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Annual Research Report 2009
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Centre for Fish and Fisheries Research
www. cffr.murdoch.edu.au
Centre for Fish and Fisheries Research
ANNUAL REPORT 2009
Cover Page:
Australind boat ramp at Leschenault Estuary - photo by Peter Coulson
Inside Cover Page:
Lionfish – photo by Simon Allen
Credits:
Editor: Neil Loneragan
Layout and Design: Nathalie Kennedy / Murdoch Design
Data Collection and Preparation: Neil Loneragan and Nathalie Kennedy
All written material may be used without permission provided correct reference
to persons quoted and the University is included.
November 2010
CONTENTS
1. MANAGEMENT BOARD ..............................................................................3
2. ADMINISTRATIVE DETAILS .......................................................................3
Centre members as at 31 December 2009 ....................................................3
Director’s report .......................................................................................5
Committee membership/ Community service ................................................8
3. RESEARCH ACTIVITIES .......................................................................... 12
3.1 Ecosystems and Fisheries Management ................................................. 13
3.1 a)
Marine, estuarine and freshwater systems..................................... 13
3.1 b)
Oceanographic processes ............................................................ 18
3.1 c)
Resource partitioning and trophic interactions ................................ 18
3.1 d)
Fisheries dynamics .................................................................... 19
3.1 e)
Modelling ecosystems and fisheries .............................................. 20
3.1 f)
Socio-economics of fishing .......................................................... 21
3.1 g)
Sustainable aquaculture and fish health ........................................ 21
3.2
3.2
3.2
3.2
3.2
Biodiversity and conservation of aquatic systems ................................. 22
a)
Shallow water habitat classification and faunal assemblages ............ 22
b)
Studies on macroalgae diversity .................................................. 23
c)
Marine protected areas ............................................................... 24
d)
Species of conservation significance ............................................. 25
3.3
Biological processes and evolution ..................................................... 29
3.3 a)
Growth, reproduction and feeding ................................................ 29
3.3 b)
Genetics and evolution ............................................................... 32
3.3 c)
Lampreys ................................................................................. 34
4. PUBLICATIONS for 2009 ......................................................................... 37
5. POSTGRADUATE STUDENTS AND THEIR RESEARCH TOPICS ........................ 49
6. HONOURS STUDENTS AND THEIR RESEARCH TOPICS ................................ 53
7. SUMMARY OF RESEARCH FUNDING .......................................................... 55
7.1 List of projects and research income for 2009 ........................................ 55
8. ACKNOWLEDGEMENTS ........................................................................... 61
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Centre for Fish and Fisheries Research - Annual Research Report 2009
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Centre for Fish and Fisheries Research - Annual Research Report 2009
ADMINISTRATIVE DETAILS
1. MANAGEMENT BOARD
Chair
Director
Centre member
Centre member
Centre member
Centre member
Centre member
Centre member
Head of school
External representative
Postdoctoral representative
Postgraduate student representatives
Professor Stuart Bradley
Professor Neil Loneragan
Professor Norm Hall
Professor Ian Potter
Dr Howard Gill
Dr Jennie Chaplin
Associate Professor Lynnath Beckley
Associate Professor Alan Lymbery
Associate Professor Carolyn Jones
Associate Professor Rod Lenanton
Dr David Morgan
Mr Peter Coulson
Mr Chris Hallett
2. ADMINISTRATIVE DETAILS
Centre members as at 31 December 2009
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)
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
Rod Lenanton PhD
Michael Krützen PhD
Hector Lozario 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 MPhil (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)
Steeg Hoeksema PhD (SELS)
David Morgan PhD (SELS)
Research staff
David Holliday (SELS)
Florian Mayer (SELS)
Claire Smallwood (SELS)
Gordon Thomson (SELS)
Kristin Wouters (SELS)
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Centre for Fish and Fisheries Research - Annual Research Report 2009
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)
Matthew Harvey (SELS)
Marina Hassan (HS/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)
MPhil/MSc students
Valissa Buchanan (SELS)
Simon Wee (SELS)
Jeff Whitty (SELS/JCU)
Honours students
Nicholas Breheny (SELS/DoF)
Rowen Burch (SELS)
Gin Swen Ham (SELS)
Adrian Hordyk (SELS)
AE
AIMS
CSIRO
DEC
DoF
ECU
HS
JCU
LB
SELS
UAdel
UTAS
UW
UWA
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/ECU)
Natalie Toon (SELS)
Mike Travers (SELS/DoF)
James Tweedley (SELS)
Julien Tyne (SELS)
Lauren Veale (SELS)
Kristel Wenziker (SELS/DEC)
Sharon Yeo (SELS/CSIRO)
Broderic Hosie (SELS/DoF)
Vanessa Jaiteh (SELS)
Nicholas Konzewitsch (SELS)
Michelle Lo (SELS)
Natalie Millar (SELS)
Faculty of Arts and Education (* through Asia Research Centre)
Australian Institute of Marine Science
Commonwealth Scientific and Industrial Research Organisation
Department of Environment and Conservation
Department of Fisheries
Edith Cowan University
Faculty of Health Sciences
James Cook University
Faculty of Law and Business
Faculty of Sustainability, Environmental and Life Sciences
University of Adelaide
University of Tasmania
University of Washington
Unversity of Western Australia
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Centre for Fish and Fisheries Research - Annual Research Report 2009
DIRECTOR’S REPORT
Director’s report
The research areas of staff and students in the Centre for Fish and Fisheries Research
(CFFR) 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). These areas 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.
We are very fortunate in having Professor Ken Pollock join the CFFR in October 2009 to
lead the development of a quantitative training program in fisheries and natural resource
assessment, with funding from Fisheries Research and Development Corporation (FRDC),
the Department of Fisheries and Murdoch University. In 2009, the staff and students of
the Centre have continued to publish a substantial number of papers in international
journals (39 in 2009 and 27 in press for 2010), two books, three book chapters,
35 technical reports and/or popular articles in 2009 and nine in press for 2010.
The
activities of research students continue to be a vital part of the Centre’s success, with
51 Postgraduate and seven Honours students currently enrolled as well as two PhD and
two Honours students officially completing their theses in 2009.
Some of the research highlights in marine fisheries and ecosystem research include: the
development of approaches to classify marine habitats using hyperspectral data and
documenting the detailed spatial patterns of reef use at Ningaloo for marine conservation
and
development
planning
as
part
of
the
CSIRO
Ningaloo
Cluster;
developing
Ecopath/Ecosim ecosystem models for the central west coast to evaluate the effects of
spatial closures on food webs in this system; 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 WA Departments of Environment and Conservation (DEC), Fisheries and 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, Peel-Harvey) have
changed over the last three decades.
The studies of the genetics of a number of fish
species, including that of the Black Bream Acanthopagrus butcheri which was restocked
into the Blackwood River Estuary, are continuing to yield data that are important for the
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Centre for Fish and Fisheries Research - Annual Research Report 2009
DIRECTOR’S REPORT cont…
conservation of those species. Research on the biological oceanography of the Leeuwin
Current continued, particularly on larval fish recruitment.
Staff and students in the CFFR 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, the Whale Sharks of Ningaloo, Freshwater Sawfish in the Kimberley,
and on Fairy Penguins in Cockburn Sound. Research on the interactions of dolphins with
trawling in the Pilbara, funded by FRDC, the Department of Fisheries and the fishing
industry, found that the catch rates of dolphins had declined with modifications in net
designs and that further reductions in catch rates may be possible. Remote sensing and
tagging technology have been used to understand the movement and home ranges of
Whale Sharks, Fairy Penguins and Freshwater Sawfish. Research on sawfish was filmed by
National Geographic for inclusion in the Hooked Monster Fish series. Monitoring of
Australia’s only critically endangered (EPBC Act 1999) freshwater fish species, 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 were heavily involved in organising the very successful joint 8th IndoPacific Fish Conference and 2009 Australian Society of Fish Biology conference and
workshop in Perth in June 2009 and the 3rd Ningaloo Research Symposium. We have also
hosted a number of international visitors (Professor John Hoenig – Virginia Institute of
Marine Science, Dr Michael Krüetzen – University of Zurich, Dr Pilar Olivar – Institute of
Marine Science, Barcelona, Dr Zeb Hogan – University of Nebraska / National Geographic,
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, Associate Professor
Page 6
Centre for Fish and Fisheries Research - Annual Research Report 2009
William Sherwin – University of New South Wales, Dr Margaret Platell – University of
Newcastle and Dr Brendan Ebner - Griffith University).
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
Page 7
Centre for Fish and Fisheries Research - Annual Research Report 2009
AWARDS/COMMITTEE MEMBERSHIP
Committee
membership/
Community service
Stephen Beatty

8th Indo-Pacific/Australian Society for Fish
Biology Conference organizing committee

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 Executive Board (until June 09)

School Advisory Committee (Industry)

Editor – School Annual Report
Faculty of Sustainability, Environmental and
Life Sciences:

Marine Science Deputy Programme Chair
(until June 09)

Board member, Centre for Fish and
Fisheries Research
Other Organisations:

African Journal of
Marine Science
(Editorial Board)

Australian Marine Sciences Association
(Vice-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)

Indo-Pacific
Fish
Conference
2009
(International
Scientific
Advisory
Committee member)

Indo-Pacific Fish Conference 2009 (Reef
Fish Biology Symposium Convenor)

Sustained Indian Ocean Biogeochemical
and Ecological Research (International
Scientific Committee member)

Monitoring Recreational Fisheries -Victoria
DPI and FRDC (Technical Advisory
Committee member)
Lars Bejder

Board member of the Society for Marine
Mammalogy

Chair of the Education Committee for the
Society of Marine Mammalogy

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
Invited and funded participant at the
International Whaling Commission’s 61st
annual meeting. Scientific Committee on
Sustainable
whale-watching.
Madeira,
Portugal. June, 2009
Invited and funded participant at the
Behavioural Response Study workshop, La
Spezia, Italy. April 2009.
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
Joseph Christensen

Secretary of the Australian Association for
Maritime History
Howard Gill

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
Australian Marine Sciences Association
of
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
Page 8
Centre for Fish and Fisheries Research - Annual Research Report 2009
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

BSB Research Committee

WA Fisheries Research Advisory Board

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

Co-Convenor, 8th Indo-Pacific Fish
Conference and 2009 Australian Society of
Fish Biology Conference and Workshop
Alan Lymbery

Zoological Parks Authority Research Board

Editor, Pacific Conservation Biology

Managing Editor, Biodiversitas

School of Veterinary and Biomedical
Sciences, Honours Committee
David Morgan

8th Indo-Pacific/Australian Society for Fish
Biology Conference organising committee

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
Brad Norman

National Geographic Emerging Explorer
2008

CEO, Ecocean (Australia)

Director, Ecocean (USA)
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:

Academic Chair: Marine Science
(University level) – until July 2009;
Deputy Academic Chair from July
2009

Director of the Coral Bay Research
Station

University Dive Officer (University level)
General Community Service

President: North West Research
Association

Member: Council of the Royal Society of
WA

Member: Committee of the Australian
Marine Sciences Association (WA Branch)
Page 9
Centre for Fish and Fisheries Research - Annual Research Report 2009
AWARDS/COMMITTEE MEMBERSHIP cont…




