smith, A 2010, Parasites, emerging disease and wildlife conservation, International Journal for Parasitology, 40(10), 1163-1170

Thompson, R.C.A, Smith, A, Lymbery, A, Averis, S, Morris, K, Wayne, A 2010, Giardia in Western Australian wildlife, Veterinary Parasitology, 170(3-4), 207-211

Travers, M, Potter, I, Clarke, K, Newman, S, Hutchins, J 2010, The inshore fish faunas over soft substrates and reefs on the tropical west coast of Australia differ and change with latitude and bioregion, Journal of Biogeography, 37(1), 148-169

Tyne, J, Loneragan, N, Krutzen, M, Allen, S, Bejder, L 2010, An integrated data management and video system for sampling aquatic benthos, Marine & Freshwater Research: 61(9), 1023-1028



Valesini, F, Hourston, MH, Wildsmith, MW, Coen, NC, Potter, I 2010, New quantitative approaches for classifying and predicting local-scale habitats in estuaries, Estuarine, Coastal and Shelf Science, 86(4), 645-664

Wen, Z., K. H. Pollock, J. D. Nichols,and P. Waser 2010, Augmenting superpopulation, capture–recapture models with Population pssignment data. Biometrics Online.

Wiszniewski, J, Beheregaray, L, Allen, S, Moller, L 2010, Environmental and social influences on the genetic structure of bottlenose dolphins (Tursiops aduncus) in southeastern australia, Conservation Genetics, 11(4), 1405-1419

Yang, RY, Reid, A, Lymbery, A, Ryan, U 2010, Identification of zoonotic Giardia genotypes in fish, International Journal for Parasitology, 40(7), 779-785

Zanguel, N, Lymbery, A, Lau, J, Suzuki, A, Yang, RY, Ng, JN, Ryan, U 2010, Identification of novel Cryptosporidium species in aquarium fish, Veterinary Parasitology, 174(1-2), 43-48

Other publications in 2010 Allen, S.J., Loneragan, N.R. 2010. Reducing

dolphin bycatch in the Pilbara finfish trawl fishery. Final Report for the Fisheries Research and Development Corporation of Australia Project 2008/036. Murdoch University, 59 pp. ISBN: 978-0-86905-926-5

Beatty, S.J., Morgan, D.L., Klunzinger, M., Lymbery, A.J. 2010, Aquatic macrofauna of Ellen Brook and the Brockman River: fresh water refuges in a salinised catchment. Centre for Fish & Fisheries Research, Murdoch University Report to the Ellen Brockman Integrated Catchment Group.

Beatty, S., Morgan, D., Sarre, G., Cottingham, A. & Buckland, A. 2010, Assessment of the distribution and population viability of the Pearl Cichlid in the Swan River catchment, Western Australia. Freshwater Fish Group & Fish Health Unit (Centre for Fish & Fisheries Research, Murdoch University), report to the Swan River Trust.

Beckley, L.E., Smallwood, C.B., Moore S.A. & Kobryn, H.T. 2010. Ningaloo Collaboration Cluster: Human use of Ningaloo Marine

Park, Ningaloo Collaboration Cluster Final Report No. 2. 166 pp.

Christensen, J., Between history and science: history of marine animal populations, Marine Adaptation Bulletin, 2(4): 7.

http://arnmbr.org/content/images/uploads/MAB_v2_i4_Summer2010_11.pdf.

Holliday, D. & Beckley, L.E. 2010. Biological oceanography of the west Kimberley shelf: Macro-zooplankton and larval fishes, Report prepared for Woodside Energy, 40pp.

Holyoake, C., Finn, H., Stephens, N., Duignan, P., Salgado, C., Smith, H., Bejder, L., Linke, T., Daniel, C., Lo, H.N., Ham, G.S., Moiler, K., Allen, S., Bryant, K. and McElligott, D. 2010, Technical report on the Bottlenose dolphin (Tursiops aduncus) unusual mortality event within the Swan Canning Riverpark, June-October 2009. Murdoch University.

Loneragan, N.R., Jenkins, G., Taylor, M. (2010) Opportunities for finfish stock enhancement and restocking in Western Australia. Report to the Aquaculture Development Council of Western Australia. Pp. 39.

Loneragan, N.R., Babcock, R.C., Lozano-Montes, H., Dambacher, J.M. 2010, Evaluating how food webs and the fisheries they support are affected by fishing closures in Jurien Bay, temperate Western Australia. Final Report for the Fisheries Research and Development Corporation of Australia Project 2006/036. Murdoch University, ISBN 978-1-921605-62-8. 160pp.

Morgan, D.L. & Beatty, S.J., 2010, Interannual variation of the fish fauna associated with Snake (Uralla) Creek, Fitzroy River, Kimberley, Western Australia. Centre for Fish & Fisheries Research, Murdoch University, report to Liveringa Pastoral Co.

