MB 3200 201 9 Marine Conservation .docx

MB 3200
201 9
Marine
Conservation
Biology
1
MB3200
Marine Conservation Biology
Marine Biology and Aquaculture,
Australia’s endangered handfish

College of Science and Engineering,
James Cook University
2019 Subject Manual
2
SUBJECT CO-ORDINATOR
Geoff Jones (142-225)
Consulting hours: Thursday 9:30am – 2:00pm
Email: [email protected]
LECTURER, ENQUIRIES & WEB MANAGER
Prof. Jeff OBBARD
Email: [email protected]

CONTRIBUTING LECTURERS
Dr Lisa Bostrom-Einarsson (JCU)
Dr Andrew Chin (JCU)
Dr Philip Munday (JCU)
Professor Garry Russ (JCU)
Dr Hugh Sweatman (AIMS)
Dr Lynne van Herwerden (JCU)
Dr David Williamson (JCU)
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CONTENTS
1. ABOUT THIS SUBJECT
...............................................................................................
............. 4
2. CLASS ORGANIZATION AND TIMETABLE
........................................................................... 10

3. LECTURE TOPICS AND RECOMMENDED READING
…………….. ....................................... 0
4. THREATENED MARINE SPECIES: STATUS REPORTS
………….… ..................................... 9
5. TUTORIALS
……………..….………………………………………..……... 28
6. EXAMINATION INFORMATION AND STUDY
QUESTIONS ………….. 63
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1. ABOUT THIS SUBJECT

Marine Conservation Biology is a 3rd year BSc subject intended
for students majoring in the fields
of marine biology, ecology, conservation biology or
environmental impact assessment. It runs in
the second semester (July-November) and consists of 25
lectures and 12 tutorials that are a mix of
practical exercises, debates, discussions and presentations.
Attendance at all tutorials is
compulsory and attendance at all lectures is highly
recommended. To enter this subject you
should have completed Marine Biology to second year level.
There are no inadmissible subject
combinations.
1.1 WHY MARINE CONSERVATION BIOLOGY?
So you have chosen to do Marine Conservation Biology!
Congratulations on your wise choice.
There is an urgent need to focus science and research on
conservation issues in the marine
environment. Many marine ecosystems are on the verge of
collapse, many habitats have been
decimated and many believe we are on the threshold of a
human-induced mass extinction event.

The mission of this subject is to develop scientific skills and
enhance employment prospects to
confront the biodiversity crisis in the marine environment.
Conservation biology is the application of scientific
methodology to the conservation of biological
diversity. It is an ecological science that targets the causes and
seeks remedies to the disastrous
global decline in biodiversity that we have already seen on land
and are beginning to see in our
harbours and oceans. Marine conservation biology is a
relatively new and rapidly changing
discipline in marine biology. New concepts are developing, new
hypotheses are being tested and
alternative views debated - all fuelled with a sense of urgency
as evidence of the widespread
decimation of marine habitats and decline of marine species
accumulates at an alarming rate.
We will start this subject with some of the general ideas on
conservation and biodiversity that were
largely developed for terrestrial species and see which of these
principles can be applied to marine
organisms. We will then examine new approaches that target
threats to marine habitats and

species, with an emphasis on novel alternatives to terrestrial
conservation practices. Both single
species and whole ecosystem approaches to marine conservation
will be addressed. Particular
attention will be devoted to the effectiveness of marine reserves
for biodiversity conservation and
the design of reserve networks. In addition, we will take a close
look at the endangered species
concept and how it can be effectively applied to threatened
marine species.
For some species and habitats conservation may be too late. If
the dire predictions concerning the
demise of seagrass beds, mangroves and coral reefs turn out to
be correct, and if all the major
fisheries of the world continue to collapse at the same alarming
rate, we will see the discipline
metamorphose from the principles of conservation (of what we
have) to the restoration (of what we
had). To this end, this subject will culminate with a look at the
emerging principles and practices of
rehabilitating severely impacted populations and habitats.
1.2 SUBJECT CONTENT:

This subject will take an ecological approach to human impacts
on and conservation of marine
habitats and species, from a local (Australia), regional (South
East Asia) and global (Planet Earth)
perspective.
• It will describe the ecological effects of overfishing,
sedimentation and nutrient enrichment,
habitat loss, pollution, marine introductions and climate change.
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• Case studies on the types and scales of human impacts on
coral reefs, seagrass beds, kelp
forest and pelagic ecosystems will be examined.
• Sampling designs and ecological indicators will be developed
for assessing the magnitude
and scale of impacts on marine habitats.
• Current practices employed in the conservation and
management of marine habitats and
endangered marine species will be examined.
• A central focus will be on the ecological principles and

practice of designing marine
reserves and determining how well they work.
• The subject will examine the meanings of the terms 'rare' and
'endangered' for marine
organisms, focussing on factors associated with the risk of
extinction.
• Small population theory and conservation genetics will be
discussed for large and/or highly
exploited marine organisms, including sharks, other large
predatory fishes, reptiles, marine
birds and mammals.
• The final topic of interest will be restoration ecology - the
principles and practice of
enhancing populations of rare species and restoring damaged
biological communities.
• Tutorials will facilitate the debate of all current issues in
marine conservation.
1.3 LEARNING OBJECTIVES:
At the end of this subject, a student should have the ability to:
• Appraise the status of marine conservation biology and
emerging theory.

• Assess the key threats to marine species and ecosystems,
including overfishing, habitat
loss and fragmentation, pollution and climate change.
• Compare the effectiveness of different approaches for
protecting marine biodiversity,
including the endangered species concept, marine reserves and
integrated coastal zone
management.
• Examine the roles of population enhancement and habitat
restoration in circumstances
where conservation efforts have failed.
• Practice methods to undertake literature searches and
synthesize information on critical
issues in marine conservation and criticize published materials.
• Apply skills in environmental impact assessment and
ecological surveys of tropical
organisms.
• Evaluate the status of potentially endangered marine species
and formulate management
plans.
• Demonstrate debating and presentation skills in evaluating
controversies and knowledge in

marine conservation biology.
1.5 STRUCTURE OF THE SUBJECT
The basic structure of this subject is outlined below. While we
will try to keep to this logical order in
the weekly schedule (section 2.2), occasionally lectures have to
be swapped around to fit in guest
lecturers. Full lecture notes, copies of slides and screencasts
can be accessed through LearnJCU.
Attendance of lectures is highly recommended as updated
information is provided, breaking news
is presented and assistance with assignments is given.
Attendance at tutorials is compulsory and
you receive credit for attending, participating and handing in
the tutorial worksheet. To participate it
is important that you read over relevant material prior to your
tutorial. Refer to appropriate sections
of the manual or log onto the LearnJCU website a few days
before each tutorial.

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1.5.1 Lecture Topics
Section A: General introduction to marine conservation biology
and biodiversity
“Scope of marine conservation biology” (Lecture 1)
“History of conservation biology and relevance to the marine
environment” (Lecture 2)
“What is biodiversity and how is marine biodiversity
threatened?” (Lecture 3)
Section B: Threats to marine biodiversity
“Overfishing – top down destruction of marine ecosystems”
(Lecture 4)
“Nutrient enrichment – bottom up destruction of marine
ecosystems” (Lecture 5)

“Marine introductions – diversity of effects on marine
ecosystems” (Lecture 6)
“Ocean warming – global impacts on marine habitats and
species” (Lecture 7)
“Ocean acidification - the next big problem for coral reefs”
(Lecture 8)
Section C: Marine environmental impact assessment
“Marine environmental impact assessment” (Lecture 9)
“Marine organisms as environmental indicators” (Lecture 10)
“Monitoring the Great Barrier Reef” (Lecture 11)
Section D: Marine reserves: conserving marine biodiversity
“Marine reserves: do they work?” (Lecture 12)
“Marine reserve design: choosing sites, sizes and spacing”
(Lecture 13)

“Do green zones work? Assessing the ecological effects of
management zoning in the Great
Barrier Reef Marine Park” (Lecture 14)
“Marine reserves and conservation in the Philippines” (Lecture
15)
“Larval connectivity and the design of marine protected area
networks” (Lecture 16)
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Section E: Rarity, small populations and conservation genetics
“Endangered species concept for threatened marine organisms”
(Lecture 17)
“Extinction, resilience and the characteristics of marine
populations” (Lecture 18)
“Rarity and extinction risk in coral reef fish communities”