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
Page 10
Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH ACTIVITIES
Photos by Simon Allen and Peter Coulson
Page 11
Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH ACTIVITIES cont…
3. RESEARCH ACTIVITIES
Research objectives
The main ongoing objectives of the Centre for Fish and Fisheries 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:
1. Ecosystems and Fisheries Management (including fish health and sustainable aquaculture);
2. Biodiversity and Conservation of Aquatic Systems (including studies of species of
conservation significance); and
3. Biological Processes and Evolution (including population biology and genetics), to better reflect
the role of our research in providing knowledge for Ecosystem Based Fisheries Management and
marine and freshwater conservation planning.
The research activities of the Centre are reported under these themes below:
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Centre for Fish and Fisheries Research - Annual Research Report 2009
3.1
Ecosystems and Fisheries Management
3.1 a) Marine, estuarine and freshwater systems
Estuarine Fish Community Studies
Peel-Harvey and Leschenault estuaries
The studies of the fish faunas of the Peel-Harvey and Leschenault estuaries, which are funded by
WAMSI, South West Development Commission and Murdoch University, are progressing very well.
These WAMSI studies are being supervised by Dr Peter Coulson, Dr Steeg Hoeksema and Prof Ian
Potter, who are being very ably assisted by PhD student Lauren Veale. The initial aim of the project
was to determine the ichthyofauna compositions of these systems and to elucidate the factors that
influence them. These contemporary data are now being compared with those obtained in earlier
studies when conditions in the estuary were very different. For example, extensive sampling was
conducted in the Peel-Harvey Estuary in the early 1980s when this system was highly eutrophic and
in the 1990s after a large artificial channel (Dawesville Channel) to the ocean had been constructed.
Thus, such comparisons will enable hypotheses to be tested regarding the influence of extreme
macroalgal growth and greatly increased tidal exchange with the ocean on species composition,
density and diversity.
By the end of 2009, the
fish faunas at numerous
sites in the Peel-Harvey
and Leschenault estuaries
had been sampled in six
consecutive seasons and
will be sampled for a
further two seasons until
the autumn of 2010. On
the basis of the data
analysed thus far, the
overall density of fish is
similar to that in the
1990s, but less than in the
1980s, when the system
Ben French, Ian Potter, Peter Coulson, Thea Linke, Fiona Valesini and Ashlee Jones
contained
massive
at the Marine Science Centre in Fremantle
macroalgal
growths.
In
Photo provided by Peter Coulson
contrast, the number of
fish species has increased
since the 1980s, as a result of a greater number of marine species, which reflects the fact that,
through the construction of the Dawesville Channel, there is now a greater influx of such species
from the ocean.
The ichthyofaunas of each of the five regions of the Peel-Harvey Estuary, comprising the natural
entrance channel and two regions of each of the two large basins, were all dominated by a small
number of species. However, the fish faunal composition varies among these different regions
particularly the natural (Mandurah) entrance channel compared with that of the basin regions. Thus,
for example, while the Sandy Sprat Hyperlophus vittatus contributes nearly 80% to the total number
of fish caught in the entrance channel, this clupeid is not abundant in any other region of the estuary.
The Weeping Toadfish Torquigener pleurogramma, which is such a nuisance to anglers when present
in large numbers, is now the most abundant species in the large basins of the Peel Harvey Estuary,
contributing over half and nearly three quarters to the total fish catch in two of the main regions of
the estuary. The very large numbers of this marine species in the Peel-Harvey Estuary probably
reflects the influence of a greatly increased tidal exchange with the ocean and thus more marine
conditions since the construction of the Dawesville Channel and the greater access provided to the
estuary by that channel. The second most abundant fish species in the basins of the Peel-Harvey
Estuary is the Western Gobbleguts Apogon rueppellii. This mouth-brooding species, which completes
its life in estuaries, is frequently associated with aquatic vegetation and thus, its increased
Page 13
Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH ACTIVITIES cont…
abundance maybe linked to the prevalence of seagrass and macroalgae, which has increased in
recent years.
On the basis of the data collected during the during the first six seasons of sampling, seven of the
eight most abundant species in the Leschenault Estuary during this period likewise ranked among the
most abundant species in the 1990s. However, the Spotted Hardyhead Craterocephalus mugiloides,
which now ranks fifth in terms of abundance, was not found in the earlier period. This atherinid has
not previously been found in any estuary to the south of the Peel-Harvey Estuary, but is abundant
further to the north in Western Australia. Thus, this sub-tropical/tropical species appears to have
recently colonised the Leschenault Estuary, possibly having been transported southwards from the
regions of the Peel-Harvey and Swan Estuary in which it is abundant.
While the number of fish species in the Leschenault Estuary is similar to that in this system in the
1990s, the species composition has changed between the two periods. This is partly due to the
consistently large catches now taken of C. mugiloides and of another Hardyhead Atherinomorous
vaigiensis. The ongoing collection of samples and further analyses will elucidate the extent to which
the characteristics of the ichthyofauna of the Leschenault Estuary have changed during the last two
decades and whether any changes can be attributed to the deterioration in the condition of the
estuary that local residents believe has reoccurred.
Figure (left). Lauren Veale and Steeg Hoeksema seine netting in the Peel-Harvey Estuary. (Right) Lauren Veale
and Peter Coulson sorting a seine net catch from the Peel-Harvey Estuary containing mainly Banded Toadfish.
Photos by Peter Coulson
South coast estuaries
A detailed study of the environmental and ichthyofaunal characteristics of five estuaries on the south
coast of Western Australia has now been completed. This study, which was undertaken by Ben
Chuwen, Steeg Hoeksema and Ian Potter, was funded by the South Coast Natural Resource
Management, the Fisheries Research and Development Corporation and Murdoch University. The five
estuaries represented the different types of estuaries found along this coast, with the Broke, Irwin
and Wilson inlets being seasonally-open to the ocean, Oyster Harbour being permanently-open and
the Wellstead Estuary being normally-closed. Each of these estuaries has a distinct riverine and large
basin area and, when open to the ocean, has a short and narrow entrance channel.
The environmental characteristics of the five estuaries varied markedly, even between estuaries of
the same type. These differences reflected variations in the relationship between the volume of fluvial
discharge, which is determined by a combination of the amount of local rainfall, catchment size and
extent of clearing of native vegetation, and the amount of intrusion by marine waters, which is
largely controlled by the size and duration of the opening of the estuary mouth. Some idea of the
extent of these variations among estuaries is provided by the values for salinity in the basins of the
different estuaries. Thus, salinity never reached that of full strength sea water and did not vary
markedly during the year in Wilson Inlet, whereas it substantially exceeded that of seawater at times
in Wellstead Estuary and underwent very pronounced seasonal and inter-annual changes in Broke
Inlet.
The marked differences among the environmental variables in the five estuaries, and particularly in
their salinities, account for the species compositions of the nearshore waters of those estuaries being
significantly different. However, each of those ichthyofaunas was dominated to a remarkable extent
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Centre for Fish and Fisheries Research - Annual Research Report 2009
by three species of atherinid, i.e. Atherinosoma elongata, Leptatherina wallacei and
L. presbyteroides, and three species of gobiid, i.e. Pseudogobius olorum, Afurcagobius suppositus
and Favonigobius lateralis, all of which are able to complete their life cycle within these systems.
Thus, while those six species collectively contributed between 92.9 and 99.7% to the total number of
fish caught in each estuary, their relative abundances differed among estuaries, reflecting differences
in such factors as the status of the estuary mouth, extent of macrophyte cover and salinity regime.
For example, F. lateralis and L. presbyteroides, which are also represented by marine populations,
were most abundant in the permanently-open Oyster Harbour, which, in terms of substrate and
salinity, most closely resembles that of the nearshore marine environment.
In contrast to the situation in nearshore waters, the fish faunas of
the more offshore and deeper waters of the basins of the five
estuaries were dominated by marine species, but to varying
degrees. These ichthyofaunal differences reflected, in part, the
extent and duration of the opening of the estuary mouth, with, for
example, the prevalence of marine stragglers in Oyster Harbour,
the single permanently-open estuary, being the greatest of any
estuary. Furthermore, ichthyofaunal composition was also
influenced by the extent of macrophyte growth, with the Estuary
Cobbler Cnidoglanis macrocephalus being most abundant in Wilson
Inlet in which macrophytes were particularly dense, which may
provide particularly important habitat for that species, particularly
the juveniles of this eel-tailed catfish.
Prof Ian Potter on Wilson Inlet
Photo by Ben Chuwen
Irrespective of estuary type, the ichthyofaunal composition of the deeper waters of the riverine and
basin regions of each estuary differed markedly. This difference was very largely attributable to the
consistently far greater abundances of the Black Bream Acanthopagrus butcheri and the Sea Mullet
Mugil cephalus in the rivers than in the basins. The first of these species is only found in estuaries
and typically spawns in the riverine reaches of these systems, while the second migrates through
estuaries to their upper reaches and sometimes even into freshwater.
During the course of past studies of estuaries in south-western Australia, it became increasingly
evident that some estuaries became markedly hypersaline, with, for example, salinities reaching 65
in Stokes Inlet, 145 in Hamersley Inlet and even 296 in Culham Inlet. As these estuaries are also all
normally-closed to the ocean, it was thus considered appropriate to develop a definition that took
into account the above characteristics which are generally not covered by traditional definitions of
estuaries. This resulted in the following definition, which is being published in Estuarine, Coastal and
Shelf Science 87, 497-500 (2010):
“An estuary is a partially enclosed coastal body of water that is either permanently or
periodically open to the sea and which receives at least periodic discharge from a
river(s), and thus, while its salinity is typically less than that of natural sea water and
varies temporally and along its length, it can become hypersaline in regions when
evaporative water loss is high and freshwater and tidal inputs are negligible.”
Invertebrates in Estuaries
During 2009, we had the pleasure and value of visits by Professors Bob Clarke and Richard Warwick
from the Plymouth Marine Laboratory in the United Kingdom. Their expertise was invaluable in
refining our statistical approaches to analysing faunal community data and developing our
understanding of the implications of the results of our studies on the benthic macroinvertebrate and
nematode faunas in our estuarine and coastal waters. Richard also helped Mathew Hourston describe
ten new species of nematodes.
Mathew Hourston, who was supervised by Fiona Valesini and Ian Potter, submitted his PhD thesis in
2009. The thesis was well received by the three examiners, who all recommended that Mathew be
awarded his PhD subject to minor changes. Mathew, together with Richard Warwick, Ian Potter and
Fiona Valesini, have been using the data collected by Mathew during his PhD to quantify the extent to
which the diversity, density and composition of nematode assemblage vary within the Swan-Canning
Estuary and between that estuary and nearshore coastal marine waters. The results of these
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Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH ACTIVITIES cont…
analyses are emphasising that, in terms of its composition, the nematode fauna in the Swan-Canning
Estuary constitutes two distinct groups, with the division occurring at the point where salinities
change most markedly during the year. The compositions of both of these estuarine groups differ
markedly from those found in nearshore coastal waters.
Since completing her PhD, Michelle Wildsmith has established her own consultancy company in
conjunction with Matt Harvey, another PhD graduate from Murdoch University. During her PhD,
Michelle sampled the same sites that Tom Rose sampled in the Peel-Harvey and Swan-Canning
Estuaries for his PhD in the 1980s. The comparisons between the recent and past data provide
overwhelming evidence that the benthic environment in these estuaries has declined during the last
two decades. The evidence for this deterioration includes a decline in the abundances of species
sensitive to detrimental environmental changes, such as crustaceans, and increases in those of
species that are far more tolerant, e.g. polychaetes.
Freshwater ecosystems
Team Sawfish is a long running project
by the Freshwater Fish Group and
involves many researchers from around
Australia and Indigenous organisations
and communities in the Kimberley. The
Murdoch researchers involved include
Dr David Morgan, Dr Jenny Chaplin, PhD
candidate Nicole Phillips and MPhil
candidate Jeff Whitty, as well as former
Murdoch researcher, Dr Dean Thorburn.
During 2009, the team’s research on the
genetics, ecology and movement patterns
(tagging) of Freshwater Sawfish in the
Fitzroy River was aired on National
Geographic’s
Monsterfish
series
on
Foxtel.
The show’s host Dr Zeb Hogan is on a
quest to find the world’s largest
Dave Morgan discussing the new born Freshwater Sawfish pup
freshwater fish, of which the giant
with National Geographic’s Zeb Hogan
Photo by Jatuporn Athasopa
Freshwater Sawfish is a contender. Nicole
was filmed at Murdoch while David, Jeff,
and the Yiriman Rangers, were filmed on location in the Kimberley. The team also produced a
number of publications during 2009 and presented their research at a number of conferences
(IPFC/ASFB 2009 in Fremantle) and workshops (Fitzcam meeting in Fitzroy Crossing; Jarlmadangah
Community). David also went to Brisbane as part of a scientific review committee on the export of
live Freshwater Sawfish. Collaborating researchers on the project included Stirling Peverell (Qld DPI
& F), Dr Colin Simpfendorfer (JCU), Dr Rory McAuley (DoF), and the team would also like to
acknowledge the help from the general community in the Kimberley, and funding body DEWHA.
Other freshwater research
The Freshwater Fish Group welcomed international (USA) PhD candidate Michael Klunzinger to the
group. Michael is on a quest to find the fish hosts of the parasitic stage of the vulnerable Carter’s
Freshwater Mussel and to determine the ecology of the species. He is supervised by Associate
Professor Alan Lymbery, Dr David Morgan and Dr Stephen Beatty. His research has highlighted our
lack of knowledge on this species as well as demonstrating the decline of various populations. Alan,
David and Stephen also co-supervised another international (Iran) PhD candidate, Mahmoud
Rashnavidi. Mahmoud is in the final stages of completing his thesis and should be submitting early in
2010. Mahmoud’s work has demonstrated the impacts of salinisation on the fishes, their food, and
their parasites with the Blackwood River.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
A number of projects by the Freshwater Fish Group continued during 2009. This included the
influence of surface water and groundwater expression (Yarragadee Aquifer) in the Blackwood River,
which is the longest running monitoring of fish movement patterns in south-western Australia (20052009). The research, which is led by Dr Beatty and Dr Morgan is demonstrating the importance of
groundwater expression in maintaining relictual populations of freshwater fish in a salinised
environment
and
the
importance of perennial flows
from groundwater during the
drier months in maintaining
migratory routes for fishes.
PhD candidate Fiona McAleer
is also working on the project
and is investigating the
ecology of the region’s largest
freshwater
fish,
the
Freshwater Cobbler, in this
unique environment.
This
project is funded jointly by
the Department of Water and
the
Federal
Government
under the $12.9 billion Water
for the Future Plan.
Stephen
Beatty,
David
Morgan and Mark Allen also
worked with Geocatch to
Freshwater fishes of the Swan-Canning catchment
control feral Goldfish in the
Poster by Gavin Sarre
Vasse River, and to aid in
catchment plans for the
Carbunup and Buayanyup Rivers through a baseline fish and crayfish survey of these catchments.
They also continued their long association with the Cape to Cape Catchments Group in assessing the
movement patterns of fishes in the Margaret River, as well as in the control of feral Goldfish and
Yabbies in a tributary of the river. Further Goldfish controls were implemented in the Warren River in
association with Southern Forests Landcare. Other feral fish work included the Rosy Barbs in
Jingarmup Brook (with Geocatch).
David and Stephen, in collaboration with Dr Brendan Ebner (Griffiths University) completed a
Department of Water funded study into the importance of groundwater in maintaining fish
populations in the Pilbara. They examined the fishes of the Fortescue and Yule Rivers and compared
this with the group’s previous research in these systems at the turn of the century. Not only did they
find that the Fortescue is the most diverse river in the Pilbara for freshwater fishes, but these
groundwater dependant pools are important nurseries for estuarine species. Pools that have
connection to groundwater were considerably more diverse and stable (fauna wise) than pools
without groundwater expression. An important result, noting that there is increasing pressure to
develop water resources in the Pilbara to quench the thirst of the expanding mining industry. They
have also found what may be two new species of fish.
David and Stephen, in collaboration with former Murdoch researcher Dr Gavin Sarre, produced a
poster on the freshwater fishes of the Swan River for community groups, which was funded by the
Northam Shire Council, Lotterywest and Avon Valley Environment Society, to be put on display next
to Northam Pool. This resulted from a collation of fish distributions from over 180 sample sites
throughout the Swan-Avon-Canning catchments by the group. The team has also commenced a
project in collaboration with the Swan River Trust on determining the ecological impacts of the