Morgan, D., Beatty, S., Lymbery, A., Adams, M., Murphy, J. & Keleher, J. 2010. Aquatic fauna values of the Mitchell and Quickup Rivers. Centre for Fish & Fisheries Research, Murdoch University, report to the Water Corporation of Western Australia.

Veale, L., Coulson, P., Hoeksema, S., Tweedley, J., Hall, N. & Potter, I. 2010.


The characteristics of the fish and assemblages of the Leschenault Estuary. Inter-period comparisons and their management implications. Report for the South West Development Commission Report. Murdoch University, Perth, Western Australia.

Conference and workshop

presentations in 2010 Beatty, S, Morgan, D 2010, Unique inland

fishes of south-western Australia: how may climate change exacerbate current impacts?, Australian Society for Fish Biology, Annual Meeting, Australian Society for Fish Biology Annual Conference, Melbourne

Beatty, S, Morgan, D 2010, Freshwater fishes in a biodiversity hotspot: use of multiple sampling techniques reveals groundwater sustains remnant populations in south-western Australia, 13th International River Symposium, International River Symposium, Perth, Western Australia

Beatty, S, Morgan, D 2010, Freshwater fishes in a biodiversity hotspot: use of multiple sampling techniques reveals groundwater sustains remnant populations in south-western Australia, FSAM 2010 (Fish Sampling with Active Methods), FSAM, Ceske Budejovice

Beckley, L 2010, Marine scientific research in the Indian Ocean. 9th Ausmarine Conference and Exhibition, Ausmarine, Perth, Australia

Beckley, L 2010, Rottnest Island: Coastal ecosystem conservation in an urban playground?, Urban Ecology Conference, Urban Ecology, Perth

Beckley, L.E. & Prior, S.P. 2010. Thirty years down the line – Change in the recreational fishery in the Blackwood Estuary, Western Australia. History of Marine Animal Populations Asia II: diverse case-studies, common themes. Perth, Australia

Beckley, L, Smallwood, C 2010, Spatial distribution, seasonal variability and zoning compliance of recreational fishing in Ningaloo Marine Park, north-western Australia, Australian Marine Sciences National Conference., Australian Marine Sciences National Conference, Wollongong

Beckley, L, Smallwood, C, Moore, S, Kobryn, H, 2010, Spatio-temporal distribution of reef use and applications for monitoring in Ningaloo Marine Park., Australian Marine Sciences National Conference., Australian Marine Sciences National Conference, Wollongong

Cannell, B.L., Bradley, S., Wooller, R., Sinclair, J. and Sherwin. W. 2010. 2008: The year of the global financial crisis and the Perth penguin crisis? Seventh International Penguin Conference, Boston.

Christensen, Joseph ‘History of Recreational Fishing in Western Australia: using the records of saltwater angling to examine changes in marine animal populations’, Oceans Past III: Stories from the sea- history of marine animal populations and their exploitation, Trinity Long Room Hub, Trinity College Dublin, 18-20 November.

Christensen, Joseph (with Kevin James McElroy), ‘Socio-economic assessment of scalefish fisheries (inshore demersal) in the West Coast Bioregion’, WAMSI Node 4 synthesis workshop, Western Australian Fisheries and Marine Research Laboratories, 6 December.

Christensen, J. Pilot study to develop a socio-economic assessment of fisheries (recreational and commercial) in the West Coast Bioregion’, Western Australian Marine Sciences Institute (WAMSI) and Australian Marine Sciences Association (AMSA) show-and-tell symposium, Western Australian Maritime Museum, 9 February.

Christensen, J. 2010, Pilot study to develop a socio-economic assessment of fisheries (recreational and commercial) in the West Coast Bioregion’, WAMSI Node 4 synthesis and integration workshop, Western Australian Fisheries and Marine Research Laboratories, 17 June.

Christensen, J. History of recreational fishing in Western Australia: using the records of saltwater angling to address HMAP hypotheses. HMAP Asia II: diverse case studies, common themes, Lion Mill, Mt Helena, 11 June.

Hallett, C. 2010. Assessing the health of estuaries: an Australian perspective (or “How do we catch up?”). Plenary presentation, 13th International River Symposium, Perth.



Hallett, C., Valesini, F. 2010. A fish-based Estuarine Health Index for the Swan Estuary, WA. 13th International River Symposium, Perth.

Hallett, C., Valesini, F. Developing a multimetric estuarine health index for the Swan Estuary, Western Australia: An approach for selecting fish community metrics in the absence of independent measures of ecological condition. Estuarine and Coastal Sciences Association conference, Figueira de Foz, Portugal.

Jensen, F.H., Beedholm, K., Wahlberg, M., Bejder, L. and Madsen, P.T. (2010) Short-range communication of bottlenose dolphins in a shallow, noisy habitat. In: 2nd Pan-American/Iberian Meeting on Acoustics, 15--19 November, Cancun, Mexico.