(Lecture 19)
“Small population theory and metapopulation dynamics”
(Lecture 20)
“Conservation of genetic diversity in the marine environment”
(Lecture 21)
“Shark conservation in tropical marine waters” (Lecture 22)
Section F: Restoration of marine populations and communities
“Enhancement of marine populations as a conservation tool”
(Lecture 23)
“Reversing human impact: restoration of marine communities”
(Lecture 24)
“Habitat restoration on coral reefs” (Lecture 25)
The end...
“Questions, answers, (Lecture 26)

1.5.2 Tutorial topics (see Section 5 for details)
1. Verbal Debate: “The biodiversity dilemma: species versus
ecosystems!”
Section 5.1 and Learn JCU
2. Computer-based tutorial: “Coral reefs in crisis: over 50 years
of escalating threats”
Section 5.2 and LearnJCU.
3. Debate: “Climate change: advocate or skeptic?”
Section 5.3 and LearnJCU
4. Computer-based tutorial: “Marine reserves: do they work?”
5. Information session: How to write-up the Marine Reserves
Report”
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6. Do in your own time, post your video to the MB3200
Facebook page Stories from home: Post
a video of yourself giving a 5min talk on a recent paper from
your home country or state.
7. Computer-based tutorial: “World Map: approaches to
selecting sites for marine reserves”
8. Paper critique: “Marine reserves have rapid and long-lasting
effects”
9. Computer workshop: “Classifying threatened marine species
using RAMAS Red List”
10-11. Student poster presentations: “Threatened marine
species”
1.6 ASSESSMENT
Final examination 40%

In subject assessment (total) 60%
In subject assessment:
(1) Marine reserves report (20%)
Section 5.4 [Due Thursday 02 January]
(2) Threatened species status report and poster presentation
(25%) Section 4.1
There are two parts to this assignment:
Status report (20%) [Due Thursday, 16 January]
Poster presentation (5%) [Tutorials 10]
(3) Tutorial Attendance/Participation (10%)
Submitting assignments
You are required to submit all assignments online in LearnJCU
by the due date (see LearnJCU
guide for instructions). There is no need to submit hard copies.
You may submit draft versions of

your assignments to check for levels of close matching with
other documents that may indicate
plagiarism (see section below on plagiarism). Don’t worry about
a close match when it only
involves reference lists!
Please do not email assignments to the subject coordinator.
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Endangered leafy sea dragon
It is recommended that you keep both hard copies and electronic
copies of all your
assignments in case you have computer issues or lose your
memory stick. When working
on assignments, make sure you save regularly, keep backups
and print out draft copies.
Try to begin assignments as soon as you have the material
required. Requests for extensions

should not be made more than one week before an assignment
due date. Also, these requests
should not be made to the class co-ordinator. Fill out an
extension request form at Academic
Services (Building 34, Room 212) and, if for medical reasons,
attach a copy of a medical
certificate.
Late assignments: For every day an assignment is late, it will be
marked out of 1 percentage point
less. That is, an assignment worth 15% will be marked out of
14% if it is one day late, and 13% if it
is 2 days late etc. After one-week, late assignments will not be
accepted.
Assignment marking and feedback
We will endeavour to have assignments marked and provide
feedback approximately 2 weeks
after the due date (as long as you submit assignments on time!).
Assignments will be marked
according to the marking scheme provided (in the folder for
each assessment) so please refer to
the marking scheme as you work on each assignment. Both
generic and specific comments on

your assignments will be provided in LearnJCU to assist you in
the future.
We are happy to discuss requirements and marking criteria
before you hand in assignments. For a
quick response, email [email protected]
Plagiarism
Plagiarism is the act of taking and using another's work as one's
own (including published works,
information from web sites and assignments by other students).
It includes doing the following
without the due acknowledgment or clear indication of origin:
directly copying any part of anyone
else's work; using very close paraphrasing or summarising of
another's work; using or developing
an idea or thesis derived from another's work; using the
experimental results that have been
obtained by someone else.
Plagiarism is serious! Take special care not to copy from each
other, from assignments submitted
in previous years or for other subjects, or from published works
or websites. It is not allowable to
copy text, even if you cite the original document. Plagiarism

may result in the offending piece of
assessment being rejected by markers and may lead to
disciplinary action. To detect plagiarism,
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electronic versions of your assignments will be scanned using
software designed to detect
repeated tracts of text.
2. CLASS ORGANIZATION AND TIMETABLE
2.1 LECTURE TIMES AND TUTORIAL GROUPS
Lecture: Thursday 9:00 – 11:50 am
Tutorial Thursday 1:00 – 2:50 pm
NB. You will be scheduled into 1 of 3 compulsory tutorial
groups, which are an integral part of this
subject. Choose one that suits your timetable and sign up to the
group on LearnJCU. There will be

a 1-2hr tutorial each week, either a discussion tutorial or a
computer workshop (alternating through
the semester). Check the weekly schedule (section 2.2) to
confirm where your tutorial is each
week.
2.2 WEEKLY SCHEDULE
LECTURES TUTORIALS
Week/
Date
TUESDAY 09:00 - 11:50 TUESDAY 13:00 – 14:50
Week 1
14
November
Lecture 1.

“Scope of marine conservation
biology”
Lecture 2.
“History of conservation biology and
relevance to the marine
environment”
Lecture 3.
“What is biodiversity and how is
marine biodiversity threatened”
No tutorial this week.
Log on to LearnJCU and explore subject materials in your
own time. Familiarise yourself with subject structure
and deadlines!
Week 2
28
November
Lecture 4.

“Overfishing – top down
destruction of marine
ecosystems”
Lecture 5.
“Nutrient enrichment – bottom up
destruction of marine ecosystems”
Lecture 6.
“Marine introductions – diversity of
effects on marine ecosystems”
Tutorial 1
Verbal Debate: “The biodiversity dilemma: species versus
ecosystems!” Section 5.1 and LearnJCU
Week 3
05
December
Lecture 7.
“Ocean warming – global
impacts on marine habitats

and species”
Lecture 8.
“Ocean acidification – the next big
problem for coral reefs”
Lecture 9.
“Marine environmental impact
assessment”
Tutorial 2
Literature search: “Coral reefs in Crisis: Over50 years of
escalating threats” Section 5.2 and Learn JCU
Week 4
05
December
Lecture 10.
“Marine organisms as
environmental indicators”
Lecture 11.

“Monitoring the Great Barrier Reef”
Lecture 12.
“Marine reserves: do they work?”
Tutorial 3
Verbal debate: “The global warming controversy:
advocate or skeptic?” Section 5.3 and LearnJCU
Week 5
12
December
Lecture 13.
“Marine reserve design:
choosing sites, sizes and
spacing”
Lecture 14.
Do green zones work? Assessing the
ecological effects of management
zoning in the Great Barrier Reef
Marine Park

Lecture 15.
Marine reserves and conservation in
the Philippines
Tutorial 4
Computer-based tutorial : Marine reserves: do they
work”? Section 5.4 and LearnJCU
1
Week/
Date
LECTURES
Thursday 09:00 - 11:50
TUTORIALS
Thursday 13:00 – 14:50
Week 6
19
December

Lecture 16:
Larval connectivity and the
design of marine protected
area networks
Lecture 17:
Endangered species concept
for threatened marine
organisms
Lecture 18:
Extinction, resilience and the
characteristics of marine
populations
Tutorial 5
Information session: How to write-up the
Marine Reserves Report
26

December
PUBLIC HOLIDAY
Tutorial 6
Do in your own time, post your video to the MB3200
Facebook page Stories from home: Post a video of
yourself giving a 5min talk on a recent paper from your
home country or state.
Week 7
02 January
Lecture 19:
Rarity and extinction risk
in coral reef fishes
Lecture 20:
Small population theory and
metapopulation dynamics
Lecture 21:
Conservation of genetic diversity

in the marine environment
Tutorial 7
Computer-based tutorial: “World Map: approaches to
selecting sites for marine reserves”
Week 8
07 January
Lecture 22:
Shark conservation and
management
Lecture 23:
Enhancement of marine
populations as a conservation
tool
Lecture 24:

Reversing human impact:
restoration of
marine communities
Tutorial 8
Paper critique: Marine reserves have rapid and long-
lasting effects Section 5.7 and LearnJCU
Week 9
14 January
Lecture 25:
Habitat restoration on coral
reefs
Lecture 26:
Questions & answers
Tutorial 9
Computer workshop: Classifying threatened marine

species using RAMAS Red List
Week 10
21 January
Tutorial 10
Poster presentations: Threatened marine species
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3. LECTURE TOPICS AND RECOMMENDED READING
There are links to recommended readings on LearnJCU, in the
folder for each lecture under
‘Subject Materials’, and also under ‘Readings’. For most of the
lectures, we provide a complete

written summary of the lecture and the lecture slides as pdfs.
All lectures are recorded and
screencasts will be provided on LearnJCU.
LECTURE 1: SCOPE OF MARINE CONSERVATION
BIOLOGY
This lecture defines the subject matter for conservation biology
as a discipline and outlines the
structure and scope of the subject.
New TR (2000) Conservation biology: an introduction for
Southern Australia. Chapter 1, pp 1-21.
Oxford University Press
Soule MF (1991) Conservation: tactics for a constant crisis.
Science 253:744-749
Vitousek PM, Mooney HA, Lubchenco J, Melillo JM (1997)
Human domination of earth's
ecosystems. Science 277:494-499
Halpern BS et al. (2008) A global map of human impact on
marine ecosystems. Science
319:948952

LECTURE 2: HISTORY OF CONSERVATION BIOLOGY
AND ITS RELEVANCE TO THE
MARINE ENVIRONMENT
The purpose of this lecture will be to briefly review the history
of terrestrial conservation biology
and evaluate whether or not terrestrial theory has any
applicability to marine organisms. It
discusses why terrestrial models relating to reserve design and
small population theory have
limited applicability to marine organisms. It suggests that
marine conservation biology requires a
substantially different emphasis.
Simberloff D (1988) The contribution of population and
community biology to conservation science.
Annual Review of Ecology and Systematics 19:473-511
Diamond JM (1975) The island dilemma: lessons of modern
biogeographic studies for the design
of nature reserves. Biological Conservation 7:129-146
LECTURE 3: WHAT IS BIODIVERSITY AND HOW IS

MARINE BIODIVERSITY THREATENED?
This lecture discusses the various meanings of the term
biodiversity in an attempt to come to grips
with the fundamental goal of conservation biology. It discusses
how we measure biodiversity, from
genes to ecosystems and evaluates current opinion as to the
primary threats to biodiversity in
terrestrial environments. The threats to marine biodiversity are
contrasted with terrestrial
environments. Key threats, including overfishing, nutrient
enrichment, habitat destruction, marine
introductions and global warming are evaluated.
Mora C, Tittensor DP, Adl S, Simpson A, Worm B (2011) How
many species are there on earth
and in the ocean? Public Library of Science, Biology 9:635-45
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Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GAB,
Kent J (2000) Biodiversity hotspots
for conservation priorities. Nature 403: 853-858

Worm B et al. (2006) Impacts of biodiversity loss on ocean
ecosystem services. Science
314:787790
LECTURE 4: OVERFISHING – TOP DOWN DESTRUCTION
OF MARINE ECOSYSTEMS
This lecture will describe the catastrophic state of marine
fisheries, and highlight both the direct
and indirect effects of fishing on marine ecosystems.
Jackson JBC et al. (2001) Historical overfishing and the recent
collapse of coastal ecosystems.
Science 293:629-638
Hilborn R et al. (2003) State of the world’s fisheries. Annual
Review of Environment and
Resources 28:359-399
Pitcher TJ, Cheung WWL (2013) Fisheries: Hope or despair?
Marine Pollution Bulletin 74:506516.
LECTURE 5: NUTRIENT ENRICHMENT – BOTTOM UP
DESTRUCTION OF MARINE
ECOSYSTEMS

The seagrass decline represents the greatest loss of any single
habitat in the sea. This lecture
documents the global decline in seagrass beds and the reasons
for the decline, focussing on
nutrient enrichment and turbidity. The ecological consequences
for other organisms dependent
upon seagrass are also discussed.
Orth RJ et al. (2006) A global crisis for seagrass ecosystems.
Bioscience, 56: 987-996
Diaz RJ, Rosenberg R (2008) Spreading dead zones and
consequences for marine ecosystems.
Science 321:926-929
LECTURE 6: MARINE INTRODUCTIONS – DIVERSITY OF
EFFECTS ON MARINE
ECOSYSTEMS
The accidental transfer of marine organisms by ships has
reached epidemic proportions. This
lecture describes the ecological consequences of marine
introductions, documenting the total
change of habitats in some harbours and estuaries. Potential

methods for eliminating accidental
transport are discussed.
Carlton JT (1996) Pattern, process, and prediction in marine
invasion ecology. Biological
Conservation 78:97-106
Carlton JT and Geller JB (1993) Ecological roulette: the global
transport of non-indigenous marine
organisms. Science 261:78-82
Grosholz E (2002) Ecological and evolutionary consequences of
coastal invasions. Trends in
Ecology and Evolution 17:22-27
LECTURE 7: OCEAN WARMING – GLOBAL IMPACTS ON
MARINE HABITATS AND
SPECIES
This lecture the latest information on ocean warming and the
mechanisms by which this will impact
on coral reefs.

2
Walther GR et al. (2002) Ecological responses to recent climate
change. Nature 416: 389-395
Pratchett MS et al. (2008) Effects of climate-induced coral
bleaching on coral-reef fishes -
ecological and economic consequences. Oceanography and
Marine Biology: An Annual
Review 46:251-296
LECTURE 8: OCEAN ACIDIFICATION – THE NEXT BIG
PROBLEM FOR CORAL REEFS
This lecture will outline the predicted effects of increasing CO2
on the pH of the ocean and
emerging information to suggest it will have a catastrophic
effect on organisms with calcium
carbonate skeletons. Increasing evidence suggests fish sensory
systems will also be disrupted.
Munday PL, Jones GP, Pratchett MS, Williams AJ (2008)
Climate change and the future for coral
reef fishes. Fish and Fisheries 9: 261-285
Doney SC et al. (2012) Climate change impacts on marine

ecosystems. Annual Reviews in Marine
Science 4:11-37.
LECTURE 9: MARINE ENVIRONMENTAL IMPACT
ASSESSMENT
Developing models that reliably predict the ecological cost of
human activities requires that we
build up an understanding of how these activities affect natural
populations and communities.
Reliable models will enable us to forecast detrimental human
impacts before they occur, minimize
effects as they occur and/or enhance recovery after they have
occurred. To do this we need to: (1)
Distinguish effects on populations and communities from
normal background variability; (2)
Measure and assess the spatial and temporal scales over which
impacts and recovery may occur;
(3) Develop an understanding of the mechanisms that cause the
effects. This lecture discusses
these issues.
Kaly UL and Jones GP (1997) Minimum sampling design for
detecting the magnitude and scale of

human impacts on coral reefs. Proceedings of the Eighth
International Coral Reef
Symposium, Panama 2:1479-1483
Underwood AJ (1995) Detection and measurement of
environmental impacts. In: Coastal marine
ecology of temperate Australia (Underwood, A.J. & Chapman,
M.G., editors), University of
NSW Press
LECTURE 10: MARINE ORGANISMS AS
ENVIRONMENTAL INDICATORS
“Indicator” species are “organisms which have certain
characteristics making them suitable for
detecting and forecasting impacts at some level of biological
organization, from biochemical to
ecosystem” (Soule & Kleppel 1988). A wide variety of criteria
for the selection of ideal indicator
species have been advocated. The aims of this lecture are: (1)
To critically examine the criteria for
the selection of indictor species; (2) Argue against the
“shopping list” approach in favour of a
smaller number of criteria stemming from the practical
limitations of sampling, and the ecological

and social importance of the species present in the community.
Jones GP and Kaly UL (1995) Criteria for selecting marine
organisms in biomonitoring studies.
pp. 39-56, In: Detecting Ecological Impacts: Concepts and
applications in coastal habitats
(Schmitt RJ, Osenberg CW eds), Academic Press, San Diego
3
Noss RF (1990) Indicators for monitoring biodiversity: a
hierarchical approach. Conservation
Biology 44:355-364
LECTURE 11: MONITORING THE GREAT BARRIER REEF
In this guest lecture, the leader of the AIMS long-term
monitoring team will describe how one goes
about monitoring the health of the largest barrier coral reef
system in the world.
De’ath G, Fabricius KE, Sweatman H, Puotinen M (2012) The
27-year decline of coral cover on the

Great Barrier Reef and its causes. Proceedings of the National
Academy of Sciences
109:17995-17999.
Sweatman H, Delean S, Syms C (2011) Assessing loss of coral
cover on Australia’s Great Barrier
Reef over two decades, with implications for longer term-
trends. Coral Reefs 30:521–531.
LECTURE 12: MARINE RESERVES: DO THEY WORK?
Marine reserves or marine protected areas (MPA’s) have
become one of the major tools for the
management of coastal marine habitats and exploited marine
organisms. They continue to be
established in the belief that they can protect a “representative”
range of species and habitats,
where single-species approaches to marine conservation are
doomed to fail. The first aim of this
lecture is to describe the ecological effects of marine reserves:
(a) How do they affect the
abundance and structure of exploited populations, both within
and outside protected areas?; (b)
What are the community-wide effects of marine reserves?