introduced Pearl Cichlid (Geophagus brasiliensis) in Bennett Brook in the Swan River catchment
(pictured on the poster). David, Stephen, Alan Lymbery and Michael Klunzinger also commenced an
investigation into the fishes of the Brockman River and Ellen Brook in the Swan catchment. This
work, which is funded by Lotterywest through the Ellen Brockman Integrated Catchment Group, is
demonstrating that areas of groundwater discharge are maintaining threatened and isolated
populations of fishes and mussels that have been eliminated from many catchments.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH ACTIVITIES cont…
The Water Corporation provided funding to the
group to determine the risks associated with the
interbasin transfer of water between two
catchments in the Denmark region.
With
Denmark’s water supply nearing capacity, there
is an urgent need to secure additional water
resources.
This project is examining the
migration patterns of fishes in the Denmark and
Hay rivers, the parasites of fishes in these
rivers, and the genetics of fishes. The genetic
and morphological work, in collaboration with Dr
Mark Adams and Dr Michael Hammer (SA
Nannoperca sp. Nov – a new species of pygmy perch
Museum), has confirmed the presence of a new
discovered by David Morgan and Stephen Beatty
species of pygmy perch in the area (pictured).
Photo by Stephen Beatty
In collaboration with the Department of Water,
the team has purchased a swim tunnel to examine the swimming abilities of freshwater fish in the
south-west. Honours student James Kelleher will commence this work as an Honours project in
2010; information that is a key consideration in the design of fishways. With regard to fishways,
David Morgan aided in filling the knowledge gaps and design of a fishway for the Camballin Barrage
in the Fitzroy River of the Kimberley. The group has demonstrated the impact of this barrier to
migrating fishes, in particular to the endangered Freshwater Sawfish. David also led research into
the importance of groundwater in maintaining freshwater fish diversity in Snake Creek, with the help
of the Yiriman Rangers. This work was funded by Liveringa Pastoral Co. and is a continuation of the
study that commenced in 2008. Remarkable species diversity was found in this major tributary of
the Fitzroy River, and the stability of the fish fauna is highlighted by the little evidence of interannual
variation. The abundances of Freshwater Crocodiles are extremely high in this system and it is a
critical nursery for many species, including Freshwater Sawfish.
3.1 b) Oceanographic processes
The highlight of the year was the submission of the PhD thesis of David Holliday examining timing,
sources and pathways for the incorporation of larval fishes into an evolving eddy of Leeuwin Current
eddies. This comprehensive work was based on depth-integrated and depth-stratified samples
collected from the RV Southern Surveyor and he matched these biological data with water mass
characteristics and trajectories and velocities of currents measured with oceanographic drifters and
the shipboard Acoustic Doppler Current Profiler. His thesis also included part of an extensive study of
the Leeuwin Current ecosystem conducted between Cape Leeuwin and North West Cape. He focused
on the southern part of the system and its extensive eddy field, while Natalie Millar completed her
Honours project on the larval fish assemblages in the northern part of the study area. Other work
entailed ascertaining the distribution of rock-lobster phyllosoma larvae over the entire west coast
from neuston samples collected in the Leeuwin Current system. Nick Breheny completed his Honours
project on the larval fish assemblages associated with the annual spawning aggregations in Cockburn
Sound and adjacent embayments.
Lynnath Beckley spent considerable time working towards an expansion of collaborative biological
oceanographic research into the remote Kimberley region off northern Australia. Some success was
achieved with a dedicated research cruise by the RV Southern Surveyor now scheduled for April
2010. She also continued her role as Australian representative on the Scientific Steering Committee
for the international programme on Sustained Indian Ocean Biogeochemical and Ecological Research.
The science plan for basin-wide research has evolved considerably and has six focal areas for
biological oceanography including Indian Ocean boundary currents and equatorial circulation.
3.1 c) 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
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Centre for Fish and Fisheries Research - Annual Research Report 2009
and Dr Luke Twomey (Oceanica Consulting), and involves using dietary analysis 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.
Thea gave oral seminars of her work at the South-West Catchment Council conference in Busselton,
8th Indo Pacific fish conference/ASFB workshop and the Coastal and Estuarine Research in Perth, the
46th annual AMSA conference in Adelaide and the ICES Annual Conference in Berlin during 2009.
3.1 d) Fisheries dynamics
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 (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.
Nick Konzewitsch completed an Honours project with Neil Loneragan and Natalie Toon, examining the
behaviour of lobsters in the field during the migration phase (whites – November) and more
stationary phase (reds – March). He found that behaviour around the traps was similar in the whites
and the reds phase but that much more activity was recorded during the whites. Lobsters in both
phases were able to leave the traps through the escape gapes. In addition, Nick found that lobsters
did not enter the trap when an octopus was inside the trap.
Aggregation dynamics of orange roughy
For his Honours, Adrian Hordyk developed a methodology for recognizing orange roughy marks and
estimating the volume of schools from scientific surveys of the Cascade Plateau, south-east of
Tasmania. His research, supervised by Neil Loneragan and Jeremy Prince, was successful in
developing a documented, repeatable system for estimating the volume of orange roughy
aggregations from technology on commercial vessels. His study is one of the few studies to
document changes in aggregation size during a spawning season and also examine the biological
characteristics of the aggregation. The results of his work lead to the orange roughy assessment
being revised for one year in which a high biomass of roughy had been estimated from another
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Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH ACTIVITIES cont…
approach. His research relied on data collected by scientific observers working on commercial fishing
vessels and was facilitated through discussions with Geoff Diver (Biodiversity).
3.1 e) Modelling ecosystems and fisheries
Ecosystem modelling work has focused on developing both qualitative and quantitative ecosystem
models for marine and estuarine systems in Western Australia. 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. The management
strategy evaluation studies, which are being conducted by PhD student Emily Fisher and her
supervisors, involves predicting, through computer simulation, the likely effectiveness of alternative
fisheries management options.
An important element of the MSE study is to develop a user-friendly program interface for the
computer model. This was facilitated by using a “scenario-testing” workshop, during which
undergraduate students at Murdoch University, who are undertaking a fisheries unit, used
preliminary
versions
of
the
computer
model
to
make
“management decisions” based
on stock status information
presented by the model. The
data obtained from the workshop
revealed that, when using the
program, the decisions made by
students differed according to the
initial status of the simulated
stock, strongly suggesting that
the program is effective for
communicating stock assessment
information.
Figure A - A preliminary version of part of the program interface of
The agent-based modelling (ABM)
the agent-based model developed by students Rowena Burch and
studies are aimed at providing a
Calais Tink and their supervisors Norm Hall and Alex Hesp. The
visual tool for engaging and
screen displays simulated movements of fish and fishers over an
artificially-generated habitat landscape. Statistics on the changing
communicating stock assessment
demography of the fish population, fishers’ catches and their
information to recreational fishers
behaviour are recorded during the simulations.
(see below). These studies were
initiated by Rowena Burch, who
received a first class degree for her Honours thesis, which she submitted towards the end of 2009
and are being continued by Calais Tink for her PhD. The agent based model is being used to explore
the consequences of localised interactions between individual fish and recreational fishers. With the
help of Kane Moyle from RecFishWest, Rowena, Calais and Alex undertook a detailed survey with
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Centre for Fish and Fisheries Research - Annual Research Report 2009
experienced dhufish and snapper fishers. The information gained from that survey was invaluable for
parameterising the model and increasing our understanding of how fishers interact with these
species. The students and researchers are most grateful to RecFishWest and FRDC for their support.
3.1 f) Socio-economics of fishing
Socio-Economics and Environmental History
Professor Malcolm Tull (Murdoch Business School) continued to direct WAMSI Node 4.5 ‘Socioeconomic implications of implementing EBFM in the West Coast Bioregion’ in 2009. Following the
appointments of Dr Seamus McElroy to the UWA Business School as Senior Research Fellow in Node
4.5.2 ‘Modelling Recreational Fisher Behaviour’, and Joseph Christensen as Postdoctoral Researcher
for Node 4.5.3 ‘Socio-Economic Assessment of Fisheries in the West Coast Bioregion’, project
development reached an advanced stage, and assorted research activities were initiated. The Node
4.5 projects aim to improve understanding of the behavioural responses of commercial, charter and
recreational fishers within the West Coast Bioregion over the long-term under different scenarios of
economic and demographic growth, resource exploitation regimes, and stock recovery, and to
enhance understanding of the social, economic and environmental values of the fishery that informs
the management process, assists with resource allocation decisions, and enables long-term
monitoring programs of socio-economic values. This research will facilitate the incorporation of
socio-economics into the EBFM framework.
Progress continued in the HMAP Asia
research
project
on
the
environmental history of fisheries in
the South-East Asian and Australian
regions. The highlight of the year was
the workshop ‘HMAP Asia: Towards a
Regional Synthesis’ held at Murdoch
University
in
February
2009.
Presentations
at
the
workshop
included papers on the history of
shark fishing in Indonesia, whaling in
the Philippines, the Taiwanese tuna
fishery, Madras fish curing yards,
south-east Australian trawl fishery
and the Shark Bay snapper fishery,
with attendees including invited
experts John Butcher from Griffith
University,
and
HMAP
Director
Professor Poul Holm from Trinity
Workshop HMAP Asia: towards a Regional Synthesis
College, Dublin. Prof Malcolm Tull and
Photo provided by Malcolm Tull
Dr
Joseph
Christensen
also
participated in the ‘Oceans Past II’
conference at the Aquatic Ecosystem Research Laboratory, University of British Columbia, Vancouver,
in May 2009. Research will continue in 2010. PhD student Jo Marie Acebes arrived at Murdoch in
August 2009 to commence her study into the history of indigenous whaling in the Philippines.
3.1 g)
Sustainable aquaculture and fish health
The research focus of the Fish Health Unit is the health of cultured and wild aquatic species and the
environment in which they are found. We currently have research projects addressing the causes and
consequences of stream salinisation, the development of sustainable inland saline aquaculture, and
understanding parasitic diseases of wild and cultured aquatic species.
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RESEARCH ACTIVITIES cont…
Stream salinisation
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.
Michael Klunzinger has commenced 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. Michael’s study will provide
valuable information for the conservation of this unique species.
Inland saline aquaculture
We have continued our work, 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. This is
currently being further tested in pen and paddock trials.
Parasitic diseases of aquatic species
Marina Hassan, after successfully completing her PhD in 2008 on the parasites of native and
introduced freshwater fishes in the south-west of Western Australia, returned to the Fish Health Unit
in 2009 to complete a short project funded by the Water Corporation. Marina identified parasites
which may pose a risk to resident fish populations during water transfer between river catchments.
Susan Gibson-Kueh continued her PhD on infectious diseases of cultured barramundi. Susan has been
collecting samples from barramundi farms in Australia and throughout South East Asia and busily
examining pathology slides. We were also funded by Zamira Life Sciences to conduct a series of trials
on the efficacy of a probiotic treatment in protecting against bacterial diseases in barramundi. This
work produced some interesting results and we are planning to undertake further trials
Dr Dina Zilberg is currently at Murdoch University as a Visiting Fellow for an 18 month sabbatical.
Dr Zilberg visits us from the The Jacob Blaustein Institutes for Desert Research, Ben-Gurion
University of the Negev, Israel, where she holds a senior lectureship in Aquatic animal health. Dina is
here to develop further her skills in fish pathology and is currently investigating Mulloway and
Yellowtail kingfish health in Western Australia, supported by the Aquaculture Development Council
and Indian Ocean Fresh.
3.2
Biodiversity and conservation of aquatic systems
3.2 a) Shallow water habitat classification and faunal assemblages
Development of indices of health and a food web for the Swan-Canning Estuary
Chris Hallett is in the third year of a PhD study with Dr Fiona Valesini, Dr Steeg Hoeksema and
Prof Ian Potter, and is developing and evaluating a multi-metric biotic index of estuarine health for
the Swan-Canning Estuary, based on a suite of characteristics (metrics) of the fish assemblages in
this system. This will be the first biotic index to be developed for estuaries in Western Australia, and
will provide a robust and affordable management tool for assessing and monitoring estuarine health,
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Centre for Fish and Fisheries Research - Annual Research Report 2009
and communicating the findings to the wider public. The approach developed in this study is widely
applicable and could be used to assess the ecological health of any other estuary.
Chris has recently used a novel statistical approach for identifying those fish metrics which are the
most sensitive to ecosystem change in the Swan-Canning Estuary, and which will be used to build the
final index. These metrics reflect aspects of species diversity and community composition, dominance
and nursery and trophic function. Chris is currently in the process of developing reference conditions
for each selected metric, which represent the “best available” values against which the previous,
current and future health of the estuary can be assessed and compared. He is using a number of
historical data sets for fish assemblages in the Swan-Canning Estuary to undertake this task, which
have been collected by various researchers in the CFFR since the late 1970s. The next steps for
Chris’s study involve calculation of the final health index, then validation of index sensitivity and
reliability.
Chris gave oral seminars of his work at the South-West Catchment Council conference in Busselton,
8th Indo Pacific fish conference/ASFB workshop in Perth and the Coastal and Estuarine Research
Federation conference in Oregon during 2009.
Amanda Buckland, who completed her Honours at James Cook University, started her PhD in the
CFFR during 2009 under the supervision of Drs Steeg Hoeksema, Fiona Valesini and Luke Twomey.
Her project is partly focussed on building on aspects of the work undertaken by Thea Linke, and will
develop a broader food web for the Swan-Canning Estuary that incorporates all fish species recorded
in the middle and upper reaches of the system. She will be using complementary data derived from
(i) traditional gut content analyses of fish and (ii) stable isotope analyses of those fish and their prey
to establish trophic interrelationships in the estuary and how they might change with regions and
seasons. Amanda will also be examining the composition of the benthic macroinvertebrate
assemblages in the Swan River, contrasting the fauna in the well oxygenated shallows with that of
the deeper waters that now regularly suffer from low dissolved oxygen concentrations, and
comparing these data to those recorded by previous CFFR researchers in the mid-1990s. The
outcomes of her work will thus provide valuable insights into the trophic functioning of the SwanCanning Estuary, and how it is potentially impacted by the effects of environmental perturbations
such as anoxia in particular reaches of the system. Amanda gave presentations of her work at a
research showcase hosted by the Swan River Trust and at the annual AMSA student workshop during
2009.
Relationships between faunal assemblages and habitat types in Broke Inlet
James Tweedley, who commenced his PhD in 2007 and is being supervised by Dr Fiona Valesini,
Dr Steeg Hoeksema and Prof Ian Potter, is examining the relationships between habitat types and
fish and benthic macroinvertebrate faunas in the nod-pristine Broke Inlet on the south coast of
Western Australia. James has employed a quantitative classification scheme to identify the various
nearshore and offshore habitats in Broke Inlet, and has sampled the fish and benthic
macroinvertebrate fauna at representatives of those habitats on a seasonal basis since spring 2007.
He completed this faunal sampling in winter 2009, and has since been examining the trends between
differences in habitat types and those in fish and invertebrate assemblage composition. It is
envisaged that the outcomes of his study will be used to produce a tool for managers and ecologists
that will enable them to predict the habitat type and characteristic fish and benthic macroinvertebrate
species at any site in the estuary during any time of year.
James gave presentations of his work at both the South-West Catchment Council conference in
Busselton and the 8th Indo Pacific fish conference/ASFB workshop in Perth during 2009.
3.2 b) Studies on macroalgae diversity
Dr John Huisman continues his studies on Western Australian marine macroalgae, with a focus on the
north-west. Recent or in press publications have included an annotated checklist of the species
occurring on the offshore atolls (Huisman et al., 2009b), rediscovery of an extremely rare alga from
near the Perth region (Huisman et al., 2009a), an ultrastructural study of an unusual endophyte
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RESEARCH ACTIVITIES cont…
(Pueschel & Huisman, 2010), and two publications examining the effects of the Leeuwin Current
(Phillips & Huisman, 2009; Westera et al., 2009). In addition, Wells et al. (2009) makes a major
contribution to the recognition of invasive marine species by presenting them in a field guide format.