Klunzinger M.W., Walker K., Lymbery A.J. and Thomson G. 2010, Glochidia tooth morphology of the freshwater mussel Westralunio carteri (Iredale, 1934) of south-west. Western Australia Proceedings of the 17th International Congress of UNITAS MALACOLOGICA, World Congress of Malacology, Phuket, Thailand.

Kobryn, H, Wouters, KW, Beckley, L, Heege, T 2010, Ningaloo Marine Park: Coral Reef and Coastal Zone Maps achieved with hyperspectral, remotely sensed data, Australian Marine Sciences Association 48th Annual Conference, Australian Marine Sciences Association, Fremantle

Lymbery, A.J., Klunzinger, M.W., Morgan, D.L. and Beatty, S.J. 2010, Factors affecting the decline of a freshwater mussel and its host fish in Western Australia. Proceedings of the 12th International Congress of Parasitology, Melbourne.

Smallwood, C, Beckley, L, 2010, Spatial distribution, seasonal variability and zoning compliance of recreational fishing in Ningaloo Marine Park, north-western Australia, Australian Marine Sciences National Conference., Australian Marine Sciences National Conference, Wollongong

Stanton, M, Mann, J, Bienenstock, E, Gibson, Q, Sargeant, B, Bejder, L, Singh, L 2010, Snapshot or movie: How sampling methods bias dolphin social network metrics, 30th International Network for Social Network Analysis (INSNA) International Sunbelt Social Network Conference (2010),

International Network for Social Network Analysis (INSNA), Trento, Italy

Stephens, NS, Palmer Holyoake, CP, Duignan, P, Finn, HF, Salgado, C, Bejder, L 2010, An unusual mortality event involving Bottlenose Dolphins (Tursiops aduncus) within the Swan Canning Riverpark June-October 2009, Australian Society for Veterinary Pathology Annual Conference, NA, NA, 80-80

Thompson, R., Lymbery, A. and Smith, A. 2010, Parasites, emerging disease and wildlife conservation. Proceedings of the 12th International Congress of Parasitology, Melbourne.

Tonge, J M, Moore, S, Beckley, L, Ryan, M 2010, Place attachment at southern Ningaloo., Marine Science in Western Australia "Show and Tell" Symposium, Marine Science in Western Australia "Show and Tell" Symposium, Fremantle

Tonge, J., Moore, S.A., Beckley, L.E. & Ryan, M. 2010. The place attachment of visitors to Ningaloo Marine Park, north-western Australia. 16th International Symposium on Society and Natural Resource Management. Corpus Christi, USA.

Tull, M. 2010, HMAP Asia: Diverse Case-Studies, Common Themes. Oceans Past III: Stories from the sea- history of marine animal populations and their exploitation. Trinity Long Room Hub, Trinity College Dublin, 18-20 November.

Tull, M. 2010, Node 4.5: Socio-Economics of EBFM. WAMSI Node 4 synthesis and integration workshop, Western Australian Fisheries and Marine Research Laboratories, 17 June.

Tull, M. 2010, Node 4.5: Socio-Economics of EBFM. WAMSI Node 4 synthesis workshop, Western Australian Fisheries and Marine Research Laboratories, 6 December.

Tull, M. 2010, HMAP Asia II: Diverse Case-Studies, Common Themes. HMAP Asia II: diverse case studies, common themes, Lion Mill, Mt Helena, 11 June.

Tweedley, J.R. 2010, The fauna of Broke Inlet: Some comparisons with holarctic estuaries. 8thAustralian Marine Science Association (AMSA) Marine Science Student Workshop 2010. Rottnest Island, Australia


Tweedley, J.R. and Valesini, F.J. 2010, Evaluating the effectiveness of a habitat classification scheme for south-western Australia estuaries in Broke Inlet. 8th

Australian Marine Science Association (AMSA) Marine Science Student Workshop 2010. Rottnest Island, Australia

Tweedley, J.R., Valesini, F.J., Hoeksema, S. & Potter, I.C. (2010). Relationships between habitats types and faunas in Broke Inlet (SW Australia). WAMSI and AMSA-WA Marine Science in Western Australia: Show and Tell Symposium. Fremantle, Australia

Tweedley, J.R. 2010, North vs South: Comparing the estuarine environment and faunal assemblages of Broke Inlet, south-western Australia to those in the northern hemisphere. The Royal Society of Western Australia 12th Annual Postgraduate Symposium. Perth, Australia.

