Composition and abundance of freshwater fish - SAFE Project

69 Pages·2013·1.99 MB·English

Composition and abundance of
freshwater fish communities across a
land use gradient in Sabah, Borneo
© Clare Wilkinson
“In all works on Natural History, we constantly find details of the marvellous adaptation of animals to
their food, their habits, and the localities in which they are found”. Alfred Russel Wallace

© Clare Wilkinson © Clare Wilkinson

Clare Wilkinson
September 2013

A thesis submitted in partial fulfilment of the requirements for the degree
of Master of Science and Diploma of Imperial College London

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Declaration of own work

I declare that this thesis (insert full title)

Composition and abundance of freshwater fish communities across a
land use gradient in Sabah, Borneo

is entirely my own work and that where material could be construed as the
work of others, it is fully cited and referenced, and/or with appropriate
acknowledgement given.

Signature ……………………………………………………..

Name of student: Clare Wilkinson

Name of Supervisor: Dr. Robert Ewers

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CONTENTS
1. INTRODUCTION…………………………………………………………...9
1.1. Tropical freshwater fish diversity……………………………………..9
1.2. Threats to freshwater fish in Borneo………………………………...10
1.3. The Stability of Altered Forest Ecosystems (SAFE) Project………10
1.4. Project aims and objectives…………………………………………..11

2. BACKGROUND…………………………………………………………...12
2.1. Capture Mark Recapture of Freshwater fish……………………….12
2.1.1. Sampling and tagging methods……………………………………...12
2.1.2. Modelling fish abundance……………………………………………13
2.2. Freshwater fish in Borneo……………………………………………15
2.2.1. Overview of species…………………………………………………..15
2.2.2. Role in tropical forest streams……………………………………….16
2.3. Effects of land use change on freshwater fish in Borneo………...16
2.3.1. Logging………………………………………………………………...16
2.3.2. Conversion…………………………………………………………...18
2.4. Study Site: A land use gradient in Eastern Sabah, Borneo……..19
2.4.1. Yayasan Sabah Concession Area…………………………………19
2.4.2. Virgin Jungle Reserve……………………………………………….20
2.4.3. Benta Wawasan Oil Palm plantation………………………………20

3. METHODS………………………………………………………………....21
3.1. Framework……………………………………………………………..21
3.2. Data Collection………………………………………………………..21
3.2.1. Project design and location………………………………………….21
3.2.2. Trapping………………………………………………………………..22
3.2.3. Tagging protocol………………………………………………………23
3.2.4. Forest quality variables in the riparian zone……………………….24
3.2.5. Stream variables………………………………………………………25
3.3. Data analyses…………………………………………………………26
3.3.1. Dispersal……………………………………………………………….26
3.3.2. Abundance estimation………………………………………………...26
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3.3.3. Comparison of abundance across the land use gradient………….28
3.3.4. Methodological comparison…………………………………………..29
3.3.5. Community level comparisons across the land use gradient……..29

4. RESULTS…………………………………………………………………..31
4.1. Fish dispersal…………………………………………………………..31
4.2. Indices if land use gradient…………………………………………...32
4.3. Population modelling and estimation………………………………..33
4.4. Comparison of abundance across the land use gradient…………34
4.5. Methodological comparison………………………………………….37
4.6. Community similarity and species turnover rates………………….39

5. DISCUSSION……………………………………………………………...43
5.1. Response of fish to logging and conversion to oil palm…………..43
5.1.1. Species level…………………………………………………………..43
5.1.2. Community level………………………………………………………45
5.2. Dispersal……………………………………………………………….48
5.3. Capture Mark Recapture of fish……………………………………..48
5.4. Review of fish capture techniques at SAFE………………………..50
5.5. Project limitations and further research…………………………….51
5.5.1. Project design…………………………………………………………51
5.5.2. Land use variables……………………………………………………52
5.5.3. Capture Mark Recapture……………………………………………..53
5.6. Conclusion…………………………………………………………….54

6. REFERENCES……………………………………………………………55
7. APPENDICES…………………………………………………………….65
I – Model selection by species/site in Mark………………………...65
II – GLM Abundance estimate model selection……………………67
III – Effects of year and land use on relative species abundance.69