Generalisations will be illustrated using
case studies on marine reserves from three different habitats: (i)
Coral reefs; (ii) Temperate rocky
shores; and (iii) Temperate sub-tidal rocky reefs. The second
question to consider is whether or
not the database strong enough to support the claims made for
marine reserves.
Gell FR and Roberts CM (2003) Benefits beyond boundaries:
the fishery effects of marine
reserves. Trends in Ecology and Evolution. 18:448-455
Jones GP, Cole RC, Battershill CN (1993) Marine reserves: do
they work? pp. 29-45. In: Battershill
CN (ed) Proceedings of the 2nd International Temperate Reef
Symposium, Auckland, 1992
Lester SE et al. (2009) Biological effects within no-take marine
reserves: a global synthesis.
Marine Ecology Progress Series 384:33-46.
LECTURE 13: MARINE RESERVE DESIGN: CHOOSING
SITES, SIZES AND SPACING
Now that we know marine reserves work, the next obvious
questions are: How big should they be?

What shape should they be? Where should they be? How many
should there be? How should they
be arranged in space? Our goal in seeking answers to these
questions is how to achieve
maximum protection for the greatest number of species. There
has been considerable attention to
these questions in the design of nature reserves on land,
although the theory has not often been
put into practice. We introduce WORLDMAP, a software
package designed to trial different
selection strategies for maximizing biodiversity in reserves. The
goal is to find a selection algorithm
that maximises the representation of species in marine reserves
and provides the greatest
concordance among different taxa. We introduce a tutorial in
which we compare
complementarity, diversity hot spot and endemicity hotspots for
both fish and corals in Kimbe Bay,
Papua New Guinea. These approaches are contrasted with
simple random selection of reserve
sites.
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Beger M, Jones GP, Munday PL (2003) Conservation of coral
reef biodiversity: a comparison of
reserve selection procedures for corals and fishes. Biological
Conservation 111:53-62
McNeill SE (1994) The selection and design of marine protected
areas: Australia as a case study.
Biodiversity and Conservation 3:586-605
McNeill SE and Fairweather PG (1993) Single large or several
small marine reserves? An
experimental approach with seagrass fauna. Journal of
Biogeography 20:429-440
Pressey RL, Humphries CJ, Margules CR, Vane-Wright RI,
Williams PH (1993) Beyond
opportunism: key principles for systematic reserve selection.
Trends in Ecology and Evolution
8:124-128
Reid WV (1998) Biodiversity hotspots. Trends in Ecology and
Evolution 13:275-289
LECTURE 14: DO GREEN ZONES WORK? ASSESSING THE
ECOLOGICAL EFFECTS OF
MANAGEMENT ZONING IN THE GREAT BARRIER REEF
MARINE PARK

This lecture will examine the long-term effects of the rezoning
of the Great Barrier Reef (GBR)
Marine Park in 2004, when 33% of the reef was protected in
“no-take areas”. The effects of
reserve status on the abundance, biomass and reproductive
potential of targeted marine fishes will
be addressed. It will examine the evidence for “fishery
squeeze” (overfishing in response to
reducing the area for fishing) and the net effects of reserve
status on fish abundance on the GBR.
The lecture will also examine effects of reserve status on the
abundance of non-target species,
including overall fish community structure and coral cover. It
will examine the evidence for
noncompliance or fishing in green zones by surveying lost or
discarded fishing gear. Finally, it will
examine whether marine reserves can reduce the level of coral
disease by minimizing mechanical
damage due to fishing.
Lamb JB, Wenger AS, Devlin MJ, Ceccarelli DM, Williamson
DH, Willis BL. (2016) Reserves as
tools for alleviating impacts of marine disease. Philosophical

Transactions of the Royal
Society B 371:20150210
McCook LJ, Ayling AM, Cappo M, Choat JH, Evans RD,
DeFreitas DM, Heupel M, Hughes TP,
Jones GP, Mapstone B, Marsh H, Mills M, Molloy F, Pitcher
CR, Pressey RL, Reichelt R,
Russ GR, Sutton S, Sweatman HPA, Tobin R, Wachenfeld DR,
Williamson DH (2010)
Adaptive management of the Great Barrier Reef: A globally
significant case study in marine
protected area networks. Proceedings of the National Academy
of Science 43:18278-18285
Williamson DH, Ceccarelli DM, Evans DM, Jones GP, Russ GR
(2014) Habitat dynamics, marine
reserve status and the decline and recovery of coral reef fish
communities. Ecology and
Evolution 4:337-354
LECTURE 15: MARINE RESERVES AND CONSERVATION
IN THE PHILIPPINES
Dr Russ summarizes 20 years of research on the effectiveness of
marine reserves in protecting
fish stocks at two heavily fished sites in the Philippines. He has

recorded a continual increase in
fish biomass since the reserves were established and predicts
populations may need to be
protected for 30-40 years before full recovery will be observed.
Evidence for spill-over effects that
may enhance adjacent fished areas is presented. The need for
inter-generational management
strategies is stressed.
Russ GR and Alcala AC (1996) Do marine reserves export adult
fish biomass? Evidence from Apo
Island, central Philippines. Marine Ecology Progress Series
132:1-9
5
Russ GR and Alcala AC (1999) Management histories of
Sumilon and Apo marine reserves,
Philippines, and their influence on national marine resource
policy. Coral Reefs 18:307-319
Russ GR, Miller KI, Rizzari JR and Alcala AC (2015) Long-
term no-take marine reserve and
benthic habitat effects on coral reef fishes. Marine Ecology
Progress Series 529:233-248

LECTURE 16: LARVAL CONNECTIVITY AND THE DESIGN
OF MARINE PROTECTED AREA
NETWORKS
An understanding of the degree of connectivity between marine
populations is critical to
conservation, but remains unknown for the vast majority of
marine organisms. The degree of larval
dispersal has implications for assessing the susceptibility of
populations to overfishing, their ability
to recover, the spread of disease and so on. Critical design
features for marine reserves, such as
reserve size and spacing, will ultimately be reliant on
information on larval dispersal. This lecture
describes new approaches for assessing larval dispersal,
including larval marking, otolith
microchemistry and new genetic techniques.
Almany GR et al. (2017) Larval fish dispersal in a coral reef
seascape. Nature Ecology and
Evolution 1:1-7
Harrison HB, Williamson DH, Evans RD, Almany GR, Thorrold
SR, Russ GR, Feldheim KA, van

Herwerden L, Planes S, Srinivasan M, Berumen ML, Jones GP
(2012) Larval export from
marine reserves and the recruitment benefit for fish and
fisheries. Current Biology 22:1023–
1028.
Jones GP, Srinivasan M, Almany GR (2007) Population
connectivity and conservation of marine
biodiversity. Oceanography 20:100-111
Sale PF et al. (2005) Critical science gaps impede use of no-
take fishery reserves. Trends in
LECTURE 17: ENDANGERED SPECIES CONCEPT FOR
THREATENED MARINE
ORGANISMS
The goal of this lecture is to discuss endangered species
concepts and whether or not they can be
applied to the large majority of marine populations. The IUCN
red-list categories are defined and
the data requirements discussed. We give a demonstration of
RAMAS, a software package for

determining the status of potentially threatened marine species.
Other characteristics of potentially
threatened marine species are discussed.
Jones GP, Kaly UL (1995) Conservation of rare, threatened and
endemic marine species in
Australia. Status of the marine environment report for Australia,
Technical Annex 1: The
marine environment, pp. 183-191
Mace GM, Lande R (1990) Assessing extinction threats:
towards a re-evaluation of IUCN
threatened species categories. Conservation Biology 5:148-157
LECTURE 18: EXTINCTION, RESILIENCE AND THE
CHARACTERISTICS OF MARINE
POPULATIONS
This lecture discusses the concepts of rarity and extinction for
marine organisms. The relative
threats of global, local and ecological extinction are discussed.
Different kinds of rarity are
described, including low local abundance and small geographic
range. The lecture discusses why

many organisms are naturally rare and whether or not such
organisms are endangered. Other
6
characteristics of marine populations that are relevant to their
conservation organisms are
described.
Carlton JT, Geller JB, Reaka-Kudla ML, Norse EA (1999)
Historical extinctions in the sea. Annual
Review of Ecology and Systematics 30:515-538
Dulvy NK, Sadovy Y, Reynolds JD (2003) Extinction
vulnerability in marine populations. Fish and
Fisheries 4:25-64
McClenachan L, Cooper AB, Carpenter KE, Dulvy NK (2012)
Extinction risk and bottlenecks in the
conservation of charismatic marine species. Conservation
Letters 5:73-80
Roberts CM, Hawkins JP (1999) Extinction risk in the sea.
Trends in Ecology and Evolution
14:241-246