Tweedley, J., Valesini, F., Hoeksema, S. & Potter, I. 2010, Classifying habitats in Broke Inlet using enduring environmental variables. The Royal Society of Western Australia 12th Annual Postgraduate Symposium. Perth. Australia. (Poster)

van Keulen, M., Paling, E.I. and Verduin, J.J. 2010, Influence of planting density on success of seagrass transplantation and long-term observations of a large-scale transplanting exercise in Cockburn Sound, Western Australia. 9th International Seagrass Biology Workshop, Phuket, Thailand

Verduin, J.J., Paling, E.I. and van Keulen, M. 2010, Seagrass rehabilitation; requisites to successful, long term, mitigation outcomes. 9th International Seagrass Biology Workshop, Phuket, Thailand

POSTGRADUATE STUDENTS


5. POSTGRADUATE STUDENTS AND THEIR RESEARCH TOPICS PhD students (completed in 2010) Ben Chuwen Fish faunas of deeper, offshore waters in estuaries on the south coast of Western Australia, including aspects of the biology of Black Bream Acanthopagrus butcheri. Supervisor: Ian Potter (SELS) Chris Hallett Development of an estuarine health index for the Swan-Canning Estuary and Wellstead Estuary. Supervisors: Ian Potter, Fiona Valesini and Steeg Hoeksema (SELS) David Holliday Incorporation of larval fishes into a developing anticyclonic eddy of the Leeuwin Current: timing, sources and pathways. Supervisor: Lynnath Beckley (SELS) and Ming Feng (CSIRO) Mathew Hourston The ecology of free living nematodes in nearshore marine and estuarine sediments on the microtidal lower west coast of Australia. Supervisor: Ian Potter and Fiona Valesini (SELS) Anne Lif Lund Jacobsen, The south-east (trawl) fishery in Australia from 1915 to 1980. Supervisors: Elaine Stratford (UTas) and Malcolm Tull (LB) Andrew Rowland The biology of Samson fish Seriola hippos with emphasis in the sport fishery in Western Australia. Supervisor: Howard Gill (SELS) Claire Smallwood Spatial patterns and temporal patterns of recreational use at Ningaloo Reef, north-western Australia. Supervisors: Lynnath Beckley and Susan Moore (SELS)

PhD students (enrolled/examined /submitted/pending correction in 2010) Jo Marie Acebes Historical catches of large marine vertebrates in the Sulu-Sulawesi Sea: changing perceptions and conservation management implications in the Philippines. Supervisors: Malcolm Tull (LB) and James Warren (AE*) Mark Allen Balancing artisanal fishing and conversation goals in a newly established network of marine protected areas in Raja Ampat, Papua. Supervisors: Neil Loneragan (SELS) and Mark Erdmann (Conservation International) Farhan Bokhari The effects of salinity on riparian arthropod communities and consequences for ecosystem function. Supervisor: Alan Lymbery (HS) Samantha Bridgwood Physical factors determining the structure of seagrass meadows in Warnbro Sound, Western Australia. Supervisors: Mike van Keulen (SELS), Marion Cambridge (UWA) Amanda Buckland Trophic interactions of fish species in the Swan-Canning Estuary and Peel-Harvey Estuary. Supervisors: Steeg Hoeksema, Ian Potter, Fiona Valesini (SELS) and Luke Twomey (Oceanica) Janja Ceh The role of microbial communities in reef-building corals of Ningaloo Reef, Western Australia Supervisors: Mike van Keulen (SELS), David Bourne (AIMS) Warren Chisholm The stability of shallow coastal sediments with and without seagrasses Supervisors: Mike van Keulen, Eric Paling, Jennifer Verduin (SELS) Natasha Coen Implications of habitat type for the hyperbenthos for four morphologically divergent estuaries in south-western Australia.


Supervisors: Ian Potter and Fiona Valesini (SELS) Alan Cottingham Factors influencing the life-history characteristics of the Black Bream Acanthopagrus butcheri in the Swan-Canning Estuary. Supervisors: Alex Hesp and Norm Hall (SELS) Rainbo Dixon A taxonomic revision of the brown algal genus Sargassum (Fucales: Sargassaceae) from Australia. Supervisor: John Huisman, Mike van Keulen (SELS), Fred Gurgel (UAdel) Emily Fisher An exploration of the effectiveness of alternative strategies for managing fish species with different biological characteristics. Supervisors: Alex Hesp and Norm Hall (SELS) Ben French The determination of the diets of Snapper and Silver Trevally, the construction of a food web for the demersal fish community in South-Western Australia and biology of Harlequin Fish. Supervisors: Ian Potter and Margaret Platell (SELS) Sarah Fretzer Analysing the effects of anthropogenic activities on different aquatic ecosystems in Western Australia and identifying ecosystem-based management policies that provide long-term sustainability. Supervisors: Norm Hall (SELS), Jeffrey Dambacher (CSIRO), Hector Lozano-Montes (CSIRO), Brent Wise (DoF) Michelle Gardner Genetic determination of the stock structures of pink snapper (Pagrus auratus) and baldchin groper (Choerodon rubescens). Supervisors: Jennie Chaplin and Ian Potter (SELS) Susan Gibson-Kueh Diseases of Asian seabass and barramundi. Supervisors: Phil Nicholls and Alan Lymbery (HS) Michelle Ingram The effect of salinity on the resilience of riparian ecosystems. Supervisor: Alan Lymbery (HS)