Ongoing works include a book describing the marine flora of north-western Australia, which should be
completed in 2010 or early 2011 and will be published as part of the ‘Algae of Australia’ series. This
study has revealed several new genera and many new species, some of which are being described
separately (e.g., Huisman et al., 2010 in press). PhD student Rainbo Dixon is continuing her studies
of the brown alga Sargassum, incorporating DNA sequence analyses in an attempt to clarify the
species relationships in this difficult genus.
3.2 c) Marine protected areas
Mark Allen is in the last stages of his field program, examining the diversity of the fish fauna in the
Raja Ampat region of eastern Indonesia. His research, supervised by Prof Neil Loneragan, is funded
by Conservation International through a grant for his PhD and the Conservation International Bird’s
Head Seascape Project. He has developed a methodology for rapid-underwater visual census of
fished reef populations and has surveyed the reefs in four areas designated as Marine Protected
Areas in the region.
The two large projects being conducted at Ningaloo Marine Park under the auspices of the CSIRO
Wealth from Oceans Ningaloo Collaborative Cluster progressed well during 2009. The prime focus of
the project on high resolution mapping of human use of Ningaloo Reef, led by Associate Professor
Lynnath Beckley, was completion of the PhD thesis by Claire Smallwood incorporating aerial and
coastal survey data and results from interviews with users of the Ningaloo Marine Park. The clear
seasonality in use of the marine park and the dramatic spatial expansion of recreational activities
during the winter tourist season are hallmarks of the data set. The land tenure arrangements
adjacent to the marine park strongly influence the use of the park and travel network analysis
highlighted the nodal nature of use of the Marine Park and rapid distance decay from access points.
Florian Mayer completed some modelling work on how a range of environmental, spatial and
temporal variables (roads/tracks, accommodation availability, coastal geomorphology, zoning scheme
etc) explained the variation seen in the aerial and coastal survey data. Towards the end of the year,
attention focussed on preparing the final report and drafting manuscripts for submission to journals
in 2010.
The Ningaloo Cluster project using the high resolution, remotely-sensed, hyperspectral dataset for
Ningaloo Reef, led by Dr Halina Kobryn, made good progress with respect to the spatial mapping of
the shallow-water habitats. Kristin Wouters produced numerous exciting data products including
probability maps for different benthic covers (corals, macro-algae, sand etc) and bathymetric
variables such as slope and aspect which are particularly important in the ecology of shallow water
marine benthos. A comprehensive field trip to Ningaloo in April enabled ground truthing to be
completed. Attention was also placed on the terrestrial habitats along the coast adjacent to the
marine park with further work completed on the extent of the labyrinth of four wheel drive tracks
that has proliferated in the region.
Another highlight of 2009 was the completion by Matt Harvey of his PhD thesis on the subtidal
benthic habitats at Rottnest Island as determined from hyperspectral imagery. He developed
techniques to separate the spectra produced by the different benthic substrates in the shallow
waters, produced high resolution maps of the distribution of the shallow-water marine benthic
habitats (<15 m depth) and examined a range of management scenarios where such data could
assist with management of the Rottnest Island Reserve.
During the year, Lynnath Beckley continued her collaborative work with marine conservation planners
and biological oceanographers, led by Prof Hugh Possingham’s group at the University of Queensland
and a multi-authored paper on pelagic protected areas was published in the high impact journal
Trends in Ecology & Evolution. Another multi-authored manuscript, using the dynamic pelagic
ecosystem of the Benguela region off southern Africa as a case study for pelagic conservation, has
been submitted for publication.
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3.2 d) Species of conservation significance
Cetacean Research
The members of Murdoch University’s Cetacean Research Unit (MUCRU), within the Centre for Fish
and Fisheries Research, work on both applied and empirical conservation-based research projects.
This includes assessing abundance and habitat use of a variety of dolphin populations, analysing
cetacean social structure and mitigating against dolphin by-catch. Other areas of research include
foraging ecology, population genetics and assessment of anthropogenic impacts on cetaceans
through development and tourism. In 2009, we further expanded our research program and
collaborations, and strengthened existing partnerships with industry and government agencies.
Group members and collaborators:
As of December 2009, Murdoch University’s Cetacean Research Unit consisted of Simon Allen
(Research Fellow), Research Leader Dr Lars Bejder (Research Leadership Fellow), Valissa Buchanan
(MSc candidate), Claire Daniel (PhD student through UNSW), Dr Hugh Finn, Vanessa Jaiteh (Honours
student), Shannon McCluskey (PhD candidate), Holly Smith (PhD candidate) and Julian Tyne (PhD
candidate). Murdoch University collaborators include: Profs Stuart Bradley and Neil Loneragan;
Dr Kate Bryant; Ms. Bec Donaldson; Dr Carly Holyoake; and Dr Nahiid Stephens.
External collaborators include: Dr Padraig Duignan (University of Melbourne), Prof James Higham
(University of Otago), Associate Prof Dave Johnson (Duke University), Dr Michael Krützen (University
of Zürich; Adjunct Prof Murdoch University), Dr David Lusseau (University of Aberdeen), Associate
Prof Peter Madsen (University of Aarhus, Denmark; Adjunct Prof Murdoch University), Associate
Prof Doug Nowacek (Duke University), Dr Guido Parra (Flinders University), Dr Chandra Salgado
(Curtin University), Associate Prof William Sherwin (University of New South Wales) and Dr Magnus
Wahlberg (University of Southern Denmark; Adjunct Prof Murdoch University).
Research Activities undertaken by MUCRU are as follows:
Marine Mammal Health research
In 2009, a “Marine Mammal Health Project” was initiated,
spearheaded by Dr Carly Holyoake. This project was
formed in collaboration between Murdoch University
Cetacean Research Unit and Murdoch University’s School
of Veterinary and Biomedical Sciences. The project strives
to assess and monitor the health of marine mammals in
Western Australia and, in doing so, supports both the
early detection of adverse impacts from natural and
anthropogenic pressures, and the ability to distinguish
between these different pressures. The project has the
following components: investigations of mortality events,
biomonitoring and tissue banking. As part of this work,
Post-mortem examinations of dead dolphins
Drs Holyoake, Stephens and Finn have been investigating
from the Swan River
the deaths of six dolphins within the Swan-Canning
Photo provided by MUCRU
Estuary in 2009, as well as the death/disappearance of
dolphins resident within the inner waters around Bunbury, based on post-mortem examinations and
analyses of histopathology, contaminants, water quality, and photo-identification data. Their research
involves close collaboration with the Swan River Trust and WA Department of Environment and
Conservation.
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RESEARCH ACTIVITIES cont…
Dolphin population abundance, habitat use, conservation genetics and prey species in the southwest:
Cetacean research in the south-west of WA in 2009 focused on bottlenose dolphins (Tursiops sp.).
The overall aim here 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). Four 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 Holly Smith).
This work includes mark-recapture techniques to estimate
dolphin population size. Holly has also been analysing 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.
Bottlenose dolphin tossing an octopus
Photo provided by Holly Smith
2) Investigate the factors affecting the distribution of dolphin prey species (PhD candidate Shannon
McCluskey).
Shannon’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.
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 a) a species identification of the dolphins in Bunbury and
wider south-west Western Australia and b) an estimation of the level of gene flow between dolphin
populations along the coast of south-western Western Australia.
and 4) Evaluate the viability of the local dolphin population using models and results from Projects 13 (PhD project - student to be appointed).
Baseline abundance and residency patterns of bottlenose dolphins, Tursiops sp., Binningup, Western
Australia
The Water Corporation is constructing a 100GL (per annum) reverse osmosis seawater desalination
plant north of Binningup in Western Australia. The Corporation is funding research into dolphin
abundance and residency/movement patterns near the proposed brine-saline water discharge site.
This research, carried out by MSc candidate Valissa Buchanan and Dr Lars Bejder, aims to obtain
baseline information on bottlenose dolphins near the proposed discharge site prior to the desalination
plant discharging the brine-saline water into the ocean. This will allow for future comparisons of
dolphin abundance, subsequent to the brine-saline water being discharged.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
Fisheries interaction:
Research Fellow Simon Allen and
Professor
Neil
Loneragan
have
recently completed their draft report
to FRDC on reducing dolphin bycatch
in the Pilbara trawl fishery. The
primary objectives of this research
were: (1) to conduct a fine-scale
analysis of spatial and temporal
aspects of dolphin bycatch and fishing
effort; (2) to evaluate dolphin
behaviour around trawl nets and the
efficacy of different net designs in
reducing the chance of harm and
mortality to dolphins; and (3) to
assess dolphin species identity and
population
structure
across
the
Bottlenose dolphins (Tursiops truncatus) feeding on fish
fishery-impacted
area.
In
escaping from a trawl net
collaboration with Simon Allen and Neil
Photo by Simon Allen
Loneragan, Vanessa Jaiteh will be
awarded her Honours degree on “An Assessment of Dolphin Behaviour and Bycatch Mitigation
Techniques in the Pilbara Finfish Trawl Fishery, Western Australia” in 2010.
Cultural transmission of tool-use in bottlenose dolphins:
Tool use in cetaceans has only been documented in one population – the bottlenose dolphin
population in Shark Bay, WA. Some of these dolphins use marine sponges as a protective glove to
protect their rostra when they probe for prey in the substrate. All “spongers” are maternally related –
they share the same mitochondrial DNA, which is transmitted only through the female line. Research
Fellow Simon Allen, graduate student Julian Tyne and Dr Bejder of MUCRU are collaborating with
Dr Michael Krützen (University of Zürich) and Assoc. Prof. William Sherwin (University of New South
Wales) to discern whether tool-use is a genetic trait, governed by ecological factors or transmitted
culturally (through social learning by offspring from their mothers).
Population Consequences of Acoustic Disturbances
Acoustic disturbance of marine mammals has become a topic of great concern and interest to
biologists and managers worldwide. In 2009, Deirdre McElligott and Lars Bejder completed a
literature review into the effects of noise on wildlife. Previously, the National Research Council
developed a conceptual framework, the Population Consequences of Acoustic Disturbance (PCAD), to
tackle the difficult task of tracing acoustic disturbance through the life history of a marine mammal
and then to determine the consequences for the population. The concept of the model was designed
to serve as a guideline which may eventually enable researchers to relate marine mammal
behavioural responses caused by man-made noise to long term viability of the exposed population.
This literature review aimed to identify current knowledge and data gaps in each section of the PCAD
model and illustrate where research is most needed. This research effort was a collaborative effort
with Associate Prof Doug Nowacek and Dr Dave Johnston (Duke University, USA).
Little penguins research
Population viability analysis of the Perth metropolitan population of little penguins involves Professors
Stuart Bradley and Ron Wooller, and Dr Belinda Cannell at Murdoch University, in collaboration with
Professor William Sherwin and Dr Jennifer Sinclair at UNSW. Recently Professor Ken Pollock has been
collaborating with us to develop estimates of population size on the islands.
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RESEARCH ACTIVITIES cont…
Little Penguins in Perth Metropolitan waters are an important ecotourism and natural resource for
WA. They breed on Penguin and Garden islands. They forage in waters heavily impacted by
commercial and recreational vessels, and bounded by heavy industry. This project is using genetic,
demographic and movement data to model the population and predict its viability in the face of a
range of threats from human activities. The model will enable management strategies to be
evaluated to secure the future of the population.
The project has been funded by the Australian Research Council Linkage Scheme, Department of
Environment and Conservation, Fremantle Ports, Department of Defence, Tiwest and Winifred Violet
Scott Estate Trust Fund. This is the final year of the project.
The following activities were completed in 2009
1.
Nestboxes on Penguin Island were checked fortnightly to obtain information including timing
and success of breeding, body condition and mortality rates.
2.
Satellite tags were successfully deployed on 17 penguins from Penguin Island and one
penguin from Garden Island. Tags were attached to penguins during the incubation period,
giving insight into the foraging areas of penguins when they can remain at sea for five or
more days.
3.
Unmarked penguins continued to be marked with microchips in 2009. An island-wide
estimate of the population has been determined for 2007 and 2008. Survival analyses are
underway.
4.
More community members were recruited
for walking the foreshores looking for dead
penguins. 23 dead penguins were found at
sites either on Penguin Island or on the
foreshores of the mainland. Autopsies were
performed on 17 penguins.
5.
To determine if the Little Penguin on Penguin
Island are genetically distinct from other
colonies, we analysed over 200 penguin
blood samples from colonies in Perth, Albany
and
the
Recherche
Archipelago.
Microsatellite analyses showed that the
populations near Perth are significantly
differentiated from the other WA populations.
Little Penguin
Photo provided by Belinda Cannell
6.
Blood samples were collected from more parents and chicks on Penguin Island for assessing
genetic parentage. DNA sexing using 3 primers, 2945F, cfR and 3224R showed a sex ratio of
F:M 1.1:1.
7.
Preliminary PVA modelling was initiated based on data collected from other populations of
little penguins and other closely related species. This preliminary work suggests that the
population appears to be at serious risk of extinction. However, the results from this
preliminary modelling also suggest that a satisfactory baseline model needs robust estimates
of breeding success and age-related mortality (from the final results for Aim1). The complete
demographic dataset has been formatted in a database management system throughout
2009, to allow for the final simulations to be completed.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
Whale Shark Research
Whale shark research by Brad Norman and ECOCEAN continued in the Ningaloo Marine Park (NMP)
throughout 2009, which was one of the best whale shark ‘seasons’ on record.
The photoidentification monitoring program coordinated by Brad through ECOCEAN, in collaboration with
Murdoch University, was successful in identifying a total of 193 individual whale sharks in 2009. Of
these individuals, 112 had been sighted in previous years at NMP (see Holberg et al., 2009), and 91
were ‘new’ and previously unrecorded individuals.
Brad continued his collaboration with Professor Rory Wilson (University of Swansea) and PhD student
Adrian Gleiss to deploy innovative data-logging tags, known as ‘Daily Diaries’, on Whale Sharks (see
Gleiss et al., 2009). These studies, with Dr David Morgan, are providing fine scale information on the
movement, physiology and environment of Whale Sharks. Research in collaboration with Curtin
University, ECOCEAN and the Earthwatch Institute, also investigated the visitor expenditure and
satisfaction with the whale shark ecotourism industry at Ningaloo (see Jones et al. 2009).
In 2009, Brad obtained funding from the Thyne Reid Education Trust, to secure two Honours
Scholarships (the Thyne Reid ECOCEAN Scholarships) for Murdoch University. The scholarships were
awarded to Rowena Burch and Vanessa Jaiteh – both of whom have successfully completed their
studies at Murdoch.
The Whale Shark program on increasing public awareness of the conservation concerns facing this
species and engaging the wider public in the global Whale Whark ‘citizen science’ photo-identification
monitoring project, managed by Brad Norman through ECOCEAN, was awarded the WA Science
Award ‘Science Outreach Program of the Year’ for 2009. Brad Norman was awarded the 2009 Perth
Convention Bureau Murdoch University Professional Development Scholarship to attend the annual
meeting of the Society for Conservation Biology in China and share his latest research findings, and
provide the opportunity to build relations with the authorities and encourage monitoring and
ultimately protection for Whale Sharks in China, one of the only countries that still hunts this species.
3.3
Biological processes and evolution
3.3 a) Growth, reproduction and feeding
Fish population biology studies
The acquisition of sound quantitative data for the biological characteristics of fish species, such as
their age and growth, reproductive biology and diet, has been a major focus of staff and students in
the CFFR for many years. These data have been used to explore the environmental and
anthropogenic factors that influence those characteristics and the evolutionary significance of
differences in the biology of both closely-related and distantly-related species. They have also been
used for stock assessment and modelling.
During 2009, biological studies continued in marine waters on the Samson Fish Seriola hippos, the
Foxfish Bodianus frenchii, the Orange Roughy Hoplostethus atlanticus and three species of cooccurring wrasse, Coris auricularis, Notolabrus parilus and Opthalmolepis lineolatus. The
corresponding studies in estuaries focussed on the Western-Striped Trumpeter Pelates octolineatus,
the Black Bream Acanthopagrus butcheri, the Estuary Cobbler Cnidoglanis macrocephalus, the King
George Whiting Sillaginodes punctata, the Australian Herring Arripis georgianus, the Yelloweye Mullet
Aldrichetta forsteri and the Sea Mullet Mugil cephalus. In addition, studies on two ray species, the
Western Shovelnose Ray Aptychotrema vincentiana and the Southern Eagle Ray Myliobatis australis,
and on two shark species, the Port Jackson Shark Heterodontus portusjacksoni and the Australian
Angelshark Squatina australis are nearing completion. The staff supervising these projects gratefully
acknowledge the crucial role of Honours and PhD students in these studies. Details are given below of
the studies of some of the above species.
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RESEARCH ACTIVITIES cont…