LECTURE 19: RARITY AND EXTINCTION RISK IN CORAL
REEF FISHES
In this lecture, we use published descriptions of species’
geographic ranges and abundances to
examine patterns of commonness and rarity among coral reef
fish species. We then use these
patterns to test predictions generated by hypotheses of the
causes of rarity. The specific questions
we have addressed are as follows: (1) What are the global
patterns in the geographic ranges of
coral reef fishes?; (2) How do geographic ranges relate to
location, latitude, body size, dispersal
ability and/or habitat specialization?; (3) Is there a positive
relationship between geographic range
and abundance in coral reef fishes?; and (4) Does local
abundance relate to body size or habitat
specialization?
Hawkins JP, Roberts CM, Clark V (2000) The threatened status
of restricted range coral reef fish
species. Animal Conservation 3:81-88
Jones GP, McCormick MI, Srinivasan M, Eagle JV (2004) Coral
decline threatens fish biodiversity

in marine reserves. Proceedings of the National Academy of
Sciences, 101: 8251-8253
Jones GP, Caley MJ, Munday PL (2002) Rarity in coral reef fish
communities. In: Coral reef fishes:
new insights into their ecology? PF Sale (ed.), pp. 81-101.
Academic Press
LECTURE 20: SMALL POPULATION THEORY AND
METAPOPULATION DYNAMICS
The purpose of small population theory is to provide, using
simulations, sound quantitative
predictions about the likelihood of extinction under different
conditions. If successful it can be
applied to the endangered species concept, providing an
objective basis for placing species on
and taking them off endangered species lists. In this lecture I
will consider the different kinds of
theoretical approaches used for determining population viability
and whether or not these are
applicable to marine populations.
Hopf JK, Jones GP, Williamson DH, Connolly SR (2016)
Fishery consequences of marine

reserves: short-term cost for long-term gain. Ecological
Applications 26:818-829.
doi:10:1890/15-0348.1
Hopf JK, Jones GP, Williamson DH, Connolly SR (2016)
Synergistic effects of marine reserves
and harvest controls on the abundance and catch dynamics of a
coral reef fishery. Current
Biology 26:1543-1548
Nunney L and Campbell KA (1993) Assessing minimal viable
population size: demography meets
population genetics. Trends in Ecology and Evolution 8:234-239
Shaffer ML (1981) Minimum population sizes for species
conservation. Bioscience 31:131-134
7
LECTURE 21: CONSERVATION OF GENETIC DIVERSITY
IN THE MARINE ENVIRONMENT
The objectives of this lecture are to give you a brief overview
of: (1) some of the techniques

available for assessing genetic structure of populations; (2)
what these techniques are beginning
to tell us about the genetic structure of marine populations; and
(3) review possible processes
causing loss of genetic diversity.
Allendorf FW, England PR, Luikart G, Ritchie PA and Ryman N
(2008) Genetic effects of harvest
on wild animal populations. Trends in Ecology and Evolution
23:327-337
Hauser L, Adcock GJ, Smith PJ, Bernal Ramirez JH and
Carvalho GR (2002) Loss of
microsatellite diversity and low effective population size in an
overexploited population of
New Zealand snapper (Pagrus auratus)
Kuparinen A and Merila J (2007) Detecting and managing
fisheries-induced evolution. Trends in
Zhou S, Smith ADM, Punt AE, Richardson AJ, Gibbs M, Fulton
EA, Pascoe S, Bulman C, Bayliss
P and Sainsbury K (2010) Ecosystem-based fisheries
management requires a change to the
selective fishing philosophy. Proceedings of the National

Academy of Sciences
107:94859489
LECTURE 22: SHARK CONSERVATION IN TROPICAL
MARINE WATERS
This guest lecture examines the life history characteristics and
threats to shark populations and
species in tropical waters. It emphasizes the different processes
that have lead to massive
population declines in many species.
Barker MJ, Schluessel V (2005) Managing global shark
fisheries: suggestions for prioritizing
management strategies. Aquatic Conservation: Marine and
Freshwater Ecosystems
15:325347
Baum JK, Myers RA, Kehler DG, Worm B, Harley SJ, Doherty
PA (2003) Collapse and
conservation of shark populations in the Northwest Atlantic.
Science 299:389-392
Dulvy NK et al. (2008) You can swim but you can’t hide: the
global status and conservation of
oceanic pelagic sharks and rays. Aquatic Conservation: Marine
and Freshwater Ecosystems

18:459-482
Worm B et al (2013) Global catches, exploitation rates and
rebuilding options for sharks. Marine
Policy 40:194-204
LECTURE 23: ENHANCEMENT OF MARINE POPULATIONS
AS A CONSERVATION TOOL
This lecture describes the potential means to actively restore
endangered marine populations. This
includes: (1) Release of hatchery produced larvae and juveniles;
(2) Release of “wild” caught
larvae and juveniles; (3) Release of brood stock; (4) Recruit
attractors and artificial habitats; (5)
Manipulation and restoration of natural habitat; and (6)
Translocation of marine organisms within
and beyond historical range.
Brown C, Day RL (2002) The future of stock enhancements:
lessons for hatchery practice from
conservation biology. Fish and Fisheries 3: 79-94
Jones HP, Kress SW (2012) Review of the world’s active
seabird restoration projects. Journal of

Wildlife Management 76:2-9
8
Levin PS, Zabel RW, Williams JG (2001) The road to extinction
is paved with good intentions:
negative association of hatcheries with threatened salmon.
Proceedings of the Royal Society
of London B 268:1153-1158
Roberts CM, Quinn N, Tucker JW Jr, Woodward PN (1995)
Introduction of hatchery-reared
Nassau Grouper to a coral reef environment. North American
Journal of Fisheries
Management 15:159-164
LECTURE 24: REVERSING HUMAN IMPACT:
RESTORATION OF MARINE COMMUNITIES
When conservation fails to bring about return to the original
habitat, “restoration” or “rehabilitation”
may be the only viable alternative. By restoration, we mean
human intervention to rebuild or

accelerate re-growth of a habitat after a disturbance. It involves
active manipulation of the
disturbed habitat to promote the necessary successional changes
toward the “natural” state of the
community. We set out to accelerate a return to the original
assemblage structure and/or
ecosystem function. Two questions will be addressed: (1) What
ecological principles are relevant
to restoration?; That is, what are the rules that are appropriate
to assembling a community?; and
(2) What are the necessary steps in a restoration program? This
involves identifying the natural or
target condition for the habitat, developing the necessary
technologies for restoring key species,
and assessing the success of the restoration program. This will
be illustrated with a case study on
the restoration of a saltmarsh habitat.
Moy LD, Levin LA (1991) Are Spartina marshes a replaceable
resource? A functional approach to
evaluation of marsh creation efforts. Estuaries 14:1-16
Kaly UL and Jones GP (1998) Mangrove restoration: a potential
tool for coastal management in
tropical developing countries. Ambio 27:656-661

Van Katwijk MM et al. (2009) Guidelines for seagrass
restoration: Importance of habitat selection
and donor population, spreading of risks, and ecosystem
engineering effects. Marine
Pollution Bulletin 58:179-188
LECTURE 25: HABITAT RESTORATION ON CORAL REEFS
This lecture will review all the latest methods for the
rehabilitation of coral reefs, including the
different methods of promoting coral settlement, propagating
and outplanting corals and
removal of competing species such as macroalgae.
Ceccarelli et al (2018) Rehabilitation of coral reefs through
removal of macroalgae: state of
knowledge and considerations for management and
implementation. Restoration Ecology
26:827-838.
dela Cruz DW, Harrison, PL (2017) Enhanced larval supply and
recruitment can replenish reef
corals on degraded reefs. Scientific Reports 7: 13985