Ashlee Jones Characteristics of the elasmobranch fauna in the bycatch of commercial fisheries in south-western Australia. Supervisor: Ian Potter (SELS) Michael Klunzinger Biology and ecology of the freshwater mussel, Westralunio carteri. Supervisors: Alan Lymbery (HS), David Morgan and Stephen Beatty (SELS) Mark Langdon The trophic ecology of the grazing sea urchin Echinometra mathaei within Ningaloo Marine Park, Western Australia. Supervisors: Mike van Keulen and Eric Paling (SELS) Elaine Lek Comparisons between the biology of three temperate species of wrasse (Labridae) in different habitats and different regions. Supervisors: Ian Potter and David Fairclough (SELS) Thea Linke Trophic interactions in the faunas of the Swan Estuary and Wilson Inlet, Western Australia. Supervisors: Ian Potter, Fiona Valesini and Luke Twomey (SELS) Karen Marshall Enzymatic mechanism(s) involved in the partitioning of fatty acids into either catabolic or anabolic processes. Supervisors: Max Cake and Ian Potter (SELS) Fiona McAleer Fish and fish migrations in the Blackwood River Yarragadee discharge zone – including the age growth reproduction of Tandanus bostoki. Supervisors: David Morgan, Howard Gill and Stephen Beatty (SELS) Shannon McCluskey Diet and foraging patterns of bottlenose dolphins in relation to prey composition and abundance in South Western Australia. Supervisors: Neil Loneragan, Lars Bejder (SELS) and Miles Logsdon (UW) Frazer McGregor The trophic ecology & habitat requirements of the Manta Ray (Manta birostris) in lagoonal systems of Ningaloo Reef, Western Australia

POSTGRADUATE STUDENTS cont…


Supervisors: Mike van Keulen (SELS), Mark Meekan (AIMS), Anya Waite (UWA) Heather McLetchie Molecular diagnosis of crayfish plague (Aphanomyces astaci). Supervisors: Stan Fenwick and Phil Nicholls (HS) Glenn Moore Phylogeography of marine fish species of the genus Arripis with sympatric and allopatric breeding populations in Australian waters. Supervisors: Jennie Chaplin and Ian Potter (SELS) Owen O’Shea The demography and ecology of demersal stingrays at Ningaloo Reef, Western Australia Supervisors: Mike van Keulen (SELS), Mark Meekan (AIMS) Nicole Phillips Conservation genetics of Pristis sawfishes in Australian waters. Supervisors: Jennie Chaplin and David Morgan (SELS) Mahmoud Rashnavadi The ecological impacts of secondary salinisation on halo-tolerant fishes in south-western Australia. Supervisors: Alan Lymbery (HS), David Morgan and Stephen Beatty (SELS) Rebecca Roberts Economic strategies for disaster risk-reduction in coastal areas: A case study of Exmouth Gulf Supervisors: Lynnath Beckley (SELS) and Malcolm Tull (LB) Holly Smith Population dynamics and habitat utilisationin bottlenose dolphins, Bunbury, Western Australia. Supervisors: Lars Bejder, Halina Kobryn, Stuart Bradley (SELS) and Kelly Waples (DEC) Calais Tink Exploration of interactions between recreational fishers, fish and management in South Western Australia using loop analysis and agent-based modelling. Supervisors: Alex Hesp and Norm Hall (SELS)

Joanna Tonge The influence of place attachment on the management of marine parks: Ningaloo as a case study. Supervisors: Susan Moore, Lynnath Beckley (SELS) and Maria Ryan (ECU) Natalie Toon Catchability of Western Rock Lobster (Panulirus cygnus); the influence of temperature, light intensity, lobster size, moult stage and commercial fishing apparatus. Supervisors: Neil Loneragan and Howard Gill (SELS) Mike Travers Comparisons between the species compositions of the fish faunas over reefs and soft substrates in tropical waters of north-western Australia. Supervisors: Ian Potter (SELS) and Steve Newman (DoF) James Tweedley Fish faunas and habitat classification of the seasonally-open Broke Inlet. Supervisors: Ian Potter, Fiona Valesini, and Steeg Hoeksema (SELS) Julian Tyne Quantifying the effects of human interactions on spinner dolphins in resting bays in Hawaii, and assessing the effectiveness of time area closures as a proposed mitigation approach. Supervisors: Lars Bejder, Neil Loneragan and Ken Pollock (SELS) Lauren Veale The characteristics of the fish faunas of the Peel-Harvey Estuary and Leschenault Estuary with comparisons over a thirty-year period. Supervisors: Ian Potter, Steeg Hoeksema, Alex Hesp and Peter Coulson (SELS) Kristel Wenziker The population dynamics and habitat usage of Sousa chinensis and Tursiops truncatus found in the Ningaloo area. Supervisors: Mike van Keulen, Lars Bejder (SELS) and Kelly Waples (DEC) Sharon Yeo Population biology of Peronella lesueuri Supervisors: Mike van Keulen (SELS), John Keesing (CSIRO)


