the distribution, abundance and trophic ecology of the fishes of darwin harbour mangrove habitats

302 Pages·2013·12.9 MB·English

THE DISTRIBUTION,
ABUNDANCE AND TROPHIC
ECOLOGY OF THE FISHES OF
DARWIN HARBOUR MANGROVE
HABITATS
JULIE M MARTIN
B.Sc.(Hons), James Cook University, 1994
A thesis submitted in fulfilment of the requirements for the degree of Doctor of
Philosophy in the Faculty of Education, Health and Science, Charles Darwin
University.
2005
I hearby declare that the work herein, now submitted as a thesis for the degree of
Doctor of Philosophy, is the result of my own investigations and all references to
ideas and work of other researchers have been specifically acknowledged. I hearby
certify that the work embodied in this thesis has not already been accepted in
substance for any degree and is not being currently submitted in candidature for any
other degree.
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ACKNOWLEDGMENTS
I would like to thank the many people who gave me inspiration, support,
encouragement and assistance during this research. Without them, this project would
not have been possible. Most importantly, I thank my husband Andrew for
everything, and our children, Manisha and Soni, for their patient, and not so patient,
waiting while their mum finished that book.
My supervisor, Dr. Keith McGuinness, offered me insight, support and guidance
throughout the project. I greatly appreciate his patient reading and constructive
comments on all drafts of this thesis. Dr Rik Buckworth, my associate supervisor,
was also a source of inspiration, encouragement and friendship.
This project was generously supported by two government departments. The
Department of Infrastructure, Planning and Environment provided an additional
stipend, a boat and project operational costs for three years. The Fisheries Division of
the Department of Business Industry and Resource Development gave me in-kind
assistance, including (amongst many other things) office space, computing facilities
and access to vehicles. I would also like to thank the Centre for Tropical Wetlands
Management for their Post Graduate Research Grant of $500.
My technical assistant, Paul McHugh, was an inspiration. I know of few other people
who would work so tirelessly under such trying conditions (apart from PhD
students). His assistance was essential during fieldwork which ranged from wading
through knee-deep mangrove mud wielding a chainsaw (and a pistol) in the middle
of the wet season to getting up at 3.30 am to go "fishing". Many volunteers were also
generous with their assistance in the field work, especially Andrew Buick, Stephanie
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Boubaris, Tony Powell, Patrick Grey, Adrian Donati, Charles Bryce, Richard Sellers,
Neil Smit and Roland Griffin. Richard Mounsey, Mac MacCartie, Charles Bryce and
Stepanine Boubaris helped design and make trammel nets. Armando Padovan and
Rod Metcalfe provided water quality data and assisted with water quality
measurements. Thanks also to the many others at the fisheries division for your
support and friendship.
I learnt a lot and also had fun at the Fisheries Centre, UBC and I much appreciate the
help and friendship of Profs. Daniel Pauly, Villy Christensen and Carl Walters, Dr.
Reg Watson, Dr. Neil Gribble and Maria Morlin.
Thanks also to Drs. Helen Larson, Richard Willan and Chris Glasby at the NT
Museum for their help in identifying fish and prey items taken from the stomachs of
fish. My thanks should also go to the firearms trainers for trying (in vain) to teach me
the art of self-protection.
To my colleagues who revel in mud and mangroves - Kristin Metcalfe, Chandra
Salgado-Kent, Brad Comley, Grey Coupland, Justin McDonald-it was comforting
to know that you were out there too. Kristin also generously provided preliminary
data from her PhD project for use in this thesis.
There were many others who gave me encouragement and emotional support, thanks
especially to my friends Lynne Powell and Gretchen Thombum. Finally I thank my
family; Ross and Vic, John and Wendy, my mother Linda Martin, and my parents-in
law, Kathleen and Malcolm Buick for their patience and understanding ... and Dad,
are you clicking your heels?
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FOR THE FISH
Permission to use this image from Patrick Hall and Di Allison, Phish Design Cards, Hobart,
Tasmania.
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ABSTRACT
Darwin Harbour features one of the largest and most diverse mangrove communities
in northern Australia. The harbour is also the centre of a thriving recreational fishery.
This study examined the role of mangroves in the distribution, abundance and trophic
relationships of the fish of Darwin Harbour.
Fish were sampled in three different mangrove habitats in three locations in Darwin
Harbour for two years, using three methods: trammel nets, light traps and pit traps.
Forest structural complexity and aquatic environmental variables were also
measured. Diet composition was analysed and trophic groups identified using
multivariate techniques. A preliminary trophic model was also developed.