9
4. POTENTIALLY THREATENED MARINE SPECIES:
STATUS REPORTS
A large number of marine mammals and birds have gone extinct
in the last 200 years. It is also
evident that other strictly marine species such as fishes and
invertebrates are not as immune to
extinction as previously thought (Carlton et al. 1999, Roberts &
Hawkins 1999). The development
of species-specific management plans that target potentially
threatened marine species have
lagged behind other management options, such as all-purpose
marine reserves. Criteria for
classifying marine species as “threatened” or “endangered” are
particularly vague and there are no
co-ordinated management strategies that are enacted once

species are classified.
Marine species are considered potentially threatened, due to
some combination of biological
characteristics that make them naturally rare and human impacts
that are likely to reduce their
numbers even further. Species may be restricted to very small
geographic areas that are highly
disturbed. They may be over-exploited with no natural refuges
from human exploitation. They may
be restricted to shallow coastal areas and sensitive to coastal
enrichment or pollution. They may
be large, long-lived and susceptible to any level of exploitation
or disease. They may be naturally
weak competitors in the process of being replaced by exotic
species. They may be specialised
species that are sensitive to a widespread decline in the quality
of their habitat. However, the
particular problems faced by particular species are not always
clear.
The main impediment to developing species-specific
management strategies is that lack of
information on the status of potentially threatened species or
the ecosystems they rely on. That is,

what is the geographic range of the species and what are the
current population numbers and
trends? What are the biological characteristics of species that
should be considered potentially
threatened? How are these species and their demographic
parameters responding to exploitation,
pollution, habitat loss and other disturbances? At what point
should they be considered
endangered? What management actions are possible and what
are appropriate to species of
different kinds?
The aim of this exercise is to assemble up-to-date information
on the status of marine species that
either have or should be considered potentially threatened. The
following list is a selection of
species (or groups of species) from a variety of taxa and
geographic locations that either are or
might be considered endangered:
Blue whale (Balaenoptera musculus)
Southern right whale (Eubalaena australis)
Northern Pacific right whale (Eubalaena japonica)

Bowhead whale (Balaena mysticetus)
Hector’s dolphin (Cephalorhynchus hectorii)
Irrawaddy river dolphin (Orcaella brevirostrus)
Vaquita (Phocoena sinus)
Atlantic humpback dolphin (Sousa teuszii)
Mediterranean monk seal (Monachus monachus)
Australian sea lion (Neophoca cinerea)
Southern sea otter (Enhydra lutris nereis)
Manatee (Trichechus manatus)
Dugong (Dugong dugon)
Stellar sea lion (Eumetopias jubatus)
Guadalupe fur seal (Arctocephalus townsendi)
Leatherback turtle (Dermochelys coriacea)
Loggerhead turtle (Caretta caretta)
10
Kemp’s ridley sea turtle (Lepidochelys kempi)

Hawksbill turtle (Eretmochelys imbricata)
Galapagos marine iguana (Amblyrhynchus cristatus)
Sea snakes (Aipysurus spp)
Albatross species
Frigatebirds (Fregata spp.)
Petrels (Pterodroma spp)
Coelacanth (Latimeria chalumnae)
Great White shark (Carcharodon carcharias)
Whale shark (Rhiniodon typus)
Grey nurse shark (Carcharias taurus)
Pondicherry shark (Carcharhinus hemiodon)
Angel sharks (Squatina spp)
Hammerhead sharks (Sphyma)
Gulper sharks (Centrophorus)
Giant guitarfish (Rhynchobatus djiddensis) Sawfishes
(Pristis or Anoxypristis spp)
River & speartooth sharks (Glyphis spp).
Barn door skate (Raja laevis and other Raja species)

Swordfish (Xiphias gladius)
Chinook salmon (Onchorhynchus tshawytscha)
Sea horses (Hippocampus spp.)
Handfishes (Brachionichthys, Thymichthys)
Banggai cardinalfish (Pterapogon kauderni)
Goliath grouper (Epinephelus itajara)
Speckled hind (Epinephelus drummondhayi)
Warsaw grouper (Epinephelus nigritus)
Nassau grouper (Epinephelus striatus)
Northern bluefin tuna (Thunnus thynnus)
Maori wrasse (Cheilinus undulatus)
Sturgeon (Acipenser spp.)
Tidewater goby (Eucyclogobius newberryi)
Leafy sea dragon (Phycodurus eques)
Patagonian toothfish (Dissostichus eleginoides)
Hydrocoral (Millepora boschmai) and other hard corals and
gorgonians
Giant clams (Tridacna, Hippopus)
Abalone (Haliotus)

There will be a limit of just two students per species. There will
be a sign-up sheet on LearnJCU
by the end of Week 2, so you can get started on your report as
early in the semester as you’d like
to.
11
There will be two parts to this project:
4.1 STATUS REPORT
This is a written evaluation of the species. Your report should
assess the current and projected

status of this species and viable management options. You
should:
• Review historic and current trends in the geographic range and
abundance of the species
(if available) and discuss whether these figures suggest that the
species should be
considered potentially threatened.
• Review the biological characteristics of the species and
processes that have lead to the
current status.
• Consider the current status of our scientific knowledge of this
species and what are the
research priorities?
• Outline the current status of the species, in terms of
international and domestic legislation
and conservation action.
• Outline species-specific management strategies that are
appropriate for the conservation of
this species.

• Discuss options for the active restoration of this species by
captive breeding or
enhancement.
• Give your prognosis for the future of this species.
Your report should be a maximum of 2500 words. It should
begin with a title and should
subsequently be divided into two sections: (1) Executive
Summary (maximum of 500 word
summary of your main conclusions and a list of
recommendations (suitable for forwarding to a
newspaper); (2) Technical Report (maximum of 2000 words,
which is the main body of
assignment, excluding figures and tables). To provide structure
and clarity, the use of subheadings
within the technical report is highly recommended, including an
introduction at the beginning
(general concepts, background and a statement of the aims of
the report) and a conclusions and
recommendations section at the end. All text should be written
in your own words, giving the
citations to articles or web sites from which the information was
sourced. Do not copy from other

assignments, past or present. Figures and tables can be either
original or copied from published
works or websites. Make sure copied figures are clear, provide
an original caption and indicate the
source. Reproduce photographs only where essential to
illustrate a point.
12
Our marking sheet will be as follows:
Marking
category
Maximum
mark

Your
mark Comments
Executive
summary
2.5
500 word summary of main findings. Write in plain
language suitable for a press release.
Introduction 1.5
Must have a clear introduction… begin with general
concepts, finish with a specific set of aims or
questions.
General
information
4.5
You must cover all the ecological and biological
information that contributes to current status. Do not
include information that has no direct relevance to
conservation.

Management 4.5
Must have a clear set of management
recommendations
Prognosis and
conclusions
1.5
Give a clear prediction for future status of this species
with and without management action.
Research/
References
1.0
Should cite at least 20 references, including the
most important ones for the species. Use a
standard format.
Structure,
organisation,
clarity
1.5

This relates to presenting information in a logical
order.
Originality 1.0
Having an original title and including figures/tables
that you have created/modified/redrawn, informative
section headings and your own management ideas
all contribute to your mark for originality.
Figures/Tables 2.0
Marks will be given for inclusion of clear and relevant
illustrative material. Include at least 4-5
figures/tables.
Total 20.0
4.2 SEMINAR AND POSTER
You will need to prepare a poster using Microsoft PowerPoint
(including pictures, maps, figures
etc) and present a 5 minute verbal presentation of the poster

during tutorial time. Posters should
be in the form of a single slide, either in portrait or landscape
mode. Please do not prepare a
powerpoint presentation with multiple slides and do not use
animations. Posters will be projected
using a data projector, rather than printed (to save paper). Notes
on how to prepare a poster can
be found in the next section.
13
A powerpoint file of your poster must be emailed to the relevant
tutor 24 hours before your allotted
talk. An email will be sent to you to let you know who to send
your poster to.
Make sure your last name and tutorial group is in the file name
for the PowerPoint file when
it is emailed, e.g. Jones-Group1.pptx
Common faults with posters in previous years include:
(1) Writing in point form, with too little information. Use

proper sentences.
(2) Poor balance between written and illustrative material, i.e.
nearly all writing or nearly all
pictures. You need good use of both.
(3) Too much unused space - fill up the poster.
(4) Poor choice of background and font colours, so writing
cannot be clearly seen.
(5) Lack of critical evaluation or synthesis.
(6) No clear conservation initiatives.
(7) Unimaginative title and layout.
(8) Not putting your name on the poster (or the ppt file).
Common faults with presentations include:
(1) Talking to the poster rather than the audience.
(2) Reading notes.
(3) Going well under or over the allotted 5 minutes.
(4) Giving a talk that does not integrate with the poster.
Hints on making a good poster
• There should be roughly equal amounts of written and
illustrative material on your poster