MPhil/MSc students (enrolled/ examined/pending correction in 2010) Valissa Buchanan Baseline abundance and residency patterns of bottlenose dolphins, Tursiops sp., Binningup, Western Australia (MPhil) Supervisors: Lars Bejder and Ken Pollock (SELS) Krista Nicholson Population estimation of bottlenose dolphins, Tursiops sp., in Shark Bay, Western Australia (MPhil) Supervisors: Lars Bejder and Ken Pollock (SELS) Simon Wee Extent and density of roads and tracks along the Ningaloo coastline. (MSc) Supervisors: Halina Kobryn and Lynnath Beckley (SELS) Jeff Whitty Movement & habitat utilization of Pristis microdon & Glyphis sp. C. (MPhil) Supervisors: David Morgan (SELS) and Colin Simpfendorder (JCU)

HONOURS STUDENTS


6. HONOURS STUDENTS AND THEIR RESEARCH TOPICS Honours students (completed in 2010) Nicholas Breheny Larval fish assemblages associated with pink snapper spawning aggregations in embayments on the lower west coast of Australia. Supervisors: Lynnath Beckley (SELS) and Corey Wakefield (DoF) Rowena Burch Description and parameterisation of an agent-based model to explore the effects of recruitment variability on populations of Glaucosoma hebraicum in a recreational fishery. Supervisors: Alex Hesp and Norm Hall (SELS) Felicity Hart The taxonomy and pest potential of the green algal genus Codium (Bryopsidales) in Western Australia Supervisors: John Huisman and Mike van Keulen Adrian Hordyk Aggregation dynamics of orange roughy on the Cascade Plateau, south-eastern Tasmania. Supervisors: Neil Loneragan (SELS) and Jeremy Prince (Biospherics) Broderick Hosie A morphometric assessment of the relationships among assemblages of the blue swimmer crab Portunus pelagicus, in selected water bodies in south-western Australia. Supervisors: Jenny Chaplin (SELS) and Danielle Johnston (DoF) Vanessa Jaiteh An assessment of dolphin behaviour and bycatch mitigation techniques in the Pilbara Finfish Trawl Fishery, Western Australia. Supervisors: Neil Loneragan and Simon Allen (SELS) Nicholas Konzewitsch Trap behaviour of the western rock lobster, Panulirus Cygnus: in situ comparisons of the ‘white’ migratory phase and the ‘red’ residential phase and the influence of conspecifics in the laboratory.

Supervisors: Neil Lonaragan and Natalie Toon (SELS) Michelle Lo Development of methods that can be used to obtain DNA from poorly preserved sawfish rostra. Supervisors: Jennie Chaplin and David Morgan (SELS) Honours students (enrolled/ examined/submitted/ pending correction in 2010) Amy Griffiths An assessment of the effectiveness of camera traps in Australian faunal surveys Supervisor: Jennie Chaplin James Keleher The effectiveness of current fishway designs in Australia’s south west to accommodate endemic freshwater fish species. Supervisors: Alan Lymbery (HS), Stephen Beatty and David Morgan (SELS) – Class IIA. Jonathan Murphy Conservation genetics of freshwater fishes in the south west of Western Australia. Supervisors: Alan Lymbery (HS), Stephen Beatty and David Morgan (SELS) – Class I. Alicia Sutton Horizontal and vertical distribution of euphausiids associated with a meso-scale eddy of the Leeuwin Current, Western Australia Supervisors Lynnath Beckley (SELS) David Holiday (SELS) – Class I Jessica Williams Reproductive success of Flatback Turtles (Natator depressus) Supervisors: Mike van Keulen (SELS)

RESEARCH FUNDING


7. SUMMARY OF RESEARCH FUNDING 7.1 List of projects and research income for 2010

Name Project

Funding Body Duration 2010

prop’n $

Total funding

($) Allen, Simon; Bryant, Kate; Bejder, Lars; Loneragan, Neil; Kruetzen, Michael and Pollock, Ken.

Genetic Structure and Abundance of Fishery-Impacted Dolphin Populations of the Pilbara region North-Western Australia

Australian Marine Mammal Conservation Centre

2010-2011

$302,518 $361,000

Allen Simon; Bejder, Lars & Loneragan Neil

Reducing dolphin bycatch in the Pilbara Finfish Trawl Fishery

Fisheries Research and Development Corporation

2008-2010

$59,941 $150,000

Beatty, Stephen and David Morgan

Goldfish control in the Vasse River Geocatch 2010 $22,206 $22,206


Pearl cichlid ecology and control

NRM and Swan River Trust 2010 $95,321 $95,321


Rushy Creek fishway project

Department of Water 2010 $48,008 $48,008

Beckley, Lynnath; Kobryn Halina & Moore Susan

Wealth from Oceans: High resolution mapping of reef utilisation by humans at Ningaloo

Commonwealth Scientific and Industrial Research Organisation (CSIRO)

2006-2011

$32,965 490,404

Bejder, Lars Dolphin Monitoring Program at Monkey Mia, Shark Bay, WA

Department of Environment and Conservation

2007-2011

$23,655 $109,354

Bejder, Lars Megafauna line transects off Binningup

Water Corporation 2009-2011

$58,776 $222,450

Bejder, Lars Quantifying the effects of human interactions on spinner dolphins in resting bays in Hawaii, and assessing the effectiveness of time area closures as a proposed mitigation approach

US NOAA 2010-14 $18,800

Bejder, Lars Quantifying the effects of human interactions on spinner dolphins in resting bays in Hawaii, and assessing the effectiveness of time area closures as a proposed mitigation approach.