The biology and spawning aggregations of Samson Fish on the lower west coast of Australia were
studied by Andrew Rowland, supervised by Dr Howard Gill and by Dr Mike Mackie of the Department
of Fisheries, Western Australia. Their tagging studies showed that Samson Fish return to the same
spawning sites each year and at a very similar time, i.e. with a single week! They also discovered
that some Samson Fish can move very large distances, i.e. as far as from Fremantle on the lower
west coast of Australia to Kangaroo Island off the coast of South Australia, and that such movements
can occur within two months. During his studies, Andrew discovered that Samson Fish possess a
unique type of swim bladder, which enables this species to make rapid vertical movements without
suffering barotrauma-related injuries. Following the recent submission of his PhD, Andrew
commenced work at RecFishWest as a Regional Policy Officer.
Alan Cottingham recently commenced his PhD, during which he will develop aspects of the Black
Bream studies in the Swan-Canning Estuary, Perth, that formed the basis for his Honours thesis. He
will be supervised by Dr Alex Hesp and Prof Norm Hall. Alan is focussing on elucidating the factors
that have led to remarkable short-term changes in the biological characteristics of Black Bream in the
above estuary and on developing a cost-effective approach for monitoring the health of this sparid in
estuaries. Alan has also recently become involved in a project aimed at monitoring the progress of
restocked Black Bream in the Blackwood River Estuary. Hatchery-reared black bream, which were
spawned in 2001 and 2002 and whose otoliths had been marked with the chemical stain Alizarin
complexone, were released into the Blackwood River Estuary as small juveniles. Staff and students of
the CFFR, together with Greg Jenkins of Fremantle TAFE, have been monitoring the subsequent
progress of those fish. Recent results indicate that the females of the restocked fish are performing
as well as wild fish, i.e. they are growing at a similar rate and reaching maturity at a similar length
and age. Our studies thus demonstrate that restocking has a great potential to replenish the stocks
of black bream that have been severely depleted. The studies were initially funded by FRDC and
more recently by the Development and Better Interest Fund, the Department of Fisheries Western
Australia and the West Australian Fish Foundation (WAFF).
The biology of the Western Striped Trumpeter in estuarine and coastal marine waters near Perth is
being studied by PhD student Lauren Veale, who is being supervised for this aspect of her thesis by
Prof Ian Potter and Dr Peter Coulson. Lauren has now sampled this terapontid for over six
consecutive months using seine netting and line fishing and has started ageing and determining the
reproductive status of a wide size range of individuals. Her studies will focus, in particular, on
determining the relationship between the assemblages of this marine species in the Peel-Harvey
estuary and those in nearby coastal marine waters. Lauren’s studies are being conducted under the
umbrella of grants from WAMSI and the South West Development Council (SWDC).
A study of the biology of Black Bream and Estuary Cobbler in estuaries on the south coast of Western
Australia has recently been submitted by Ben Chuwen. Congratulations to Ben for his innovative
studies, which were supervised by Ian Potter and Norm Hall. Ben is continuing to study the status of
the stock of Estuary Cobbler in Wilson Inlet, a seasonally-open estuary on the south coast of Western
Australia, which supports the largest commercial fishery for this species in the state. A comparison of
contemporary data with those collected during the 1980s strongly indicate that the abundance of
Estuary Cobbler in Wilson Inlet has declined markedly since that time, a conclusion consistent with
the increase that has occurred in mortality rate.
The analysis of the results of biological studies of three species of wrasse in south-western Australian
coastal marine waters, which was undertaken by Elaine Lek for her PhD studies, is now being
finalised by Elaine for her thesis.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
This study, which is being supervised by Dr David
Fairclough (Department of Fisheries, Western
Australia) and Prof Ian Potter, was financially
supported by the Strategic Research Fund for the
Marine Environment (SRFME). The three labrid
species, Western King, Brown-spotted Southern
Maori wrasses are all of similar size (maximum
recorded lengths = 40-49 cm) and abundant over
temperate limestone reefs. Elaine has found that
each of these species live for about 10 years and
are protogynous hermaphrodites. The three
species feed on a wide range of prey, and
particularly benthic invertebrates (crustaceans
and gastropods).
A school of Southern Maori Wrasse, Ophthalmolepis
lineolatus, and a Western King Wrasse, Coris auricularis
Photo provided by Elaine Lek
Ashlee Jones, who is being supervised for her PhD by Ian Potter and Norm Hall, has been studying
the species compositions of elasmobranchs caught by commercial trawling, gillnetting and longlining
off the south-western coast of Australia. Her studies have quantified the contributions made by
bycatch and byproduct species to the total catch of elasmobranchs taken by each of these methods.
She is also studying aspects of the reproductive biology of the Port Jackson Shark, Western
Shovelnose Ray, Australian Angelshark and Southern Eagle Ray. By comparing the typical sizes at
maturity (L50) with the length-frequency distributions for the above four species, Ashlee showed that
over 90% of three of the above species taken by trawling, were caught before they had had the
potential to breed and often died before they could be returned to the water. The results of this study
have recently been accepted for publication in Fishery Bulletin.
Dietary studies
Diets of elasmobranch bycatch species
The diets of four elasmobranch species, which are abundant in the bycatch of certain commercial
fisheries in south-western Australia, were studied by Emma Sommerville for her honours project. This
study utilised the extensive samples of the sharks Heterodontus portusjacksoni and Squatina
australis and the rays Myliobatis australis and Aptychotrema vincentiana that had been collected by
Ashlee Jones for her PhD thesis. During the last two years, Emma’s data have been developed by
Emma, Margaret Platell, William White, Ashlee Jones and Ian Potter for publication. This study
demonstrated how food resources are partitioned among and within these four co-occurring species
and how the dietary composition of each species changed with season, body size and region and
differed with feeding mode. The diets of the four species were shown to differ markedly, with, for
example, the durophagous opportunist H. portusjacksoni ingesting a wide range of prey, including
gastropods, echinoderms and teleosts, whereas the specialist S. australis focused on teleosts and
cephalopods. The extent and pattern of change in dietary composition with increasing body size
varied among species, with, for example, the diet of H. portusjacksoni changing abruptly to larger,
harder-bodied prey at ~ 400 mm TL, whereas the changes in diet of S. australis were less
pronounced and more gradual. The dietary compositions of each species were shown to undergo
seasonal changes and those of M. australis and H. portusjacksoni on the lower west and south coasts
of Western Australia were found only to differ slightly. Inter- and intraspecific differences in dietary
composition would reduce the potential for competition for food among and within the four cooccurring elasmobranch species.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH ACTIVITIES cont…
Diets of temperate reef fishes
Dr Margaret Platell, Dr Alex Hesp and Prof Ian Potter collated and developed the results of three
studies on the diets of three medium to large targeted fish species, the Foxfish Bodianus frenchii, the
Breaksea Cod Epinephelides armatus and the West Australian Dhufish Glaucosoma hebraicum, which
co-occur over reefs in temperate waters of south-western Australia. The data on these species were
collected by Steve Cossington, Steve Moore and Elaine Lek for their honours studies. On the west
coast, Foxfish and Breaksea Cod spend their whole life over prominent limestone reefs, as does the
West Australian Dhufish in all but juvenile life, when it lives over low relief, limestone substrates. The
dietary composition of each species changed with increasing body size, which, in West Australian
Dhufish, was particularly pronounced at about 300 mm TL and therefore at the size when this species
shifts habitat. When the three species co-occurred over the same reefs, their dietary compositions
were significantly different, with that of the Foxfish being by far the most discrete, reflecting a far
greater ingestion of sedentary taxa. Thus, the diet of Foxfish was distinguished from those of the
other two species by containing substantial volumes of bivalve and gastropod molluscs and echinoid
echinoderms and essentially no teleosts. Although the diets of the West Australian Dhufish and
particularly Breaksea Cod were found to be dominated by teleosts, and especially those of their
larger individuals, the Dhufish ingested greater volumes of cephalopods and small crustaceans. The
pointed jaws of Foxfish, with their forwardly-directed and interlocking anterior incisors, are ideally
adapted for biting and retaining their invertebrate prey, which are attached to or reside within reef
crevices. In contrast, the mouths of the West Australian Dhufish and Breaksea Cod are broader and
rounder and contain numerous small, slender and inward-pointing teeth. The latter teeth, in
conjunction with prominent backward-curved canines in Breaksea Cod, facilitate the capture and
retention of fish prey.
Observations in situ indicate that the West Australian Dhufish is a suction feeder, while the Breaksea
Cod is predominantly a ram feeder. Although reef environments on the west and south coasts are
different, the diet of Foxfish on those coasts differed only slightly. Interspecific differences in diet,
combined with size-related changes in dietary compositions and the occupation of different habitats
by juvenile and adult West Australian Dhufish, reduces the potential for competition for food
resources among and within the individuals of Foxfish, West Australian Dhufish and Breaksea Cod
and thus helps facilitate the co-existence of these species, which historically have been abundant
over reefs in south-western Australia.
3.3 b) Genetics and evolution
A number of projects on the genetics and evolution of fish and shellfish species were conducted
during 2009.
Glenn Moore spent much of the year writing his PhD thesis on the “Aspects of the evolutionary
history of the Australasian fish family Arripidae (Australian Salmon)”. This study represents one of
only a few investigations into the evolutionary history of the temperature marine fauna of Australia.
The Eastern Australian Salmon (Arripis trutta) and Western Australian Salmon (A. truttaceus) in
particular, provide the opportunity to compare the evolutionary histories of very similar species on
the east and west coasts of Australia. Glenn’s results indicate that these two species, (together with
Giant Kahawai, A. xylabion) diverged from a common ancestor at about the same time in the mid- to
late-Pleistocene (ca. 650,000 to 700,000 years ago), which is relatively recent compared to the
estimated divergence time for some other ‘species pairs’ on the east and west coasts of Australia.
Subsequently both species appear to have undergone demographic contraction(s) and expansion(s),
probably in association with Pleistocene glacial cycles. Historical environmental data suggest that
these glacial cycles are likely to have had a much bigger impact on the temperate marine fauna on
the west coast of Australia compared to their east coast counterparts. This suggestion is supported
by Glenn’s genetic results as the Western Australian Salmon appears to have experienced a more
severe population contraction during the last glacial maximum (LGM) compared to the Eastern
Australian Salmon. Glenn’s supervisors are Dr Jennie Chaplin and Professor Ian Potter.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
Nicole Phillips entered the third year of her PhD research into the conservation genetics of three
species of sawfish (Pristis microdon, P. clavata and P. zijsron) in Australian waters. Thus far, Nicole’s
results indicate that each of these sawfish species exhibits population structuring and moderate to
low levels of genetic diversity within their Australian ranges. The results also indicate that dispersal
in one of these species, P. microdon, is strongly male-biased. This male-biased dispersal may be
related to the fact that this species uses the upper reaches of estuaries and freshwaters as a nursery
area, while the adults occur in estuarine and marine waters.
In particular, the females of
P. microdon may pup in the vicinity of their own birth site in order to increase the chances of their
offspring locating a suitable nursery area. The research is generating information that can be used to
help develop plans for the conservation of these critically endangered species. It is partially funded
by grants from the Department of Environment and Water Resources, Heritage and Arts, and is being
conducted in collaboration with Stirling Peverell (Queensland Department of Primary Industries and
Fisheries) and Dr Dean Thorburn. Nicole’s supervisors are Drs Jennie Chaplin and David Morgan.
Michelle Gardner commenced a genetic assessment of the stock structures of two important demersal
fish species, namely baldchin groper (Choerodon rubescens) and pink snapper (Pagrus auratus) in
Western Australia waters. This work will form the basis of her PhD thesis. Michelle’s preliminary
results indicate that each of these species is represented by a single stock or a series of overlapping
stocks within the west coast bioregion of Western Australia. The study is funded by WAMSI and
conducted in collaboration with the Department of Fisheries, in particular with Drs David Fairclough,
Gary Jackson and Brett Moloney.
Michelle (Shu) Lo commenced her Honours study in August 2009. Michelle is attempting to develop a
method that can be used to obtain genetic data from sawfish rostra that are over 100 years old, and
also from poorly preserved contemporary rostra. This study is the first step in a larger research
project that aims to generate information about the amount and distribution of genetic variation in
sawfish population prior to the occurrence of significant anthropogenic disturbances.
This is
important because assessments of the conservation statuses of these populations have been
hindered by a lack of information about the extent of anthropogenic impacts that have occurred,
which has in turn interfered with development of appropriate state and federal legislation required to
protect sawfish species throughout their Australian ranges. Michelle’s research is being supervised
by Dr Jennie Chaplin and assisted by Nicole Phillips, who is conducting her PhD research in this area.
Broderick Hosie conducted his Honours research during 2009. He used morphological data to
examine the relationships (connectivity) among assemblages of the blue-swimmer crab, Portunus
pelagicus, in the Swan River Estuary, Cockburn Sound, the Peel-Harvey Estuary and Comet Bay in
south-western Australia. The main catalyst for the study was a desire to understand the implications
of the closure of the fishery for P. pelagicus in Cockburn Sound on the assemblages of this species in
other nearby water bodies, as well as to test anecdotal claims that the individuals of this species in
the Swan River Estuary are relatively large. The results suggest that the sizes of male and females
of P. pelagicus in the Swan River Estuary and the adjacent Cockburn Sound are relatively large
compared to their same-sex counterparts in the Peel-Harvey Estuary and the adjacent Comet Bay.
These results could imply that there are restrictions in the movements of juvenile and adult crabs
between these two sets of water bodies, which is consistent with the results of some previous genetic
work. However, the size-differences could also be partly related to variation in the amount of fishing
effort among the sampled water bodies. The Department of Fisheries kindly provided the samples of
P. pelagicus for this study. Broderick’s supervisors were Drs Jennie Chaplin and Danielle Johnston
from the Department of Fisheries.
Ian Potter, Alex Hesp, Jennie Chaplin, Alan Cottingham, Nicole Phillips and Michelle Gardner, in
collaboration with Greg Jenkins (Challenger TAFE), continued work on a project investigating the
outcomes and implications of the restocking of the black bream, Acanthopagrus butcheri, in the
Blackwood River Estuary. The Western Australian Fish Foundation and a DBIF grant supported this
work (see also 3.3a above).
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Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH ACTIVITIES cont…
3.3 c) Lampreys
During the course of 2009, Dalal Haouchar continued the work of earlier students whose studies were
aimed at determining the complete sequence of the mitochondrial genome of representatives of both
of the Southern Hemisphere families of lampreys. Her work focused specifically on completing the
sequence for Mordacia mordax, which had posed a number of problems in the past. Dalal’s study
was supervised by Drs Howard Gill and Mike Bunce and greatly aided by Dr Matt Phillips from the
Australian National University.
Comparisons between the complete sequence of mitochondrial DNA for Mordacia mordax
(Mordaciidae) and Geotria australis (Geotriidae) and those of two divergent Northern Hemisphere
genera within the Petromyzontidae demonstrate that the order of genes in the mitochondrial DNA is
the same in all lampreys. However, it differs from those of all other vertebrates in that their control
region comprises two separate components. The results of the mtDNA studies indicate that the
Mordaciidae diverged from the group comprising the Geotriidae and Petromyzontidae approximately
150 million years ago (MYA) and that the latter two families diverged about 100 MYA.
Karen Marshall (nee Paton), who was
supervised by Professors Max Cake and Ian
Potter, continued her PhD studies in a parttime capacity despite having to relocate to
Canberra with her employment. Her studies
have focussed on the metabolic responses to
strenuous exercise of adults of the Southern
hemisphere lamprey G. australis at the
commencement of their non-feeding, upstream
spawning migration and at maturity 12 - 14
months later. Lampreys were sacrificed prior to
and
after
being
stimulated
to
swim
continuously for 12 min and at intervals during
a 3h recovery period. In early
migrants, muscle glycogen was
markedly depleted during exercise,
but became rapidly replenished, a
change inversely correlated with
serum but not muscle lactate
concentrations, the latter of which
remained elevated. These trends
were
paralleled
in
prespawning
females, but not mature males, in
Adults of the lamprey Mordacia mordax caught early in their upstream
spawning migration in Victoria
which those variables changed little
Photos by Tarmo Raadik
during the exercise/recovery regime.
As serum fatty acids declined and muscle glycogen remained high in mature males following exercise,
lipid provides the main energy source for these animals. At maturity, the glycogen declined to very