• Use both graphs and pictures
• Use contrasting background and text colours
• Use a large enough font size for the text so that people sitting
in the back of the room will
be able to read it
• Remember to put your name somewhere on the poster
• Save the PowerPoint file with your name and tutorial group as
the filename
5. DISCUSSION TUTORIALS AND COMPUTER
WORKSHOPS
5.1 TUTORIAL 1 (DISCUSSION TUTORIAL) - THE
BIODIVERSITY DILEMMA: RESEARCH
AND MANAGEMENT OF RARE SPECIES OR ECOSYSTEMS
(VERBAL DEBATE)
Conservation biology is concerned with developing methods for
maintaining biodiversity. However,
biodiversity means different things to different people. To
develop an all-encompassing definition,

Soule (1992) developed the idea of a bio-spatial hierarchy
encompassing everything from genes to
landscapes. However, it is clear that there are insufficient
resources to carry out all the required
research at all these levels. Since research and management at
some levels may be more
effective than others, we need a set of research priorities.
Historically, the major focus of research, management strategies
and funding priorities has been
on rare and endangered species, and this is likely to continue.
Central to this approach are the
IUCN Red lists and "endangered species acts", which have been
adopted in many countries.
14
However, there has been an increasing call for research into
maintaining ecosystem function (eg.
Franklin 1993). These workers believe that the species by
species approach is inadequate and too
time consuming, and the extreme view is that individual species
do not matter, provided
ecosystem function is maintained. They often point to the

failure of endangered species acts to
save species from extinctions and argue that this legislation
should be abandoned. However, the
alternative approach is not always clearly articulated and
provides no guarantee that species will
not go extinct. For the marine environment, the single-species
approach has primarily focussed on
mammals and reptiles, while ecosystem protection appears to
primarily focus on marine reserves
and integrated coastal zone management.
In this tutorial we will debate whether or not our limited
resources should go towards maintaining
threatened species (based on endangered species acts) or
maintaining degraded ecosystems.
The latter approach argues for replacing endangered species
lists and legislation with a
threatened ecosystem approach. But how do we define a
threatened ecosystem? Regardless of
your personal views, if your surname starts with a letter
between A-L, you should argue for
species, and M-Z, should argue for ecosystems. Would you
argue the same for both marine and
terrestrial systems?

You will be split up into two groups for 20min to develop your
arguments. Elect a scribe to make a
list of your key points. The two groups will then face-off to
have the debate. The purpose of the
debate is to bring out the strengths and weaknesses of both
approaches. Compromise will only be
allowed in the last 5 minutes.
The following papers provide some background (just read a
selection!):
Dulvy N (2013) Supersized MPAs and the marginalization of
species conservation. Aquatic
Conservation: Marine and Freshwater Ecosystems 23:357-362
Franklin JF (1993) Preserving biodiversity: species, ecosystems
or landscapes. Ecological
Applications 3:202-205
Mann CC and Plummer M (1995) Is Endangered Species Act
endangered? Science
267:12561258
Simberloff D (1998) Flagships, umbrellas, and keystones: is
single-species management passé in

the landscape era? Biological Conservation 83:247-257
Tracey CR and Brussard PF (1994) Preserving biodiversity:
species in landscapes. Ecological
Applications 4:205-207
Tayor MFJ, Suckling KF, Rachlinski JJ (2005) The
effectiveness of the Endangered Species Act: a
quantitative analysis. Bioscience 55:360-367
THERE IS A LINK TO REFERENCES FOR THIS TUTORIAL
ON LEARNJCU
(in the folder ‘Lectures and Tutorials’ – ‘Week 2’)
15
5.2 TUTORIAL 2 (Literature Search) - CORAL REEFS IN
CRISIS: OVER 50 YEARS
OF ESCALATING THREATS
5.2.1 Changing threats – changing research priorities
When scientists began studying coral reefs they were captivated

by fundamental ecological issues
relating to their high biodiversity and productivity. Prior to the
1970’s it was relatively rare to find
publications on human impacts on coral reef habitats and there
was little in the way of applied
research. With the first outbreak of crown-of-thorns starfish in
the 1970’s, scientists began
focussing on the possible human causes (Grigg 1992).
Increasing nutrient enrichment and
sedimentation on coral reefs lead to research programs
focussing on the possible effects of
terrestrial run-off on coral reefs (Roberts 1993). Increasing
exploitation of large reef fishes also
lead to scientists studying the impacts of exploitation on coral
reef health (Roberts 1993). The
steady introduction of marine reserves highlighted the effects of
exploitation and reserves as an
effective means of management. As time has progressed, an
ever-increasing diversity of human
impacts has been documented. Over the last few decades,
research on environmental issues on
coral reefs has grown dramatically, but the nature of this
research has changed. By 2003,
scientists were ringing the alarm bells and the worldwide

degradation of coral reefs is now widely
recognised (Hughes et al. 2004). The latest dire predictions for
coral reefs come from global
warming and ocean acidification.
The aim of this tutorial is to conduct a literature search to
document changes in the focus of coral
reef environmental research over the last 54 years. Is there
evidence that scientists have
increased their attention to the environmental stresses faced by
coral reefs? And have they shifted
their attention to different environmental issues as time has
progressed? As an indicator of the
most important impacts on reefs, how many scientific papers
have focussed on the different
threats facing coral reefs (e.g. crown-of-thorns outbreaks,
nutrient enrichment, sedimentation,
exploitation, pollution, ocean warming, sea level rise, and
acidification)? To date there has been
no integrated analysis of these trends.
There are fundamentally two ways to do research. One is to
carry out primary research, which may
involve collecting your own data from the field. The other is to

research the published scientific
database and analyse trends and generalizations from that
source. This second approach is called
meta-analysis, which aims to compare and synthesize results
from multiple studies. Meta-analyses
vary in sophistication from studies graphically examining trends
in published data to complex
statistical analyses of research outcomes.
The aim of this exercise will be to carry out an online literature
search to analyse trends in
the study of the environmental issues facing corals reefs and
quantify how coral reef
scientists have risen to the challenge.
We will use a search engine, the ISI Web of Science, to examine
trends in coral reefs science
between 1965 and 2018. This will allow us to systematically
search the contents of key journals in
marine biology and ecology, and extract a data set that will
enable us to answer the following
questions:
(1) Has the number of publications on human impacts on and
conservation of coral reefs

increased over the last 54 years?
(2) Has the proportion of all publications on coral reefs that
address environmental issues
increased over this period? That is, has there been a shift from
pure to applied ecology?
16
(3) Over the last 54 years, how much research has been directed
at the different environmental
issues? That is, what are the trends in the numbers of papers
have focussed on (a) crown-
ofthorns starfish (Acanthaster) outbreaks; (b) terrestrial run-off
(sedimentation, nutrient
enrichment); (c) chemical pollution and oil spills; (d)
overfishing (live fish trade); (e) global warming
(coral bleaching, ocean warming, sea-level rise); (f) ocean
acidification and (g) coral disease?
When did the first publications on each of these topics first
appear? Is there just an overall
increase in the amount of research on all these impacts or have
some perceived impacts come

and gone?
(4) Overall, how many studies have been published on the 6
different topics? What topics do
you think require more attention?
5.2.2 How to start?
There are potentially two ways to search the literature. One
would be to laboriously thumb through
the pages of the journals. However, we are going to use the ISI
Web of Science search engine,
which is going to be a LOT quicker. Each student will collect
their own data by searching the ISI
Web of Science.
On the JCU website, click on Library, then click on Databases
(from the menu bar below the
photo). Click W, then Web of Science. This will take you to the
ISI Web of Knowledge web site.
Check that Web of Science Core Collection is selected and not
All databases.
Under Timespan, select Custom year range, and set the year

range to 1965-2018. We will not
search 2019 because it is not over yet!
Step 1. What is the total number of papers published on coral
reefs? In the top topic field,
simply type coral* AND reef* (We add the “*” after the word
“coral” so that in the search it will pick
up papers using both the singular and plural of that word).
Then press Search and it will display all papers including the
word coral (or corals) and reef (or
reefs) between the dates requested. This will be the total
number of papers on coral reefs,
including pure ecology and applied studies.
Press Analyze results (at the top right of the list of papers), and
a new page will be displayed. In
the left-hand menu bar, select Publication Years. We do this to
display results by year, from the
year with the most publications to the year with the least. Below
the graph, change Show to 100,
make sure Minimum record count is set to 1, then click Update.
Below this, you will see the
number publications by year from the maximum to the

minimum.
Save the data as a text file and import it into Excel by clicking
on Download (at the bottom right of
the page), and then Save File and OK. In Excel, click on File
and select Open, select the text file
(it will be in the Downloads folder, unless you specified a
different location when you saved the
file), make sure Delimited is selected and click Finish.
Alternatively, open the text file in Web of
Science by clicking on Download, and then Open with and you
can then copy and paste the data
into Excel. You cannot copy the data directly from ISI Web of
Science and paste it into Excel as
Excel will treat the numbers as text and you will not be able to
use them in any calculations.
17
To get back to the first page, click on Back to previous page
(top left of page), then Search (top
left of page).