At high spring tides, the mangrove forest was used extensively by a wide range of
fish. At low tide, only resident species appeared to remain in pools, as pit trap
samples comprised the Gobiidae and Pseudomugilidae. Trammel net captures were
dominated by the Ariidae, Mugilidae, Clupeidae and Engralulidae families. Fish
captured in the light traps were dominated by Engraulidae, Clupeidae, Atherinidae
and Gobiidae. Small fish, including juveniles and larvae, were more abundant in the
seaward habitats, whereas larger fish, including predatory species, were captured
throughout the mangrove forest. This suggests that smaller fish were not seeking
refuge from predation in the shallower, more complex habitats.
Fish abundance and distribution did not appear to be influenced by small scale
variations in structural complexity (stem density and sizes) or mangrove
productivity. Instead, large scale differences in forest characteristics, such as
mangrove species composition and general topographical features, along with
aquatic environmental variables appeared to be more important.
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All habitats appeared to be important feeding areas for fish and seven trophic groups
were identified. Three major groups were separated according to feeding mode
(nekton, benthic and surface feeders) and within these, seven groups were defined by
the main prey items in their diets. The Ecopath with Ecosim trophic model, although
preliminary and based on incomplete information, synthesised information about
Darwin Harbour from a wide variety of sources, indicated information gaps and
identified areas in which future research should be focussed.
Some species, such as Toxotes chatareus and two Ariid catfish, were more strongly
associated with the higher intertidal habitats. This association may be important
ecologically, due to their high levels of predation on the sesarmid crab, Perisesarma
darwinensis, which is also found more often in the higher intertidal habitat and is
known to consume mangrove leaf litter.
Overall, the results show that a diverse array of fish use the mangroves of Darwin
Harbour. Some are economically valuable species themselves and many are prey
species for fish of recreational importance. There appear to be close trophic links
between fish and all habitats and these links must be considered in future
management of Darwin Harbour.
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TABLE OF CONTENTS
1. GENERAL INTRODUCTION ...................................................................................... 1
1.1. Background .................................................................................................................... 1
1.2. Mangrove productivity .................................................................................................. 3
1.3. Mangroves as nursery areas ........................................................................................... 5
1.3.1. Mangroves versus other habitats ............................................................................ 5
1.3.2. Habitats within the mangroves .............................................................................. 8
1.3.3. Temporal variation ................................................................................................. 9
1.4. Mangroves of Darwin Harbour .................................................................................... 11
1.5. Project aims and objectives ......................................................................................... 13
1.5.1. Specific objectives ............................................................................................... 14
2. REVIEW OF SAMPLING METHODS AND DESCRIPTION OF STUDY AREA
......................................................................................................................................... 15
2.1. Review of sampling methods ....................................................................................... 15
2.2. Description of study area ............................................................................................. 21
2.2.1. Climate ................................................................................................................. 22
2.2.2. Physical description ............................................................................................. 22
2.3. Study locations ............................................................................................................ 24
2.3.1. Location 1 ............................................................................................................ 25
2.3.2. Location 2 ............................................................................................................ 28
2.3.3. Location 3 ............................................................................................................ 29
2.4. Site Preparation ............................................................................................................ 31
2.4.1. Access .................................................................................................................. 31
2.4.2. Sampling site preparation .................................................................................... 31
2.4.3. Topographic level ................................................................................................ 32
3. HABITAT STRUCTURE AND AQUATIC ENVIRONMENTAL VARIABLES. 33
3.1. Methods ....................................................................................................................... 35
3.1.1. Habitat structure ................................................................................................... 35
3.1.2. Environmental variables ...................................................................................... 36
3 .2. Results ......................................................................................................................... 3 7
3.2.1. Habitat structure ................................................................................................... 37
3.2.2. Environmental variables ...................................................................................... 42
3.3. Discussion .................................................................................................................... 58
3.3.1. Habitat structure ................................................................................................... 58
3.3.2. Environmental variables ...................................................................................... 60
4. A COMPARISON OF FISH CATCHES AT DAWN AND DUSK USING
TRAMMEL NETS IN MANGROVE FOREST HABITATS .................................. 65
4.1. Introduction ................................................................................................................. 65
4.2. Methods ....................................................................................................................... 66
4.2.1. Data analysis ........................................................................................................ 67
4.3. Results ......................................................................................................................... 68
4.3.1. Abundance and distribution ................................................................................. 68
4.3.2. Patterns in species composition ........................................................................... 73
4.4. Discussion .................................................................................................................... 73
5. DISTRIBUTION AND ABUNDANCE OF FISH IN THE MANGROVE FORESTS
OF DARWIN HARBOUR ........................................................................................... 76
5 .1. Introduction ................................................................................................................. 7 6
5 .2. Methods ....................................................................................................................... 7 8
5.2.1. Sampling design ................................................................................................... 78
5 .2.2. Data analysis ........................................................................................................ 81
5.3. Results ......................................................................................................................... 83
5.3 .1. Abundance and distribution ................................................................................. 8 3