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LIST OF FIGURES
Figure 2.1: Map of the study site……………………………………………….. .11
Figure 3.1: Fish trapping methods, a) bottle trap, b) cast net……………….. .15
Figure 4.1: Dispersal a)all fish, b)N. everetti c)T. dourensis d)Rasbora……..23
Figure 4.2: PCA of riparian vegetation divides streams by land use…………24
Figure 4.3: Modelled abundance against land use indices……………………28
Figure 4.4: Comparison of trapping methods for focal taxa…………………...30
Figure 4.5: Multivariate ordination using PCoA of sites and species…………32
Figure 4.6: Absolute species turnover rates against indices of land use…….36

LIST OF TABLES
Table 3.1: Variables measured to indicate vegetation quality……………….17
Table 3.2: Models used to estimate abundance………………………………20
Table 4.1: Abundance estimates of focal taxa…………………………………26
Table 4.2: Results of mixed effects models comparing trapping methods…29

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LIST OF ACRONYMS

AIC Akaike’s Information Criterion
AICc Akaike’s Information Criterion corrected
ANOVA Analysis Of Variance
CMR Capture Mark Recapture
DBH Diameter at Breast Height
DVCA Danum Valley Conservation Area
GLM Generalised Linear Model
LF Logged Forest
OG Old growth (forest)
OP Oil Palm
PC1 Principle Component 1
PCA Principle Component Analysis
PCoA Principle Co-ordinates Analysis
PIT Passive Integrated Transponder
SAFE Stability of Altered Forest Ecosystems
VJR Virgin Jungle Reserve

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ABSTRACT
Malaysia has the highest levels of deforestation and production of palm oil
around the world. Due to the paucity of data on the ichthyofauna of Sabah,
understanding how this affects the diversity and abundance of freshwater fish,
is of great interest as levels of deforestation and conversion to oil palm
increase. This project used capture-mark-recapture to determine the
abundance and dispersal of three focal taxa (N. everetti, Tor dourensis,
Rasbora). Relative abundance was used to compare community similarity and
absolute species turnover rates, across the land use gradient. 200m stream
transects were established in old growth forest, logged forest and oil palm
catchments as part of the Stability of Altered Forest Ecosystems project.
Abundance of three focal taxa decreased as riparian vegetation and stream
quality decreased; despite this the highest abundance estimate was in oil
palm. Community analysis demonstrated a slight, albeit non-significant
difference between sampling years (p=0.054) and land use (p=0.098)
between sites, and relative abundance of species varied by year and land
use. Results need to be treated cautiously due to low recaptures rates and a
degree of over-dispersion in the data. The difference indicated over a land use
gradient is corroborated, but alternate hypotheses are somewhat divided in
the literature, as suggestions of differences at the mesohabitat scale and
possible barriers to migration need to be further investigated. It is
recommended that intensive research is conducted to obtain a full species list,
for the area in order to fully assess how logging and conversion affects fish
diversity and abundance in the short and long term. A critical assessment of
trapping methodologies was undertaken and recommendations as to the use
of trapping techniques are made accordingly.

Word count: 14,929
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ACKNOWLEDGMENTS
I would like to thank the SAFE project and the Sime Darby Foundation for
funding this project and allowing it to happen.

I extend great thanks to Dr. Rob Ewers, for giving me this opportunity,
supervising this project and providing invaluable advice in the field and during
the write-up.

All fieldwork was made possible by the SAFE project staff, who make working
in challenging conditions, not only possible, but fun and wanting to do more.
Minsheng and Sarah co-ordinated logistics, enabling research to run smoothly
and to schedule, whilst research assistants Sabri, James, Maria and Opong
are pro’s with a cast net, taught me Malay and enabled fieldwork to not only
happen but successfully catch nearly 3,000 fish and a terrapin! I could not
have completed field work without Rosa Gleave. She provided for support
throughout and made me laugh or a cup of tea after the hardest day’s
fieldwork.

Data contributions and priceless information were contributed from Victoria
Bignet, Sarah Luke, Holly Barclay and Anand Nainar. This enabled data and
relationships to be further explored.