low levels in females, which then depended on lipid for energy. Trends exhibited by serum alanine
concentrations imply that protein is preserved early in the migration and catabolised extensively at
maturity. In summary, G. australis employs anaerobic glycogen metabolism for energy production
during the early stages of its upstream migration, whereas, at spawning, males employ largely
aerobic respiration of lipid and females deplete their glycogen and subsequently rely on lipid. The
ability of lampreys to modify greatly their metabolic responses to accommodate the various energy
demands they encounter at different stages of their life cycle, would have contributed to the great
success of this agnathan group in temperate waters.
Page 34
Centre for Fish and Fisheries Research - Annual Research Report 2009
Prof Ian Potter will be continuing to collaborate with Prof Shaun Collin and his colleagues in studies of
the eyes of Southern Hemisphere lampreys. Their earlier work demonstrated that the characteristics
of the eyes of G. australis are ideally adapted for living in the surface waters of the ocean, where
they are found during their marine trophic phase. They found that G. australis possesses five conelike photoreceptors that are adapted for bright light vision. In contrast, M. mordax, which is highly
photophobic, possesses an eye with only a single and very large rod-like photoreceptor. Future work
will concentrate on exploring, in greater detail, the differences between the divergent eyes of these
two species and the influence of the pineal organ on behaviour. These studies have profound
implications for our understanding of vision and visual ecology in these representatives of the earliest
vertebrates. Collaboration on the lamprey work will be facilitated by the fact that Shaun Collin is
now based in Perth, having been appointed as a WA Premier’s Fellow.
Page 35
Centre for Fish and Fisheries Research - Annual Research Report 2009
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Centre for Fish and Fisheries Research - Annual Research Report 2009
PUBLICATIONS
4. PUBLICATIONS for 2009
Coastal Wetlands: An Integrated
Ecosystem Approach. Elsevier.
Teaching Publications
Books
Christensen,
J.
2009.
Recreational Fishing, in J.
Gregory and J. Gothard
eds.
Historical
Encyclopaedia of Western.
Australia
Crawley:
The
University
of
Western
Australia Press
Wells, F.E., McDonald, J.I. &
Huisman,
J.M.
2009.
Introduced Marine Species
in
Western
Australia.
Fisheries
Occasional
Publications No. 57, Dept
of Fisheries, Perth. ii + 97
pp
Book chapters
Hallegraeff, G.M., Bolch, C.J.S., Huisman, J.M.
& de Salas, M.F. In press. Planktonic
dinoflagellates. In: Hallegraeff, G.M.,
Bolch, C.J., Hill, D.R.A., Jameson, I.,
LeRoi, J.-M., McMinn, A., Murray, S., de
Salas, M. & Saunders, K. Algae of
Australia: Phytoplankton Flora of
Temperate Australian Coastal Waters.
ABRS, Canberra, CSIRO Publishing,
Melbourne, Australia.
Lang, N.J., Roe, K.J., Renaud, C.B., Gill, H.S.,
Potter, I.C., Freyhof, J., Naseka, A.M.,
Cochran, P., Espinosa Perez, H., Habit,
E.M., Kuhajda, B.R., Neely, D.A.,
Reshetnikov, Y.S., Salnikov, V.B.,
Stoumboudi, MTh. & Mayden, R.L. 2009.
Novel Relationships among Lampreys
(Petromyzontiformes) revealed by a
Taxonomically comprehensive Molecular
Data Set. Biology, Management, and
Conservation of Lampreys in North
America, American Fisheries Society, North
America, 72, 41-55.
Paling, E.I., Fonseca, M., van Katwijk, M.M. &
van Keulen, M. 2009. Seagrass
restoration. In: Perillo, G.M.E., Wolanski,
E., Cahoon, D.R., Brinson, M.M., editors,
Bowen, B., Van Keulen, M. & McComb, J.
2009. Plant diversity 1 - the greening of
the land. In: Calver, M., Lymbery, A.,
McComb, J. and Bamford, M. (Eds)
Environmental Biology. Cambridge
University Press, pp. 228-252.
Burgess, T., Twomey, L. 2009. Mysterious
diversity - the protists (including the
fungi). In: Calver, M., Lymbery, A.,
McComb, J. and Bamford, M. (Eds)
Environmental Biology. Cambridge
University Press, pp. 202-227.
Calver, M. & Bradley, J.B. 2009. Boom and
bust - population ecology. In: Calver, M.,
Lymbery, A., McComb, J. and Bamford, M.
(Eds) Environmental Biology. Cambridge
University Press, pp. 363-383.
Calver, M. & Lymbery, A. 2009. Life on the
move I – introducing animal diversity. In:
Calver, M., Lymbery, A., McComb, J. and
Bamford, M. (Eds) Environmental Biology.
Cambridge University Press, pp. 286-303.
Calver, M., Lymbery, A. & McComb, J. 2009.
Environmental biology and our time. In:
Calver, M., Lymbery, A., McComb, J. and
Bamford, M. (Eds) Environmental Biology.
Cambridge University Press, pp. 2-20.
Calver, M., Lymbery, A. & McComb, J. 2009. A
natural legacy. In: Calver, M., Lymbery, A.,
McComb, J. and Bamford, M. (Eds)
Environmental Biology. Cambridge
University Press, pp. 601-618.
Calver, M., Lymbery, A., McComb, J. &
Bamford, M. (Editors). 2009. Environmental
Biology. Cambridge University Press.
Lymbery, A. & Ayre, D. 2009. Evolutionary
theory – the origin and fate of genetic
variation. In: Calver, M., Lymbery, A.,
McComb, J. and Bamford, M. (Eds)
Environmental Biology. Cambridge
University Press, pp. 113-137.
Lymbery, A. & Calver, M. 2009. Life on the
move II - the spineless majority. In: Calver,
M., Lymbery, A., McComb, J. and Bamford,
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Centre for Fish and Fisheries Research - Annual Research Report 2009
PUBLICATIONS cont…
M. (Eds) Environmental Biology. Cambridge
University Press, pp.304-334.
Lymbery, A. & Gill, H. 2009. Coping with
cornucopia - classifying and naming
biodiversity. In: Calver, M., Lymbery, A.,
McComb, J. and Bamford, M. (Eds)
Environmental Biology. Cambridge
University Press, pp.160-181.
Refereed publications in 2009
Allen, E., Sinclair, D., Allen, S. & Peters, R.
2009. Amphibolurus muricatus (Jacky
dragon). Avian Predation. Herpetological
Review 40: 82-83.
Averis, S., Thompson, R.C.A, Lymbery, A.J.,
Wayne, A.F., Morris, K.D. & Smith, A.
2009. The diversity, distribution and hostparasite associations of trypanosomes in
Western Australian wildlife. Parasitology
136: 1269-1279.
Bartels, H., Schmiedl, A., Rosenbruch, J. &
Potter, I.C. 2009. Exposure of the gill
epithelial cells of larval lampreys to an iondeficient environment: a stereological
study. Journal of Electron Microscopy 58
(4): 253-260.
Bearham, D., Spiers, Z., Raidal, S.R., Jones,
J.B. and Nicholls, P.K. 2009. Detection of
Minchinia occulta in samples of pearl
oysters Pinctada maxima (Jameson, 1901)
infected
by
Haplosporidium
hinei.
Australian Veterinary Journal 87: 430-437.
Beckley, L.E., Muhling, B.A. & Gaughan, D.J.
2009. Larval fishes off Western Australia:
influence of the Leeuwin Current. Journal
of the Royal Society of Western Australia
92: 101-109.
Bejder, L., Samuels, A., Whitehead, H., Finn,
H. and Allen., S. 2009. Impact assessment
research: use and misuse of habituation,
sensitisation and tolerance to describe
wildlife responses to anthropogenic stimuli.
Marine Ecology Progress Series. 395: 177185.
Chapman, A., Morgan, D.L. and Gill, H.S.
2009.
Description
of
the
larval
development of Galaxias maculatus in
landlocked lentic and lotic systems in
Western Australia. New Zealand Journal of
Marine and Freshwater Research 43: 563569.
Chuwen, B.M., Hoeksema, S.D. & Potter, I.C.
2009
Factors
influencing
the
characteristics of the fish faunas in
offshore, deeper waters of permanentlyopen, seasonally-open and normally-closed
estuaries. Estuarine Coastal and Shelf
Science 81 (3): 279-295.
Chuwen, B.M., Hoeksema, S.D. & Potter, I.C.
2009.
The
divergent
environmental
characteristics
of
permanently-open,
seasonally-open
and
normally-closed
estuaries of south-western Australia.
Estuarine Coastal and Shelf Science 85:
12-21.
Coulson, P.G., Hesp, S.A., Hall, N.G. & Potter,
I.C. 2009. The western blue groper
(Achoerodus
gouldii),
a
protogynous
hermaphroditic labrid with exceptional
longevity, late maturity, slow growth, and
both late maturation and sex change.
Fishery Bulletin 107 (1): 57-75.
Finn, H. 2009. Regenesis. Pacific Conservation
Biology 15: 230.
Game, E.T., Grantham, H. S., Hobday, A.J.,
Pressey, R. L., Lombard, A. T., Beckley, L.
E., Gjerde, K., Bustamante, R.,
Possingham, H.P. & Richardson, A.J. 2009.
Pelagic protected areas: the missing
dimension in ocean conservation. Trends
in Ecology & Evolution 24(7): 360-369.
Gleiss, A.C., Norman, B., Liebsch, N., Francis,
C. & Wilson, R.P. 2009. A new prospect for
tagging large free-swimming sharks with
motion-sensitive data-loggers. Fisheries
Research 97: 11-16.
Hassan, M., Jones, B. & Lymbery, A.J. 2009. A
new species of Dermoergasilus Ho & Do,
1982
(Copepoda:
Ergasilidae)
from
freshwater fishes in the south-west of
Western Australia. Systematic Parasitology
74: 143-148.
Higham, J., Bejder, L. & Lusseau. 2009. An
integrated and adaptive management
model to address the long-term
sustainability of tourist interactions with
cetaceans, Environmental Conservation:
Page 38
Centre for Fish and Fisheries Research - Annual Research Report 2009
an international journal of environmental
science 35: 294-302.
Hoeksema, S.D., Chuwen, B.M. & Potter, I.C.
2009. Comparisons between the
characteristics of ichthyofaunas in
nearshore waters of five estuaries with
varying degrees of connectivity with the
ocean. Estuarine Coastal and Shelf Science
85: 22-35.
Holberg, J., Norman, B. & Arzoumanian, Z.
2009. Estimating population size,
structure, and residency time for Whale
Sharks Rhincodon typus through
collaborative photo-identification.
Endangered Species Research 7: 39-53.
Horn, L. E., Paling, E. I. & van Keulen, M.
2009.
Photosynthetic
recovery
of
transplanted Posidonia sinuosa, Western
Australia. Aquatic Botany 90 (2): 149-156.
Hourston, M., Potter, I.C., Warwick, R.M.,
Valesini, F.J. & Clarke, K.R. 2009. Spatial
and seasonal variations in the ecological
characteristics of the free-living nematode
assemblages in a large microtidal estuary.
Estuarine Coastal and Shelf Science 82:
309-322.
Huisman, J.M., Phillips, J.C. & Freshwater,
D.W. 2009. Rediscovery of Gelidiella
ramellosa from near the type locality in
Western Australia. Cryptogamie, Algologie
30: 1-14.
Huisman, J.M., Leliaert, F., Verbruggen, H., &
Townsend, R.A. 2009. Marine Benthic
Plants of Western Australia’s Shelf-Edge
Atolls. Records of the Western Australian
Museum Supplement 77: 50-87.
Jensen, F.H., Bejder, L., Wahlberg, M. &
Madsen, P.T. 2009. Biosonar adjustments
to target range of echolocating bottlenose
dolphins (Tursiops sp) in the wild. Journal
of Experimental Biology: 212: 1078-1086.
doi:10.1242/jeb.025619.
Jensen, F.H., Bejder, L., Wahlberg, M.,
Johnson, M., Aguilar Soto, N. & Madsen,
P.T. 2009. Masking of delphinid
communication by small vessels. Marine
Ecology Progress Series. 395: 161-175.
Jones, A.J. & Potter, I.C. 2009. Description of
the reproductive tract and gonad histology
of a second form of hermaphroditism in
the Port Jackson shark Heterodontus
portusjacksoni, Journal of the Marine
Biological Association of the UK, 89(7):
1403-1407.
Jones, T., Wood, D., Catlin, J. & Norman, B.
2009. Expenditure and ecotourism:
predictors of expenditure for whale shark
tour participants. Journal of Ecotourism 8:
32-50.
Morgan, D.L. 2009. Threatened fishes of the
world: Nannatherina balstoni Regan 1906
(Nannopercidae). Environmental Biology of
Fishes 84: 409-410.
Ochwada, F., Loneragan, N.R., Gray, C.A.,
Suthers, I.M. & Taylor, M.D. 2009.
Complexity affects habitat preference and
predation mortality in postlarval Penaeus
plebejus: implications for stock
enhancement. Marine Ecology Progress
Series 380: 161-171.
Peters, R. & Allen, S. 2009. Movement signal
choreography unaffected by receiver
distance in the Australian Jacky lizard,
Amphibolurus muricatus. Behavioural
Ecology & Sociobiology 63: 1593–1602.
Phillips, N., Chaplin, J., Morgan, D. & Peverell,
S. 2009. Extraction and amplification of
DNA from the dried rostra of sawfishes
(Pristidae) for applications in conservation
genetics. Pacific Conservation Biology 15:
128-134.
Phillips, J.C., & Huisman, J.M. 2009. Influence
of the Leeuwin Current on the Marine Biota
of the Houtman Abrolhos. Journal of the
Royal Society of Western Australia 92:
139-146.
Pueschel, C.M., Huisman, J.M. 2009.
Observations of Pihiella liagoraciphila
(Pihiellales, Rhodophyta). Phycologia
49(1): 42-47.
Renaud, C.B., Gill, H.S. & Potter, I.C. 2009.
Relationships between the diets and
characteristics of the dentition, buccal
glands and velar tentacles of the adults of
the parasitic species of lamprey. Journal of
Zoology 278: 231-242.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
PUBLICATIONS cont…
Smallwood, C.B. & Beckley, L.E. 2009.
Benchmarking recreational boating
pressure in the Rottnest Island Reserve,
Western Australia. Tourism in Marine
Environments 5(4): 301-317.
Westera, M.A., Phillips, J.C., Coupland, G.T.,
Grochowski, A.J., Harvey, E.S. & Huisman,
J.M. 2009. Sea surface temperatures of
the Leeuwin Current in the Capes region of
Western Australia: potential effects on the
marine biota of shallow reefs. Journal of
the Royal Society of Western Australia 92:
197-210.
Whitty, J.M., Morgan, D.L., Peverell, S.C.,
Thorburn, D.C. & Beatty, S.J. 2009.
Ontogenetic depth partitioning by juvenile
freshwater sawfish (Pristis microdon:
Pristidae) in a riverine environment.
Marine and Freshwater Research 60: 306316.
Wildsmith, M.D., Rose, T.H., Potter, I.C.,
Warwick, R.M., Clarke, K.R. & Valesini, F.J.
2009. Changes in the benthic
macroinvertebrate fauna of a large
microtidal estuary following extreme
modifications aimed at reducing
eutrophication. Marine Pollution Bulletin
58: 1250-1262.
Wiszniewski, J., Allen, S.J., & Moller, L.M.
2009. Social cohesion in a hierarchically
structured embayment population of IndoPacific bottlenose dolphins. Animal
Behaviour 77 (6): 1449-1457.
Wiszniewski, J., Beheregaray, L.B., Allen, S.J.
& Möller, L.M. 2009. Environmental and
social influences on the genetic structure
of bottlenose dolphins (Tursiops aduncus)
of south-eastern Australia. Conservation
Genetics DOI 10.1007/s10592-009-9968z.
Wynen, L., Larson, H., Thorburn, D., Peverell,
S., Morgan, D., Field, I. & Gibb, K. 2009.
Mitochondrial DNA supports the
identification of two endangered river
sharks (Glyphis glyhpis and Glyphis
garricki) across northern Australia. Marine
and Freshwater Research 60: 554-562.
Refereed publications in 2010 and
in press
Allen, S., Bejder, L. & Krützen, M. Accepted.
Indo-Pacific bottlenose dolphins (Tursiops
sp.) carrying conk shells (Turbinella sp.) in
Shark Bay, Western Australia? Marine
Mammal Science.
Allen, S., Constantine, R., Bejder, L., Waples,
K. & Harcourt, R. Accepted. Can't sleep,
can't eat - let's split: Indo-Pacific
bottlenose dolphin responses to tour boats
in Port Stephens, Australia. Journal of
Cetacean Research and Management.
Allen, S., Samuels, A., Constantine, R. &
Bejder, L. Accepted. Dolphin and whale
watching around Australia: Is it
'Ecotourism'? Tourism in Marine
Environments.
Beatty, S.J. & Morgan, D.L. 2010. Teleosts,
agnathans and macroinvertebrates as
bioindicators of ecosystem health in a
south-western Australian River. Journal of
the Royal Society of Western Australia 93:
65-79.
Beatty, S.J., Morgan, D.L., McAleer, F.J. &
Ramsay, A. 2010. Importance of
groundwater intrusion in maintaining
migratory routes of Tandanus bostocki
(Teleostei; Plotosidae) in a secondarily
salinised river in Western Australia.
Ecology of Freshwater Fish 19: 1-14.
Catlin, J., Jones, R., Jones, T., Norman, B. &
Wood, D. 2010. Discovering Wildlife
Tourism: A Whale Shark Tourism Case
Study. Current Issues in Tourism 13: 351361.
Catlin, J., Jones, T., Norman, B. & Wood, D.
2010. Consolidation in a wildlife tourism
industry: the changing impact of whale
shark tourist expenditure in the Ningaloo
Coast region. International Journal of
Tourism Research 12: 134-148.
Davis, A.M., Pearson, R.G., Pusey, B.J., Perna,
C., Morgan, D.L. & Burrows, D. In press.
Trophic ecology of northern Australia’s
terapontids: ontogenetic dietary shifts
and feeding classification. Journal of Fish
Biology.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
Davis, A.M., Pusey, B.J., Thorburn, D.C.,
Dowe, J.L., Morgan, D.L. & Burrows, D.
2010. Riparian contributions to the diet of
terapontid grunters (Pisces: Terapontidae)
in wet-dry tropical rivers. Journal of Fish
Biology 76: 862-879.
Donaldson, R., Finn, H., & Calver, M. In press.
Illegal feeding increases risk of boat-strike
and entanglement in bottlenose dolphins.
Pacific Conservation Biology.
Doupé, R.G., Mitchell, J., Knott, M. J., Davis,
A. M. & Lymbery, A.J. 2010. Efficacy of
exclusion fencing to protect ephemeral
floodplain lagoon habitats from feral pigs
(Sus scrofa). Wetlands Ecology and
Management 18: 69-78.
Doupé, R.G., Knott, M. J., Schaffer, J.,
Burrows, D.W. & Lymbery, A.J. 2010.
Experimental
herbivory
of
native
Australian macrophytes by the introduced
Mozambique
tilapia
Oreochromis
mossambicus. Austral Ecology 35: 24-30.
Frère, C.H., Krützen, M., Mann, J., Connor, R.,
Bejder, L. & Sherwin W.B. In press. Home
range overlap, matrilineal, and biparental
kinship drive female associations in East
Shark Bay bottlenose dolphins. Animal
Behaviour.
Huisman, J.M., De Clerck, O., Prud’homme
van Reine, W.F. & Borowitzka, M.A. In
press. Spongophloea, a new genus of red
algae based on Thamnoclonium sect.
Nematophorae Weber-van Bosse
(Halymeniales). European Journal of
Phycology.
Klunzinger, M.W., Morgan, D.L., Lymbery,
A.J., Ebner, B.C., Beatty, S.J., & Thomson,
G.J., A.J. In press. Discovery of a host for
glochidia of Velesuni angasi (Sowerby,
1867) (Bivalvia: Unionoida: Hyriidae) from
the Fortescue River, Pilbara, Western
Australia. Australian Journal of Zoology.
Freshwater fish introductions in
mediterranean-climate regions: are there
commonalities in the conservation
problem? Diversity and Distributions 16:
606-619.
Morgan, D.L. 2010. Fishes of the King Edward
River in the Kimberley region, Western
Australia. Records of the Western
Australian Museum 25:351-368.
Morgan, D.L., Allen, G.R., Pusey, B.J. &
Burrows, D.W. In press. Review of the
freshwater fishes of the Kimberley region
of Western Australia. Zootaxa.
Morgan, D.L., Tang, D. & Peverell, S.C. In
press. 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.
Parnell, J.A.N., Womersley, H.B.S., Sinkora,
D., Vaughan, A. & Huisman, J.M. In press.
W.H. Harvey’s Australian Travelling Sets of
Algae in the Herbarium of Trinity College
Dublin (TCD) and the National Herbarium
of Victoria (MEL). Biology and
Environment: Proceedings of the Royal
Irish Academy.
Pueschel, C.M. & Huisman, J.M. 2010.
Observations of Pihiella liagoraciphila
(Pihiellales; Rhodophyta). Phycologia 49:
42-47.
Reid, A., Lymbery, A.J., Ng, J., Tweedle, S. &
Ryan, U.M. 2010. Identification of novel
and zoonotic Cryptosporidium species in
marine fish. Veterinary Parasitology 168:
190-195.
Thompson, R.C.A., Smith, A., Lymbery, A.J.,
Averis, S., Morris, K.D. & Wayne, A.F. In
press. Giardia in Western Australian
wildlife. Veterinary Parasitology.,
Lymbery, A.J., Hassan, M., Morgan, D.L.,
Beatty, S.J. & Doupé, R.G. 2010. Parasites
of native and exotic freshwater fishes in
south-western Australia. Journal of Fish
Biology 76: 1770-1785.
Thompson, R.C.A., Lymbery, A.J. & Smith, A.
In press. Parasites, emerging disease and
wildlife conservation. International Journal
for Parasitology.
Marr, S.M., Marchetti, M.P., Olden, J.D.,
Garcia-Berthou, E., Morgan, D.L., Day,
J.A., Griffiths, C.L. & Skelton, P.H. 2010.
Tyne, J.A., Loneragan, N., Krützen, M., Allen,
S., & Bejder, L. 2010. An integrated data
management and video system to sample
Page 41
Centre for Fish and Fisheries Research - Annual Research Report 2009
PUBLICATIONS cont…
aquatic benthos. Journal of Marine and
Freshwater Research 61: 1023-1028.
Yang, R., Reid, A., Lymbery, A.J. & Ryan, U.M.