US Marine Mammal Commission

2010 $20,000

Bejder, Lars; Loneragan, Neil

Large-scale dolphin research program in south-west Australia

South West Marine Research Partners

2007-2010

$66,454 $289,748

RESEARCH FUNDING cont…


Name Project


prop’n $

Total funding

($) Bejder, Lars; Parra Guido & Frere Celine

Population genetics and phylogeography of Australian snubfin and humpback dolphins: defining appropriate management units for conservation-Stage 1

Australian Antarctic Division - Australian Marine Mammal Centre (AMMC)

2010 $16,836 $16,836

Bejder, Lars; Parra Gudio; Hammond Phil & Canadas A

Workshop: Spatial modelling of cetacean habitat use and abundance


2010-2011

$45,411 $45,411

Cannell, Belinda and Fiona Valesini

The effect of a boat ramp at Becher Point on the food resources of Little Penguins on Penguin Island

DEC 2010-2014

$76,210 169,774

Ceh, Janja & Mike van Keulen

Microbial communities associated with reef-building corals of Ningaloo Reef in Western Australia

WAMSI Top-up scholarship

2008-2010

$6,000 $18,000

Chaplin, Jennie & Ian Potter

Genetic (microsatellite) determination of the stock structures of snapper (Pagrus auratus) and baldchin grouper (Choerodon rubescens) in Western Australian waters.

WAMSI node 4 2008–2011

*$23,286 $137,807

Chuwen, Ben & Ian Potter

Implications of environmental change and morality estimates for sustaining fish populations in South Coast Estuaries.

Fisheries Research & Development

2006-2010

$10,077

Collin, S. P., Hunt, D. M., Foster, R. G. and Potter, I. C..

Seeing without eyes: the evolution of non-visual photoreceptors in vertebrates.

ARC Discovery Project Grant.

2008-2011

$65,000 $345,000

Hall, Norman Development of an ecosystem approach to the monitoring and management of Western Australian Fisheries


2005-2011

$165,377 $576,512

Hall, Norman Analyses of three databases of fisheries data from the Mekong River.

ACIAR 2008-2011

$54,947 $149,867


Name Project


prop’n $

Total funding

($) Hall, Norman; Ben Chuwen; Alex Hesp; Felicity Horn & Rory McCauley

Informing risk assessment through estimating interaction rates between Australian sea lions and WA temperate demersal gillnet and demersal longline fisheries


2010 $15,000 $15,000

Hall, Norman & Sarah Fretzer

Dynamics of the ecosystems of three estuaries in south-western Australia.

WAMSI 2007-2010

$11,000 $33,000

Hall, Norman & Alex Hesp

Exploration of the effectiveness of alternative management of responses to variable recruitment


2008-2012

$90,299 $256,000

Hall, Norman & Alex Hesp

Development of an agent-based model to communicate implications of recruitment variability of finfish to recreational fishers


2009-2010

$30,000 $75,000

Hall, Norman & Ian Potter

Development of bioregional level assessments of the status of community structure based on fishery dependent and/or fishery independent data

WAMSI 2007-2011

*$56,102 $281,611


Dietary studies of the fish faunas of the Peel-Harvey estuary and coastal marine waters of South-Western Australia

WAMSI 2007-2011

*$24,000 $120,000


Leschenault estuary - fish stocks assessment project

South West Development Commission -

2008-2010

*$26,603 $79,910

Hall, Norman & Peter Rogers

Development of 'A Science Strategy for the Peel-Harvey Estuary'

Peel-Harvey Catchment Council

2009-2010

$10,000 $40,000

Hodgson, Amanda & Loneragan Neil

Using Unmanned Aerial Vehicles to survey marine mammals: development of methodology and a comparison with manned aerial survey estimates


2010-2013

$133,455 $425,000



Name Project


prop’n $

Total funding

($) Huisman, John Marine Benthic Algae

of the Great Barrier Reef Rhodophyta: Acrosymphytaceae Nemastomataceae Schyzymeniaceae Dumontiaceae Ceramiaceae and Rhodomelaceae.