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5.3.2. Analysis of abundance ......................................................................................... 89
5.3.3. Diversity .............................................................................................................. 97
5.3.4. Patterns in species composition ........................................................................... 99
5.3.5. Environmental variables .................................................................................... 104
5.4. Discussion .................................................................................................................. 106
5.4.1. Species composition .......................................................................................... 106
5.4.2. Temporal patterns .............................................................................................. 111
5.4.3. Spatial patterns ................................................................................................... 113
5.4.4. Conclusion ......................................................................................................... 118
6. DISTRIBUTION OF LARVAL AND JUVENILE FISH IN MANGROVE
HABITATS OF DARWIN HARBOUR ..........................•..•...............•.•...........•....... 120
6.1. Introduction ............................................................................................................... 120
6.2. Methods ..................................................................................................................... 122
6.2.1. Light traps .......................................................................................................... 122
6.2.2. Pit traps .............................................................................................................. 124
6.2.3. Data analysis ...................................................................................................... 125
6.3. Results ....................................................................................................................... 126
6.3.1. Light traps .......................................................................................................... 126
6.3.2. Pit traps .............................................................................................................. 134
6.4. Discussion .................................................................................................................. 142
6.4.1. Lighttraps .......................................................................................................... 142
6.4.2. Pit traps .............................................................................................................. 147
6.4.3. Conclusion ......................................................................................................... 149
7. DIETS AND TROPHIC STRUCTURE OF FISH FROM MANGROVE FORESTS
IN DARWIN HARBOUR .......................................................................................... 151
7 .1. Introduction ............................................................................................................... 151
7 .2. Methods ..................................................................................................................... 155
7.2.1. Study sites and sampling methods ..................................................................... 155
7 .2.2. Diet analyses ...................................................................................................... 155
7.2.3. General description of diet.. ............................................................................... 159
7.2.4. Dietary breadth .................................................................................................. 161
7 .2.5. Trophic groups ................................................................................................... 162
7 .2.6. Habitat comparison ............................................................................................ 162
7 .3. Results ....................................................................................................................... 162
7.3.1. Overall diet description ...................................................................................... 162
7.3.2. Sesarrnid predation ............................................................................................ 167
7.3.3. Dietary breadth .................................................................................................. 169
7 .3.4. Ontogenetic changes in diet. .............................................................................. 170
7.3 .5. Trophic groups ................................................................................................... 170
7.3.6. Habitat comparison ............................................................................................ 176
7 .4. Discussion .................................................................................................................. 179
7.4.1. General diet ........................................................................................................ 179
7.4.2. Dietary breadth .................................................................................................. 184
7.4.3. Ontogenetic changes in diet ............................................................................... 185
7 .4.4. Trophic groups ................................................................................................... 186
7 .4.5. Habitat comparison ............................................................................................ 190
7.4.6. Sesarrnid predation ............................................................................................ 191
7.4.7. Conclusion ......................................................................................................... 193
8. TOWARDS A TROPIDC MODEL OF DARWIN HARBOUR .......•..................•. 195
8.1. Introduction ............................................................................................................... 195
8.2. Methods ..................................................................................................................... 197
8.2.1. Parameter estimation .......................................................................................... 198
8.2.2. Missing groups ................................................................................................... 205
8.3. Balancing the model .................................................................................................. 205
8.4. Results and discussion ............................................................................................... 206
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9. GENERAL DISCUSSION AND CONCLUSIONS ................................................. 215
9.1. Temporal patterns among fish assemblages .............................................................. 216
9.2. Spatial patterns among fish assemblages ................................................................... 219
9.2.1. Abundance and distribution ............................................................................... 219
9.2.2. Species composition .......................................................................................... 219
9.3. Patterns among fish assemblages in relation to forest structure, aquatic environmental
variables and mangrove productivity ................................................................................... 220
9.3.1. Forest area and structural complexity ................................................................ 220
9.3.2. Aquatic environmental variables ....................................................................... 222
9.3.3. Mangrove productivity ...................................................................................... 223
9.4. Diets and trophic ecology of fish assemblages .......................................................... 224
9.5. Habitats within mangroves ........................................................................................ 227
9.6. Conclusion and recommendations ............................................................................. 228
9.6.1. Recommendations .............................................................................................. 229
10. REFERENCES ........................................................................................................... 231
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