2010. Identification of zoonotic Giardia
genotypes in fish. International Journal for
Parasitology 40: 779-785.
Other publications in 2009
Beatty, S.J., McAleer, F. & Morgan, D.L. 2009.
Migration patterns of fishes of the
Blackwood River and relationships to
groundwater intrusion. For the Water
Department, Government of Western
Australia. 1-93.
Beatty, S.J., & Morgan, D.L. 2009. Synopsis of
the studies on the ecology of fishes in the
Blackwood River and the importance of
groundwater intrusion. Centre for Fish &
Fisheries Research, Murdoch University,
report to the Department of Water,
Government of Western Australia. 1-215.
Beatty, S.J. & Morgan, D.L. 2009. Goldfish
control in the Vasse River: summary of the
2008 programme. Technical Report to
Geocatch.1-9.
Beatty, S.J., Morgan, D.L. & Allen, M. 2009.
Freshwater fish and crayfish communities
of the Carbunup and Buayanyup Rivers:
Conservation significance and
management considerations. Technical
Report to Geocatch. 1-36.
Beatty, S.J., Morgan, D.L. & Allen, M. 2009.
Freshwater fish and crayfish communities
of the tributaries of the Margaret River.
Technical Report to Geocatch. 1-25.
Chaplin, J.A., Sezmis, E., Calver, M. & Moore,
G. 2009. A preliminary assessment of the
number, abundance, distribution and
characteristics of lineages of Thenus from
selected areas of Borneo East Malaysia and
Vietnam. For Lobster Harvest Co. 1-70.
Christensen, J. 2009. Recreational Fishing and
Fisheries Management: A HMAP Asia
Project Paper. Asia Research Centre
Working Papers No.157, Asia Research
Centre, Murdoch University,
http://wwwarc.murdoch.edu.au/wp/wp157
.pdf
Chuwen, B., Hoeksema, S.D., Hesp, S.A., Hall,
N.G. & Potter, I.C., 2009. The fish faunas
of south coast estuaries, Volume 1. South
Coast Natural Resource Management Inc.
Scientific Final Report, Project Number
04SC1-05e.
Chuwen, B., Hoeksema, S.D., Hesp, S.A., Hall,
N.G. & Potter, I.C., 2009. The fish faunas
of south coast estuaries, Volume 2. South
Coast Natural Resource Management Inc.
Scientific Final Report, Project Number
04SC1-05e.
Chuwen, B., Hoeksema, S.D., Hesp, S.A., Hall,
N.G., & Potter, I.C., 2009. The fish faunas
of south coast estuaries. South Coast
Natural Resource Management Inc.
Community Final Report, Project Number
04SC1-05e.
Finn, H. & Holker, M. 2009. Swan River
Dolphins. Landscope (August): 53-58.
Finn, H., Stock, W. & Valentine, L. 2009. Pine
and the ecology of Carnaby’s BlackCockatoos (Calyptorhyncus latirostris) in
the Gnangara Sustainability Strategy study
area. Technical report for the Forest
Products Commission in support of the
Gnangara Sustainability Strategy. Available
at:
http://portal.water.wa.gov.au/portal/page/
portal/gss/Reports
Holmberg, J. & Norman, B. 2009. ECOCEAN
Whale Shark Photo-identification - UNEP
MANUAL. Technical Report to United
Nations Environment Program - Regional
Seas.
Kendrick, A.J., Huisman, J.M. & Rule, M.J.
2009. ‘Marvelous Mangroves’. Landscope.
Summer edition 2009-2010. Published by
the Department of Environment and
Conservation, Western Australia, pp. 5056.
Kirby, G., Morgan, D.L. & Thorburn, D. 2009.
Fitzroy River Barrage Fishway. Technical
Report for Environs Kimberley. 1-111.
Morgan, D.L., Beatty, S.J. & Ebner, B. 2009.
Fishes in groundwater dependent pools of
the Fortescue and Yule Rivers; Pilbara,
Western Australia. For the Department of
Page 42
Centre for Fish and Fisheries Research - Annual Research Report 2009
Water, Government of Western Australia.
1-45.
Morgan, D.L., Beatty, S.J. & Sarre, G.A. 2009.
Ascending the Avon: fishes of the Northam
Pool, and the Swan-Avon catchment. 1-26.
Morgan,, D.L., Whitty, G. & Phillips, N. 2009.
Endangered sawfishes and river sharks in
the West Kimberley. For Woodside Energy.
1-52.
Nowacek, D, McElligott, D., Johnston, D. &
Bejder, L. 2009. A review of literature
relevant to the PCAD model for guidance in
developing transfer functions. Report to the
E&P Sound and Marine Life Joint Industry
Program.
Partridge, G.J., Lymbery, A.J., Hair, S.D. &
Buller, N.B. 2009. Efficacy of Bacillus
polyfermenticus KJS-2 in protecting against
infections with Streptococcus iniae in
barramundi Lates calcarifer. Report to
Zamira Life Sciences.
Phillips, N., Whitty, J., Morgan, D.L., Chaplin,
J. & Thorburn, D. 2009. Freshwater
Sawfish (Pristis microdon) movements and
population demographics in the Fitzroy
River, Western Australia and genetic
analysis of P. microdon and Pristis zijsron.
Report for the Department Environment,
Water Heritage and the Arts, Australian
Government. 1-70.
Rogers, P.P. 2009. Co-management strategies
for W.A. State Managed Fisheries using the
Exmouth Gulf Prawn (Trawl) Fishery as a
case study. For the Australian
Government, Fisheries Research and
Development Corporation. 1-123.
Tull, M. 2009. The History of Shark Fishing in
Indonesia: A HMAP Asia Project Paper.
Asia Research Centre Working Papers
No.157, Asia Research Centre, Murdoch
University,
http://wwwarc.murdoch.edu.au/wp/wp158.
pdf
Verduin, J,J., Paling, E,I. & van Keulen, M.
2009. Seagrass Rehabilitation Studies for
the Seagrass Research and Rehabilitation
Plan, Project 3. Annual Report. (Marine &
Freshwater Research Laboratory, Murdoch
University)
Yang, R., Reid, A., Lymbery, A.J. and Ryan,
U.M. 2010. Identification of zoonotic
Giardia genotypes in fish. International
Journal for Parasitology 40: 779-785.
Other publications in 2010
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. Freshwater Fish Group & Fish
Health Unit (Murdoch University) report to
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.
Chuwen, B.M., Hoeksema, S.D., Hall, N.G. &
Potter, I.C., 2010. Implications of
environmental change and mortality
estimates for sustaining fish populations in
south coast estuaries. Fisheries Research
and Development Corporation Report,
Project No. 2006/044.
Calado, A. & Huisman, J.M. In press.
Commentary: Gómez, F., Moreira, D. &
Lopez-Garcia, P. (2010). Neoceratium gen.
nov., a new genus for all marine species
currently assigned to Ceratium
(Dinophyceae). Protist 161: 35-54.
Huisman, J.M. 2010. ‘Rare Seaweed
Rediscovered’. Landscope Winter edition
2010. Published by the Department of
Environment and Conservation, Western
Australia, pp. 39-41.
Huisman, J.M. 2010. Review: (Common)
Seaweeds of India. Journal of Applied
Phycology 22: 381-383.
Huisman, J.M. In press. Review: Marine
Benthic Algae of Lord Howe Island and
the southern Great Barrier Reef.
Australian Systematic Botany
Newsletter.
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Centre for Fish and Fisheries Research - Annual Research Report 2009
PUBLICATIONS cont…
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.
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.
Conference and workshop
presentations in 2009
Beatty, S.J. & Morgan, D.L. 2009. Introduced
freshwater fishes of Western Australia:
what, where, impacts and actions. 8th Indo
Pacific Fish Conference & 2009 ASFB
Workshop & Conference, Fremantle,
Western Australia.
Beckley, L.E. 2009. Staking a claim with beach
towels: recreational usage of the Western
Australian coast. 5th Western Australian
State Coastal Conference, Fremantle,
Australia.
Beckley, L.E., Clarke, K.R. & Somerfield, P.
2009. Taxonomic distinctness of coastal
fishes around the rim of the South Indian
Ocean. Australian Marine Sciences
Association 46th Annual Conference,
Adelaide, Australia.
Beckley, L.E., Clarke, K.R. & Somerfield, P.
2009. Diversity, distinctness and
divergence of coastal fishes around the rim
of the South Indian Ocean. 8th Indo Pacific
Fish Conference and ASFB Conference,
Fremantle, Australia.
Beckley, L.E. & Lombard, A. 2009. Surely 34%
is enough? A systematic evaluation of the
incremental protection of broad-scale
habitats at Ningaloo Reef, Western
Australia. Australian Marine Sciences
Association 46th Annual Conference,
Adelaide, Australia.
Beckley, L.E., Smallwood, C.B., Moore, S.A. &
Kobryn, H.T. 2009. What do people do at
Ningaloo? Spatial and temporal mapping of
tourist usage in a large marine park, north-
western Australia. 6th International
Congress on Coastal and Marine Tourism,
Port Elizabeth, South Africa.
Beckley, L.E., Smallwood, C.B., Moore, S.A. &
Kobryn, H.T. 2009. High resolution
mapping of reef utilisation by humans in
Ningaloo Marine Park. 3rd Annual Ningaloo
Research Symposium, Ningaloo into the
future: integrating science into
management, Exmouth, Australia.
Beckley, L.E., Smallwood, C.B., Moore, S.A. &
Kobryn, H.T. 2009. What's the use? High
resolution mapping of reef utilisation and
applications to monitoring in Ningaloo
Marine Park. 84th Annual Australian Coral
Reef Society Conference, Darwin, Australia.
Bejder, L. 2009. Managing the Balance
between Conservation and Economic
Interests within MPAs for Cetaceans. First
International Conference on Marine
Mammal Protected Areas, National Marine
Fisheries Service Hawaiian Islands, Hawaii,
46-50.
Breheny, N., Beckley, L.E. & Wakefield, C.
2009. Retention of ichthyoplankton in three
adjacent marine embayments on the lower
west coast of Australia. 8th Indo Pacific
Fish Conference and 2009 ASFB
Conference, Fremantle, Australia.
Christensen, J. 2009. The Shark Bay Snapper
Fishery 1970-2008: a case-study of the
impact of recreational fishing on the decline
and recovery of a marine animal
population. Oceans Past II:
Multidisciplinary Perspectives on the
History and Future of Marine Animal
Populations. Aquatic Ecosystem Research
Laboratory, University of British Columbia,
26-28 May.
Chuwen, B., Hoeksema, S. & Potter, I.C.
2009. Factors influencing the
characteristics of the fish faunas in
offshore, deeper waters of permanentlyopen, seasonally-open and normally-closed
estuaries. 8th Indo Pacific Fish Conference
& 2009 ASFB Workshop and Conference,
Fremantle, Australia.
Cossington, S., Hesp, S.A. & Potter, I.C. 2009.
Latitudinal differences in the biology of the
foxfish Bodianus frenchii, an exceptionally
long lived, protogenous labrid. 8th Indo
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Centre for Fish and Fisheries Research - Annual Research Report 2009
Pacific Fish Conference & 2009 ASFB
Workshop and Conference, Fremantle,
Australia.
Cossington, S., Hesp, S.A. & Potter, I.C. 2009.
The biology of the Black Bream,
Acanthopagrus butcheri, in the SwanCanning Estuary has undergone shortterm, marked changes: implications for
stock assessment. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Coulson, P., Hesp, S.A., Hall, N.G. & Potter,
I.C. 2009. The temperate labrid,
Achoerodus gouldii, is a protogynous
hermaphrodite with exceptional longevity,
late maturity, and late sex change:
management implications. 8th Indo Pacific
Fish Conference & 2009 ASFB Workshop
and Conference, Fremantle, Australia.
Crisafulli, B., Hesp, S.A., Hall, N.G. &
Hoeksema, S.D. 2009. Biology of two fish
species of mullet (Mugilidae) in five very
different estuaries on the south coast of
Western Australia. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Davies, C. & Beckley, L.E. 2009.
Macrozooplankton of the inshore waters of
Christmas Island (Indian Ocean) with
specific reference to larvae of the red land
crab, Gecarcoidea natalis. Australian
Marine Sciences Association 46th Annual
Conference, Adelaide, Australia.
Ebner, B., Morgan, D.L., Whitty, J. & Beatty,
S.J. 2009. Rapid survey of fish
communities in some water holes of the
Yule, Fortescue and Fitzroy River
catchments, WA. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Fretzer, S., Hall, N.G. & Lozano-Montes, H.
2009. The impact of an artificial entrance
channel and the impact of fishing on the
ecosystem of the Peel-Harvey Estuary,
Western Australia. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Gardner, M., Chaplin, J., Hesp, A. & Potter,
I.C. 2009. Comparisons between the
biological performance and genetic
composition of restocked versus wild black
bream, Acanthopagrus butcheri, in the
Blackwood Rivery Estuary. 8th Indo Pacific
Fish Conference & 2009 ASFB Workshop
and Conference, Fremantle, Australia.
Hallett, C. & Valesini, F.J. 2009. The
development and validation of an estuarine
health index using fish community
characteristics. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Hallett, C. & Daley, R. 2009. Feeding ecology
of the southern lanternshark, Etmopterus
baxteri, and the brown lanternshark, E.
unicolor, from south-eastern Australia. 8th
Indo Pacific Fish Conference & 2009 ASFB
Workshop and Conference, Fremantle,
Australia.
Hoeksema, S.D., Chuwen, B.M. & Potter, I.C.
2009. Highly depauperate fish faunas and
extensive fish mortalities in normallyclosed estuaries on the south coast of
Western Australia which can become
markedly hypersaline. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Holliday, D., Beckley, L.E., Feng, M. &
Thompson, P. 2009. Lost at sea? The
influence of meso-scale oceanographic
features on larval fish assemblages off
south-west Australia. 8th Indo Pacific Fish
Conference and 2009 ASFB Conference,
Fremantle, Australia.
Holliday, D., Beckley, L.E., Feng, M. & Waite,
A. 2009. Shelf-ocean connectivity: the role
of eddies in cross-shelf exchange of larval
fishes off SW Australia. Australian Marine
Sciences Association 46th Annual
Conference, Adelaide, Australia.
Holliday, D., Beckley, L.E., Feng, M., Waite,
A.M., Thompson, P.T. & Olivar, M.P. 2009.
Sources of, and pathways for, the
incorporation of larval fishes into a
developing warm-core eddy of the Leeuwin
Current, SW Australia. Advancing
Limnology and Oceanography Symposium,
Nice, France.
Hood, R., Beckley, L.E. & Naqvi, S.W.A. 2009.
The emerging SIBER initiative of
IMBER/IOGOOS: Biogeochemical observing
programs and modeling needs in the
Indian Ocean. Global Ocean Observing
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Centre for Fish and Fisheries Research - Annual Research Report 2009
PUBLICATIONS cont…
System: Scientific Steering Committee
workshop XII, Perth, Australia.
Hood, R., Beckley, L.E. & Naqvi, W. 2009.
SIBER: Sustained Indian Ocean
Biogeochemical and Ecosystem Research.
Australian Marine Sciences Association 46th
Annual Conference, Adelaide, Australia.
Hordyk, A., Prince, J., Kobryn, H., Diver, G. &
Loneragan, N.R. 2009. Understanding the
spawning dynamics of orange roughy,
Hoplostethus atlanticus in south-eastern
Australia. 8th Indo Pacific Fish Conference
& 2009 ASFB Workshop and Conference,
Fremantle, Australia.
Jones, A., Hall, R.G. & Potter, I.C. 2009. A
comparison of species and size
compositions of the elasmobranch catches
from three fishing methods in southwestern Australian waters. 8th Indo Pacific
Fish Conference & 2009 ASFB Workshop
and Conference, Fremantle, Australia.
Kobryn, H.T., Wouters, K., Pinnel, N. &
Beckley, L.E. 2009. Mapping the marine
benthic habitats of Ningaloo reef lagoon.
3rd Annual Ningaloo Research Symposium,
Ningaloo into the future: integrating
science into management, Exmouth,
Australia.
Kobryn, H.T., Wouters, K., Pinnel, N., Beckley,
L.E., Harvey, M. & Heege, T. 2009.
Mapping sense of hyperspectral, remotelysensed data for habitat mapping in
Ningaloo Marine Park, Western Australia.
Australian Marine Sciences Association 46th
Annual Conference, Adelaide, Australia.
Kobryn, H.T., Wouters, K., Pinnel, N., Beckley,
L.E. & Heege, T. 2009. Marine benthic
habitats of Ningaloo Reef: mapping and
derivation from hyperspectral remote
sensing. 84th Annual Australian Coral Reef
Society Conference, Darwin, Australia.
Lek, E., Fairclough, D. & Potter, I.C. 2009. The
biology of three sympatric labrid species
from two regions in Western Australia. 8th
Indo Pacific Fish Conference & 2009 ASFB
Workshop and Conference, Fremantle,
Australia.
Linke, T., Potter, I.C., Twomey, L. & Valesini,
F. 2009. Trophic interactions in the SwanCanning Estuary. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Lymbery, A.J., Hassan, M., Morgan, D.L. &
Beatty, S.J. 2009. The role of parasites in
the decline of freshwater fishes in the
south west of Western Australia. 8th Indo
Pacific Fish Conference & 2009 ASFB
Workshop & Conference, Fremantle,
Australia.
Lozano-Montes, H.M., Loneragan, N.R.,
Babcock, R. & Jackson, K. 2009. Using
trophic flows and ecosystem structure to
model the effects of fishing in the Jurien
Bay Marine Park, temperate Western
Australia. 8th Indo Pacific Fish Conference
& 2009 ASFB Workshop and Conference,
Fremantle, Australia.
Metcalf, S., Gaughan, D., Shaw, J. & Moyle, K.
2009. Qualitative analysis of fisher
responses to management and the impact
on recreationally important species in
Western Australia. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Millar, N., Holliday, D., Beckley, L.E., Feng, M.
& Thompson, P. 2009. Larval fishes as
biological tracers of latitudinal and crossshelf connectivity off Western Australia.
Australian Marine Sciences Association 46th
Annual Conference, Adelaide, Australia.
Millar, N., Holliday, D., Beckley, L.E., Feng, M.
& Thompson, P. 2009. Influence of
latitudinal and cross-shelf transport
processes on larval fish assemblages off
Western Australia. 8th Indo Pacific Fish
Conference and 2009 ASFB Conference,
Fremantle, Australia.
Moore, S., Hesp, S.A., Hall, N.G. & Potter, I.C.
2009. Biology of the breaksea cod,
Epinephelides armatus, a serranid with an
unusual pattern of sexual development. 8th
Indo Pacific Fish Conference & 2009 ASFB
Workshop and Conference, Fremantle,
Australia.
Moore, G., Chaplin, J. & Potter, I.C. 2009. The
evolution history of Australian salmon
(Arripidae) in Australian waters. 8th Indo
Pacific Fish Conference & 2009 ASFB
Workshop and Conference, Fremantle,
Australia.
Page 46
Centre for Fish and Fisheries Research - Annual Research Report 2009
Morgan, D.L. & Beatty, S.J. 2009. Freshwater
fishes of Western Australia. 8th Indo Pacific
Fish Conference & 2009 ASFB Workshop
and Conference, Fremantle, Australia.
Newman, S.J., Skepper, C.L., Pember, M.B.,
Hesp, S.A., Hall, N.G., Young, G.C. &
Potter, I.C. 2009. Regional variation in the
demography of the mangrove jack
(Lutjanus argentimaculatus) from northwestern Australia. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Norman, B., Holmberg, J., Arzoumanian, Z.
2009. Collaborative photo-identification
monitoring of Whale Sharks on a global
scale: results to date and future
opportunities. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Norman, B., Gleiss, A., Wilson, R. 2009. A
Whale Shark "daily diary': new insights into
the biology and baits of this threatened
species. 8th Indo Pacific Fish Conference &
2009 ASFB Workshop and Conference,
Fremantle, Australia.
Peverell, S., Gribble, N., Whitty, J., Seymour,
J. 2009. Conservation management of
entrapped freshwater sawfish (Pristis
microdon) in north Queensland rivers. 8th
Indo Pacific Fish Conference & 2009 ASFB
Workshop and Conference, Fremantle,
Australia.
Pilar Olivar, M., Beckley, L.E., Holliday, D.,
Muhling, B. & Millar, N. 2009. Larvae of
Myctophidae of the South Indian Ocean and
comparisons with species shared with the
Atlantic Ocean. 8th Indo Pacific Fish
Conference and 2009 ASFB Conference,
Fremantle, Australia.
Phillips, N., Chaplin, J., Morgan, D. & Peverell,
S. 2009. Does the freshwater sawfish,
Pristis microdon, exhibit sex-biased
dispersal in Australian waters? 8th Indo
Pacific Fish Conference & 2009 ASFB
Workshop & Conference, Fremantle,
Western Australia.
Phillips, N., Chaplin, J., Morgan, D. & Peverell,
S. Conservation genetics of Pristis species
in Australian waters. 25th Meeting of the
American Elasmobranch Society. Portland,
Oregon. July, 2009.
Shaw, J., Fletcher, R., Gaughan, D. & Metcalf,
S. 2009. Ecosystems based fisheries
management; towards implementation in
Western Australia. 8th Indo Pacific Fish
Conference & 2009 ASFB Workshop and
Conference, Fremantle, Australia.
Smallwood, C.B., Beckley, L.E. & Moore, S.A.
2009. Using spatial surveys of visitors to