Australian Biological Resources Study (ABRS)

2009-2012

$25,268 $34,902

Huisman, John Macroalgae of Western Australia

DEC 2008-2010

$50,000 $150,000

Klunzinger, Michael; Alan Lymbery, Stephen Beatty and David Morgan

Providing educational tools on aquatic freshwater fauna

Lotterywest, via South East Regional Centre for Urban Landcare

2010-2011

$50,545 $50,545

Kobryn, Halina; Mike van Keulen, Lynnath Beckley, Langdon Mark and Loneragan Neil

Habitats and biodiversity of Ningaloo Reef lagoon

CSIRO Collaboration Fund

2006-2010

$52,385 $511,472

Linke, Thea & Fiona Valesini

Trophic interactions in the Swan Estuary and Wilson Inlet (Part of WAMSI project 4.3 - Trophic interactions for Ecosystem Based Fisheries Management)

WAMSI 2008-2011

$11,000 $33,000

Loneragan, Neil Trophic Models for Ecosystem Based Fisheries Management (EBFM)

WAMSI 2007-2010

*62,656 $250,626

Loneragan, Neil

Reef use, biodiversity and socio-economics for integrated MSE of Ningaloo - Science coordination and integration

CSIRO Collaboration Fund

2007-2010

$14,924 $121,012

Loneragan, Neil Evaluating how food webs and the fisheries they support are affected by fishing closures in Jurien Bay temperate Western Australia


2006-2010

$92,920 $344,885

Loneragan, Neil & Alex Hesp

Establishment of self-sustaining facility for fisheries modelling and multivariate analysis and for effective management of extremely large fisheries databases.


2008-2012

$90,000 $300,000


Name Project


prop’n $

Total funding

($) Lymbery, Alan; Michael Klunzinger

Biology and ecology of the vulnerable freshwater mussel, Westralunio carteri, of south-west Western Australia

Holsworth Wildlife Research Endowment

2010 $5,000 $5,000

Lymbery, Alan; Michael Klunzinger; Stephen Beatty and David Morgan

Protecting and restoring freshwater ecosystem health in the Serpentine River: an adaptive management approach

NRM, via Lowlands Conservation Group

2010-2011

$21,700 $21,700

Lymbery, Alan Mussels as bioindicators of fresh and estuarine ecosystem health

Murdoch University Research Capacity Fund

2010 $16,250 $16,250

Morgan, David, Stephen Beatty & Alan Lymbery

Aquatic fauna Survey, Mitchell/Hay & Quickup/Denmark Rivers

Water Corporation 2009-2010

$83,841 $273,338

Morgan, David & Stephen Beatty

Conserving with community: freshwater sawfish

NRM 2010-2011

$55,000 $110,000


Review of Kimberley endangered sharks

Woodside 2010 $42,112 $42,112


Sawfish and Wheatstone in Onslow

Chevron 2010 $286,939 $286,939

Nicholls, Philip & Bearham Douglas

Aquatic Animal Health Subprogram: development of Diagnostic tests to assess the impact of haplosporidium infections in pearl oysters


2006-2010

$44,259 $148,574

Potter, Ian Determination of Snapper and Silver Trevally and construction of a food web for the demersal fish community in South-Western Australia


2009-2011

$21,611 $74,503

Potter, Ian; Jennie Chaplin and Alex Hesp

Biological performance and genetics of restocked black bream in the Blackwood River Estuary.

DBIF – WA Fish Foundation (WAFF)

2009-2010

*$24,638 $49,277

Potter, Ian & Fiona Valesini

Development of Biotic indices for establishing and monitoring estuarine health

Department of Fisheries WA, DEC, Dept. of Water

2007-2010

*$76,679 $306,477



Name Project


prop’n $

Total funding

($) Tull, Malcolm with James McElroy and Joseph Christensen

Economic assessment of the impact of recent major changes to fisheries management in the WA West Coast demersal wetline fishery

FRDC 2008-2010

*$24,767 74,300

Van Keulen, Mike and Frazer McGregor

The trophic ecology & habitat requirements of the Manta Ray (Manta birostris) in lagoonal systems of Ningaloo Reef, Western Australia

WAMSI/BHP Billiton Top-up Scholarship

2008-2010

$11,000 $33,000

Winzer, Andrew Charles & Gill Howard

Rock lobster Post harvest Subprogram: Development of Bait Saving Strategies for the Western Rock lobster Fisheries

Fisheries Research & Development

2006-2010

$4,256 $4256

Yeo, Sharon and Van Keulen, Mike

Population biology of Peronella lesueuri

WAMSI Top-up scholarship

2009-2011

$6,000 $18,000

* funding for 2010 estimated from equal split of funding across years 2010 TOTAL FUNDING: $2,781,997, (53 projects) Total value $7,833,387 2010 Category 1 FUNDING: $1,465,926, (22 projects) Total value $4,540,752

ACKNOWLEDGEMENTS


8. ACKNOWLEDGEMENTS The CFFAER would like to acknowledge ongoing support from the following sponsors and

collaborators:

ACKNOWLEDGEMENTS cont…


And

Shark Bay Resources Nickol Bay Professional Fishers Association Winifred Violet Scott Foundation

ACKNOWLEDGEMENTS cont…


annual report 2010 - murdoch university · well as the completion of the phd thesis by claire...

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