Data analysis was made enjoyable by the great help of Jack Thorley and the
Silwood computer room. I would like to thank Beth Thomas and Sara Eckert
for reading drafts of the thesis, providing advice and cakes throughout the
time of write up.

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1. INTRODUCTION
Tropical rainforest ecosystems contain two-thirds of the world’s terrestrial
biodiversity (Gardener et al., 2009) but are one of the most threatened
ecosystems on the planet (FAO, 2006). Borneo lies within the Sunderland
hotspot and regrettably has the highest deforestation rates around the world
(Sodhi et al., 2010), with annual rates of deforestation reaching 1.3% (FAO,
2010). This deforestation has resulted in a matrix of degraded forest and
agricultural estates, with little primary forest existing outside forest reserves
and protected areas (McMorrow and Talip, 2001). In addition a shift in
agricultural practices for further economic gain now sees the highest levels of
palm oil production in Malaysia and Indonesia, in the world. Oil palm
plantations cover 1.2 million ha in the Malaysian state of Sabah in North
Borneo, with more being created on degraded, selectively logged, secondary
forest (McMorrow and Talip, 2001; Bradshaw et al., 2009; Bruhl and Eltz,
2010). Forest degradation and the increasing demand for palm oil are
accelerating forest loss. These factors, compounded with few studies
addressing the effects on biodiversity, concerns conservationists and
ecologists around the world (Laurance et al., 2012).

1.1. Tropical freshwater fish diversity
The majority of the world's freshwater fish biodiversity is contained within
tropical regions (Lowe-McConnell, 1987; Kottelat et al., 1993; Kottelat and
Whitten, 1996). Almost 10,000 species of freshwater fishes are currently
recognised (Nelson, 1994) with many more species awaiting discovery and
description (Kottelat and Whitten, 1996). The tropics of South-East Asia
possess less fish species than that of South America, but have a greater
diversity in the number of families (Kottelat et al., 1993). Malaysia (including
the states of Sabah and Sarawak in Borneo) is in the top 10 countries for
highest freshwater fish diversity, with more than 600 described species
(Kottelat and Whitten, 1996). Despite these figures, the ichthyofauna of Asia,
and particularly Borneo, remains patchy because of concentrations of studies
in easily accessible areas. The Kalabakan basin, where this project takes
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place, is not well documented due to a lack of appropriate species counts and
descriptions (Dudgeon, 2000; Martin-Smith, 1998b).

1.2. Threats to freshwater fish in Borneo
As figures above state, logging and conversion to oil palm in Sabah is
continuing and increasing at an unprecedented rate. A number of projects
have studied forest fragmentation and deforestation (Lovejoy et al., 1983;
Casant et al., 2002; Ritters et al., 2000) but few have directly quantified the
effects of fragmentation and land use change on tropical forest ecosystems
(Ewers et al,. 2011), and fewer still have focused on fish. It is therefore
essential to be able to draw comparisons between land uses, on the effects
on biodiversity at the species and community level.

The removal of tropical forest cover during timber extraction represents an
extreme form of disturbance, with potentially far-reaching effects on fish
biodiversity. Positive and negative effects have been observed on freshwater
fish abundance and community diversity across different land uses (Martin-
Smith, 1998a; Iwato et al., 2005; Nunakawa, 2005). A number of hypotheses
are therefore presented: altered allochthonous inputs and solar regulation
(Nunakawa, 2005), mesohabitats (Martin-Smith, 1998b) and significant
barriers to migration (Martin-Smith and Laird, 1998). The lack of corroboration
between studies strengthens the need to understand the impact land use
change has on freshwater fish. Until now, no study has been conducted to
quantify species abundance or community composition between streams
covered by the SAFE project.

1.3 The Stability of Altered Forest Ecosystems (SAFE) Project
The SAFE project is one of the largest, established ecological experiments
investigating responses of biodiversity to land use change and fragmentation
(Ewers et al., 2011). Based in Sabah, Malaysia, the SAFE project’s principal
aim is to quantify the effects of logging, deforestation and fragmentation on
the biodiversity and physical processes intrinsic to tropical forests. The project
makes use of the planned expansion of oil palm activities over time. While the
focus may be on the responses of forest fragmentation and conversion, the
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