better understand and manage recreational
fishing in the Ningaloo Marine Park, northwestern Australia. 8th Indo Pacific Fish
Conference and ASFB Conference,
Fremantle, Australia.
Smallwood, C.B., Beckley, L.E. & Moore, S.A.
2009. Getting out and about at Ningaloo:
understanding visitor travel networks for
better management of a fringing coral reef.
84th Annual Australian Coral Reef Society
Conference, Darwin, Australia.
Steinke, D., Ward, B., Last, P., Hebert, P.,
Johnson, J., Moore, G., Hay, A., Reader, S.
& Gomon, M. 2009. DNA barcoding of coral
reef fishes. 8th Indo Pacific Fish Conference
& 2009 ASFB Workshop and Conference,
Fremantle, Australia.
Thompson, P., Waite, A., Doblin, M., Beckley,
L.E., Strzelecki, J. & Bonham, P. 2009. The
plankton ecology of south-western
Australia: temporal and spatial patterns.
Australian Marine Sciences Association 46th
Annual Conference, Adelaide, Australia.
Toon, N., Loneragan, N. 2009. Trap behaviour
of the western rock lobster. 8th Indo Pacific
Fish Conference & 2009 ASFB Workshop
and Conference, Fremantle, Australia.
Travers, M.J., Potter, I.C., Clarke, K.R.,
Newman, S.J. & Hutchins, J.B. 2009.
Latitudinal and bioregional patterns of fish
assemblages in north-western Australian.
8th Indo Pacific Fish Conference & 2009
ASFB Workshop and Conference,
Fremantle, Australia.
Tull, M. 2009. Historical patterns of change in
Indonesia’s marine fisheries: a case study
of shark fishing. Oceans Past II:
Multidisciplinary Perspectives on the
History and Future of Marine Animal
Populations Aquatic Ecosystem Research
Laboratory, University of British Columbia,
26-28 May.
Page 47
Centre for Fish and Fisheries Research - Annual Research Report 2009
PUBLICATIONS cont…
Tweedley, J., Valesini, F., Hoeksema, S. &
Potter, I.C. 2009. Inter-relations between
fish faunas and habitat types in a
seasonally-open estuary in south-western
Australia. 8th Indo Pacific Fish Conference
& 2009 ASFB Workshop and Conference,
Fremantle, Australia.
Van Keulen, M. 2009. Biodiversity studies in
the Ningaloo Reef lagoon. 3rd Annual
Ningaloo Research Symposium, Ningaloo
into the future: integrating science into
management, Exmouth, Australia.
Veale, L., Haddy, J. & Krusic-Golub, K. 2009.
The population dynamics of the deep sea
cod, ribaldo (Gadiformes; Mora mora). 8th
Indo Pacific Fish Conference & 2009 ASFB
Workshop and Conference, Fremantle,
Australia.
Whitty, J., Phillips, N., Morgan, D.,
Simpfendorfer, C., Peverell, S., Thorburn,
D. & Field, I. 2009. Utility of rostra for the
identification of Australian sawfish species.
8th Indo Pacific Fish Conference & 2009
ASFB Workshop & Conference, Fremantle,
Australia.
Wouters, K., Kobryn, H.T., Heege, T. &
Beckley, L.E., 2009. Mapping Ningaloo Reef
using hyperspectral remote sensing:
classification approaches with varying
thematic and spatial resolutions. 84th
Annual Australian Coral Reef Society
Conference, Darwin, Australia.
Page 48
Centre for Fish and Fisheries Research - Annual Research Report 2009
POSTGRADUATE STUDENTS
5. POSTGRADUATE STUDENTS
AND THEIR RESEARCH TOPICS
PhD students (completed in 2009)
Dr Matt Harvey
Development of techniques to classify benthic
habitats using hyperspectral imagery in
oligotrophic, temperate waters.
Supervisors: Lynnath Beckley and Halina
Kobryn (SELS)
Dr Marina Hassan
Parasites of native and exotic freshwater
fishes in the south-west of Western Australia.
Supervisors: Alan Lymbery (HS), David
Morgan and Stephen Beatty (SELS)
PhD students
(enrolled/examined/submitted/
pending correction in 2009)
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*)
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 reefbuilding 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)
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)
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)
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)
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)
Farhan Bokhari
The effects of salinity on riparian arthropod
communities and consequences for ecosystem
function.
Supervisor: Alan Lymbery (HS)
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)
Samantha Bridgwood
Physical factors determining the structure of
seagrass meadows in Warnbro Sound,
Western Australia.
Supervisors: Mike van Keulen (SELS), Marion
Cambridge (UWA)
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)
Page 49
Centre for Fish and Fisheries Research - Annual Research Report 2009
POSTGRADUATE STUDENTS cont…
Sarah Fretzer
Analysing the effects of anthropogenic
activities on different aquatic ecosystems in
Western Australia and identifying ecosystembased management policies that provide longterm sustainability.
Supervisors: Norm Hall (SELS), Jeffrey
Dambacher (CSIRO), Hector Lozano-Montes
(CSIRO), Brent Wise (DoF)
Ben French
The determination of the diets of Snapper and
Silver Trevally, the construction of a food web
for the demersal fish community in SouthWestern Australia and biology of Harlequin
Fish.
Supervisors: Ian Potter and Margaret Platell
(SELS)
Ashlee Jones
Characteristics of the elasmobranch fauna in
the bycatch of commercial fisheries in southwestern 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)
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)
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)
Susan Gibson-Kueh
Diseases of Asian seabass and barramundi.
Supervisors: Phil Nicholls and Alan Lymbery
(HS)
Anne Lif Lund Jacobsen
The south-east (trawl) fishery in Australia
from 1915 to 1980
Supervisors: Elaine Stratford (UTas) and
Malcolm Tull (LB)
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)
Michelle Ingram
The effect of salinity on the resilience of
riparian ecosystems.
Supervisor: Alan Lymbery (HS)
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)
Page 50
Centre for Fish and Fisheries Research - Annual Research Report 2009
Frazer McGregor
The trophic ecology & habitat requirements of
the Manta Ray (manta birostris) in lagoonal
systems of Ningaloo Reef, Western Australia
Supervisors: Mike van Keulen (SELS), Mark
Meekan (AIMS), Anya Waite (UWA)
Holly Smith
Population dynamics and habitat utilisationin
bottlenose dolphins, Bunbury, Western
Australia.
Supervisors: Lars Bejder, Halina Kobryn,
Stuart Bradley (SELS) and Kelly Waples (DEC)
Heather McLetchie
Molecular diagnosis of crayfish plague
(Aphanomyces astaci).
Supervisors: Stan Fenwick and Phil Nicholls
(HS)
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)
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 southwestern 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)
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 northwestern 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)
Andrew Rowland
The biology of Samson fish Seriola hippos with
emphasis in the sport fishery in Western
Australia.
Supervisor: Howard Gill (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)
Claire Smallwood
Spatial patterns and temporal patterns of
recreational use at Ningaloo Reef, northwestern Australia.
Supervisors: Lynnath Beckley and Susan
Moore (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)
Page 51
Centre for Fish and Fisheries Research - Annual Research Report 2009
POSTGRADUATE STUDENTS cont…
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 2009)
Valissa Buchanan
Baseline abundance and residency patterns of
bottlenose dolphins, Tursiops sp., Binningup,
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)
Page 52
Centre for Fish and Fisheries Research - Annual Research Report 2009
HONOURS STUDENTS
6. HONOURS STUDENTS AND
THEIR RESEARCH TOPICS
Honours students
(completed in 2009)
Gin Swen Ham
Population biology of bottlenose dolphins
(Tursiops sp.) in Cockburn Sound.
Supervisors: Hugh Finn and Lars Bejder
(SELS) – Class IIA.
Natalie Millar
Larval fish assemblages in the Leeuwin
Current system, Western Australia
Supervisor: Lynnath Beckley (SELS) – Class
IIA.
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 2009)
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 agentbased model to explore the effects of
recruitment variability on populations of
Glaucosoma hebraicum in a recreational
fishery.
Supervisors: Alex Hesp and Norm Hall (SELS)
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)
Page 53
Centre for Fish and Fisheries Research - Annual Research Report 2009
Page 54
Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH FUNDING
7. SUMMARY OF RESEARCH FUNDING
7.1 List of projects and research income for 2009
Name
Beckley, Lynnath
Beckley, Lynnath
Beckley, Lynnath
Beckley, Lynnath &
David Holliday
Beckley, Lynnath; ,
Halina Kobryn & Sue
Moore
Beckley, Lynnath;
Mark Langdon; Neil
Loneragan; Mike van
Keulen & Halina
Kobryn
Beckley, Lynnath &
David Holliday
Beckley, Lynnath &
David Holliday
Bejder, Lars
Bejder, Lars
Bejder, Lars
Bejder, Lars & Neil
Loneragan
Bejder, Lars; Neil
Loneragan & Stuart
Bradley
Project
Funding Body
Duration
2009
prop’n
$
Total
funding
($)
Influence of Leeuwin
Current eddies on crossshelf transport of pelagic
larval biota
Distribution of fish larvae
in Cockburn Sound
Leeuwin Current fish
larvae (student project)
Leeuwin current eddies influence of cross-shelf
transport on biota
Human usage in
Ningaloo Marine Park
WAMSI Node 2
2007-2009
$7,000
$24,000
WA Department of
Fisheries
WAMSI Node 1
2009
$14,640
$14,640
2009
$1,000
$1,000
WAMSI
2007-2009
$11,000
$33,000
CSIRO Wealth from
Oceans Ningaloo
Collaborative Cluster
2006-2010
$65,900
$490,000
Wealth from Oceans:
Habitats and biodiversity
of Ningaloo Marine Park
CSIRO
2006-2009
$105,777
$550,424
Distribution of
phyllosoma in neuston
samples off WA
Distribution of
phyllosoma in neuston
samples off WA
Population Consequences
of Acoustic Disturbance Literature Review
Dolphin Monitoring
Program at Monkey Mia,
Shark Bay, WA
Megafauna line transects
off Binningup, WA
South West Marine
Research Project running costs
Large-scale dolphin
research program in
south-west Australia
WA Department of
Fisheries
2009
$5,000
$5,000
CSIRO/ WAMSI Node 1
2009
$5,000
$5,000
Joint Industry Program.
Oil and Gas Producers
2008-2009
$17,000
$37,000
DEC
2007-2011
$22,528
$109,354
Water Corporation
2009-2011
$92,500
$222,450
Winifred Violet Scott
Estate
2009
$18,000
$18,000
Bunbury Port Authority
2007-2010
$16,000
$60,000
Worsley Alumina
Iluka
WA Plantations
Cable Sands
City of Bunbury
Lyondell Millenium
Chemicals
Bunbury Dolphin
Discovery Centre
DEC
Millard Marine
South West
Development
Commission
2007-2010
2008-2010
2007-2010
2007-2010
2007-2010
2007-2010
$12,500
$7,000
$6,000
$7,500
$13,333
$1,500
$50,000
$21,000
$24,000
$30,000
$50,000
$6,000
2007-2010
$11,880
$42,748
2008-2010
2007-2009
2008-2010
$10,000
$3,000
$9,000
$30,000
$9,000
$27,000
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Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH FUNDING cont…
Ceh, Janja & Mike van
Keulen
Microbial communities
associated with reefbuilding corals of
Ningaloo Reef in Western
Australia
WAMSI
2008-2010
$6,000
$18,000
Chaplin, Jennie
A preliminary
assessment of the
number, abundance,
distribution and
characteristics of
lineages of Thenus from
selected geographic
regions.
Genetic (microsatellite)
determination of the
stock structures of
snapper (Pagrus
auratus) and baldchin
grouper (Choerodon
rubescens) in Western
Australian waters.
People Development
Program: FRDC
International Travel
Bursary
The nature, diversity and
potential impact of
infectious agents in
Western Australian
threatened mammals
Toxicant exposure,
population genetics, and
trophic associations of
bottlenose dolphins
(tursops sp) in the Swan
River
Fish Migrations in the
Blackwood River
(Yarragadee Aquifer
discharge zone)
Analyses of three
databases of fisheries
data from the Mekong
River.
Dynamics of the
ecosystems of three
estuaries in southwestern Australia.
Exploration of the
effectiveness of
alternative management
responses to variable
recruitment
Development of an
agent-based model to
communicate
implications of
recruitment variability of
finfish to recreational
fishers
Development of
bioregional level
assessments of the
status of community
structure based on
fishery dependent and/or
fishery independent data
Lobster Harvest
2008–2009
$11,706
$35,706
WAMSI node 4
2008–2011
$55,220
$137,807
FRDC
2009
$6,600
$6,600
ARC
2007-2009
$293,318
$903,954
Swan River Trust
2009
$17,000
$17,000
Department of Water
2005-2009
$104,239
$340,559
ACIAR
2008-2009
$59,947
$149,867
WAMSI
2007-2010
$11,000
$33,000
FRDC
2008-2012
$60,770
$256,000
FRDC
2009-2010
$22,500
$75,000
WAMSI
2007-2011
$49,290
$281,611
Chaplin, Jennie & Ian
Potter
Chuwen, Benjamin
Clark, Phillip; Richard
Thompson; Alan
Lymbery & Peter
Spencer
Finn, Hugh; Carlysle
Holyoake & Lars
Bejder
Gill, Howard; David
Morgan & Stephen
Beatty
Hall, Norman
Hall, Norman & Sarah
Fretzer
Hall, Norman & Alex
Hesp
Hall, Norman & Alex
Hesp
Hall, Norman & Ian
Potter
Page 56
Centre for Fish and Fisheries Research - Annual Research Report 2009
Hall, Norman & Ian
Potter
Hall, Norman & Ian
Potter
Hall, Norman & Peter
Rogers
Hallett, Christopher &
Fiona Valesini
Hoeksema, Steeg &
Ian Potter
Holyoake, Carly; Hugh
Finn & Lars Bejder
Huisman, John
Huisman, John
Kobryn, Halina; Mike
van Keulen & Lynnath
Beckley
Linke, Thea & Fiona
Valesini
Loneragan, Neil
Loneragan, Neil
Loneragan, Neil &
Jeremy Prince
Dietary studies of the
fish faunas of the PeelHarvey estuary and
coastal marine waters of
South-Western Australia
Leschenault estuary fish stocks assessment
project
Development of 'A
Science Strategy for the
Peel-Harvey Estuary'
The development and
validation of an estuarine
health index using fish
community
characteristics
Ecosystem health of the
Peel-Harvey Estuary data assemblage and
ecosystem monitoring
strategy
Toxicant exposure,
population genetics, and
trophic associations of
bottlenose dolphins
(Tursiops sp.) in the
Swan River
Marine Benthic Algae of
the Great Barrier Reef,
Rhodophyta:
Acrosymphytaceae,
Nemastomataceae,
Schyzymeniaceae,
Dumontiaceae,
Ceramiaceae and
Rhodomelaceae
Macroalgae of Western
Australia
Habitats and biodiversity
of Ningaloo Reef lagoon
WAMSI
2007-2011
$40,180
$120,000
South West
Development
Commission Peel-Harvey Catchment
Council
2008-2010
$20,188
$79,910
2009-2010
$30,000
$40,000
WAMSI
2008-2010
$6,000
$18,000
Caring for Our Country
2009
$45,455
$45,455
Swan River Trust Swan Canning Research
and Innovation Program
Investigators
2009
$17,000
$17,000
Australian Biological
Resources Study
2009-2012
$11,634
$34,902
DEC
2008-2010
$50,000
$150,000
CSIRO Wealth from
Oceans Ningaloo
Collaborative Cluster
2006-2010
$105 777
$510,000
Trophic interactions in
the Swan Estuary and
Wilson Inlet (Part of
WAMSI project 4.3 Trophic interactions for
Ecosystem Based
Fisheries Management)
Evaluating how food
webs and the fisheries
they support are affected
by fishing closures in
Jurien Bay, temperate
Western Australia
Applying the Ecosystem
Based Fisheries
Management (EBFM)
framework.
Assessing alternative
fishing seasons for redlegged prawns in the
Joseph Conaparte Gulf
and future directions for
collaborative research for
NPF Industry Pty Ltd
WAMSI
2008-2011
$11,000
$33,000
FRDC
2006-2009
$148,892
$344,885
WAMSI
2007-2010
$80,000
$250,626
FRDC
2009
$74,840
$74,840
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Centre for Fish and Fisheries Research - Annual Research Report 2009
RESEARCH FUNDING cont…
Loneragan, Neil &
Alex Hesp
Establishment of selfsustaining facility for
fisheries modelling and
miltivariate analysis, and
for effective
management of
extremely large fisheries
databases.
Reducing dolphin
bycatch in the Pilbara
Finfish Trawl Fishery
FRDC
2008-2012
$15,000
$85,000
FRDC, WA Fisheries,
Nickol Bay Professional
Fishers Association Inc
2008-2010
$55,000
$150,000
ARC seed money research into the
sustainability of fishes of
Snake Creek and their
swimming abilities for
future fishway design
Aquatic fauna survey of
the Ellen Brook,
Brockman River and
associated major
tributaries
Integrating inland saline
aquaculture and
livestock production
The efficacy of Bacillus
polyfermenticus KJS-2 in
protecting against
bacterial infections in
barramundi Lates
calcarifer
Aquatic fauna Survey,
Mitchell/Hay &
Quickup/Denmark Rivers
Request for funding:
Importance of
groundwater in
maintaining refuge
habitats for freshwater
fishes in the Pilbara
Continuation of studies
of the population
genetics and tracking of
the Freshwater Sawfish
(Pristis microdon) in the
Fitzroy River, Kimberley,
Western Australia 20082009 and population
genetics of P. zijsron.
Liveringa Station
2009-2013
$13,000
$183,000
Lotterywest - via The
Ellen Brockman
Integrates Catchment
Group
2009-2010
$17,140
$17,140
RIRDC
2006-2010
$10,000
$93,428
CTCBIO
2009
$7,839
$7,839
Water Corporation
2009-2010
$189,497
$189,497
Department of Water
2008-2009
$14,994
$19,994
Department of
Environment, Water,
Heritage and Arts
2009
$48,645
$48,645
Potter, Ian
Determination of
Snapper and Silver
Trevally and construction
of a food web for the
demersal fish community
in South-Western
Australia
FRDC
2009-2011
$25,685
$74,503
Potter, Ian; Jennie
Chaplin & Alex Hesp
Biological performance
and genetics of
restocked black bream in
the Blackwood River
Estuary.
Development of Biotic
indices for establishing
and monitoring estuarine
health
The nature, diversity and
potential impact of
infectious agents in
DBIF – WA Fish
Foundation (WAFF)
2009-2010
$29,566
$49,277
Department of Fisheries
WA
2007-2010
$71,338
$306,477
ARC Linkage
2007-2009
$153,118
$435,354
Loneragan, Neil;
Simon Allen & Lars
Bejder
Lymbery, Alan; David
Morgan & Stephen
Beatty
Lymbery, Alan; David
Morgan & Stephen
Beatty
Lymbery, Alan; Rob
Doupé & Gavin Sarre
Lymbery, Alan &
Gavin Partridge
Morgan, David &
Stephen Beatty
Morgan, David &
Stephen Beatty
Morgan, David &
Jennie Chaplin
Potter, Ian & Fiona
Valesini
Thompson, Andrew;
Alan Lymbery; Andy
Page 58
Centre for Fish and Fisheries Research - Annual Research Report 2009
Smith; Peter Spencer;
Keith Morris & Adrian
Wayne
Van Keulen, Mike
Van Keulen, Mike
Van Keulen, Mike
Van Keulen, Mike
Van Keulen, Mike
Western Australian
threatened mammals
The trophic ecology &
habitat requirements of
the Manta Ray (manta
birostris) in lagoonal
systems of Ningaloo
Reef, Western Australia
Population biology of
Peronella lesueuri
Ecology of Indo-Pacific
humpback dolphins in
Ningaloo Marine Park
and the Exmouth
The role of microbial
communities in reefbuilding corals of
Ningaloo Reef, Western
Australia
The population dynamics
and habitat usage of
Sousa chinensis and
Tursiops truncatus found
in the Ningaloo area
2009 TOTAL FUNDING:
WAMSI/BHP Billiton
Top-up Scholarship for
Frazer McGregor
2008-2010
$11,000
$33,000
WAMSI Top-up
scholarship for Sharon
Yeo
Winifred Violet Scott
Estate
2009-2011
$6,000
$18,000
2009
$20,000
$20,000
WAMSI Top-up
scholarship for Janja
Ceh
2008-2010
$6,000
$18,000
WAMSI Top-up
scholarship for Kristel
Wenziker
2008-2010
$6,000
$18,000
$2,395,659 Page 59
Centre for Fish and Fisheries Research - Annual Research Report 2009
Page 60
Centre for Fish and Fisheries Research - Annual Research Report 2009
ACKNOWLEDGEMENTS
8. ACKNOWLEDGEMENTS
The CFFR would like to acknowledge ongoing support from the following sponsors and collaborators:
Page 61
Centre for Fish and Fisheries Research - Annual Research Report 2009
ACKNOWLEDGEMENTS cont…
And
Shark Bay Resource
Nickol Bay Professional Fishers Association
Winifred Violet Scott Foundation
Page 62
Centre for Fish and Fisheries Research - Annual Research Report 2009
Page 63
Centre for Fish and Fisheries Research - Annual Research Report 2009
ACKNOWLEDGEMENTS cont…
Page 64
Centre for Fish and Fisheries Research - Annual Research Report 2009
Annual Research Report 2009
Centre for Fish and Fisheries Research locations
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Centre for Fish and Fisheries Research
www. cffr.murdoch.edu.au