Step 2. How many publications have there been on crown-of-
thorns starfish (Acanthaster)
and their impacts on coral reefs?
Type in the following search algorithm in the top line (note: you
need to type in the whole line
below, including the AND and OR in capitals, and the *):
[Coral* AND reef* AND Acanthaster] OR [Coral* AND Reef*
AND Crown* AND Thorn*]
This should pick up most of the papers on this topic. Click on
Analyze results. Click on
Publication years, and check it is still set to show the top 100
results, and a minimum record
count of 1. Save the data to a text file and import it into your
Excel file. You will need to rearrange
your data (using the Sort function in the Data tab) so that it is
displayed in order of year, and insert
rows for any years that are missing.
Click on Back to previous page. To find examples of key papers
on this topic, click on Create
citation report tab. This will arrange the papers from the most

cited to least cited – the better
papers should be among the most cited. Make a note of some
papers to cite in your report.
Step 3. How many publications have there been on
sedimentation and nutrient enrichment
on coral reefs?
Type in the following search algorithm (note: you need to type
in the whole line below, including
the AND and OR in capitals, and the *):
[Coral* AND reef* AND sedimentation] OR [Coral* AND
Reef* AND nutrient AND enrichment] OR
[Coral* AND reef* AND terrestrial AND run-off]
Repeat the procedure above. Transfer the data to your Excel
file.
Step 4. How many publications have there been on chemical
pollution and oil spills?
[Coral* AND reef* AND chemical AND pollution] OR [Coral*
AND Reef* AND oil AND spill*]

file.
Step 5. How many publications have there been on overfishing
or overharvesting on coral
reefs, including the effects of the live fish trade.
[Coral* AND reef* AND overfish*] OR [Coral* AND reef*
AND overharvest*] OR [Coral* AND reef*
AND live AND trade]
file.
Step 6 How many publications have there been on ocean
warming, coral bleaching and sea
level rise.
[Coral* AND reef* AND ocean AND warming] OR [Coral*
AND reef* AND bleaching] OR [Coral*
18
AND reef* AND sea AND rise]

file.
Step 7. How many publications have there been on ocean
acidification?
[Coral* AND reef* AND ocean AND acidification]
file.
Step 8. How many publications have there been on coral
disease?
[Coral* AND reef* AND disease]
file.
5.2.3 Graphing your data and submitting your answer sheet
By the end of the tutorial, you should have an Excel spreadsheet
with 9 columns – one column
with publication years, one column with the numbers of
publications on coral reefs, and a column
each for the numbers of publications on the 7 human impacts.

Graph your data to answer the
following questions:
(1) Has the number of publications on human impacts on and
conservation of coral reefs
increased over the last 54 years?
To graph this, sum across the columns for the number of
publications on the 7 human impacts
in each year. Plot this total number of papers (y-axis) against
years (x-axis) using a line graph.
(2) Has the proportion of all publications on coral reefs that
address environmental issues
increased over this period? That is, has there been a shift from
pure to applied ecology?
To graph this, divide the values you calculated in question 1 by
the number of studies on coral
reefs for each year. Graph this proportion (y-axis) against years
(x-axis) using a line graph.
(3) Over the last 54 years, how much research has been directed
at the different environmental
issues? That is, what are the trends in the numbers of papers
have focussed on (a) crown-
ofthorns starfish (Acanthaster) outbreaks; (b) terrestrial run-off
(sedimentation; nutrient

enrichment); (c) chemical pollution and oil spills; (d)
overfishing (live fish trade); (e) global warming
(coral bleaching, ocean warming, sea-level rise); (f) ocean
acidification; and (g) coral disease?
When did the first publications on each of these topics first
appear? Is there just an overall
increase in the amount of research on all these impacts or have
some perceived impacts come
and gone?
To graph this simply plot the numbers of studies on the seven
topics (y-axis) against years
(xaxis), with a different line for each of the impacts. Make sure
you label each line clearly.
(4) Overall, how many studies have been published on the 7
different topics? What topics do
you think require more attention?
To answer this, for each of the impacts, sum all the rows from
1965 to 2018. Plot a column graph
with the total number of publications (y-axis) and the seven
different impacts (x-axis).
There is an answer sheet provided on LearnJCU in the folder
‘Lectures and Tutorials’ – ‘Week 3’.

Paste your graphs into the answer sheet and answer the
questions, then submit your answer
sheet via the drop box in the Week 3 folder.
19
5.3 TUTORIAL 3 (DISCUSSION TUTORIAL) - “THE
GLOBAL WARMING CONTROVERSY:
ADVOCATE OR SKEPTIC?” (VERBAL DEBATE)
The global warming controversy is a dispute regarding the
nature and consequences of global
warming. Following the 5th Assessment Report of the
Intergovernmental Panel on Climate
Change (IPCC) there is now broad scientific agreement that
climate change is happening and is
very likely caused by human emissions of greenhouse gases.
However, because of the
uncertainties in modelling climate change, there are still many
skeptics. The aim of this tutorial will
be to debate and explore the arguments for and against human-
induced climate change and

assess the merits of the arguments on both sides.
The key conclusion of the 5th IPCC report is that it is
unequivocal that global warming is occurring;
it is ‘extremely likely’ that over half of the observed increase in
global average surface temperature
from 1951 to 2010 was caused by anthropogenic emissions of
greenhouse gases. Global mean
surface temperature has increased by 0.85 degrees Celsius from
1880 to 2012, and global mean
sea level has risen by 0.19 m from 1901 to 2010, and the
frequency and intensity of extreme
weather events (e.g. floods, droughts, wildfires and cyclones)
has increased. It is predicted that, by
the end of the 21st century (2080-2100) the following will
occur: global mean surface temperature
will increase (relative to 1986-2005) by 0.3 to 1.7 degrees
Celsius under the best (RCP2.6) of the
4 emissions scenarios, and by 2.6 to 4.8 degrees Celcius under
the worst emissions scenario
(RCP8.5); global mean sea level will rise (relative to 1986-
2005) by between 0.26 and 0.55 m
under the best emissions scenario (RCP2.6), and by between
0.45 and 0.82 m under the worst

emissions scenario (RCP8.5); and there will be an increase in
the frequency of droughts, and in
the frequency and intensity of extreme weather events such as
tropical cyclones (which include
typhoons and hurricanes).
The disputed issues include the causes of increased global
average air temperature, especially
since the mid-20th century, whether this warming trend is
unprecedented or within normal climatic
variations, and whether the increase is wholly or partially an
artefact of poor measurements.
Additional disputes concern estimates of climate sensitivity,
predictions of additional warming,
what the consequences are, and what action should be taken (if
any). The debate is vigorous in
the popular media and on a policy level.
Before coming to the tutorial we will provide you with some
articles to fuel the debate. At the
tutorial you will be randomly assigned to a position either for or
against the conclusions of the
IPCC report. In the first half hour you will be divided into two
groups to assemble your arguments,

after which we will have a class-level discussion.
20
Reading:
Cook J (2010) A scientific guide to the skeptics handbook
IPCC 5 (2014) Synthesis Report – Summary for Policymakers
Jaworowski Z (2007) CO2: The greatest scientific scandal of
our time. EIR Science
Meyer W (2012) Understanding the global warming debate
Muller RA (2012) The conversion of a climate change skeptic.
NY Times Nova
J (2009) The skeptics handbook.

Steffen W & Hughes L (2013) The critical decade: climate
change, science, risks and responses
http://www.skepticalscience.com/ - provides a summary of the
most common arguments presented
by climate change sceptics, and the scientific evidence we have
to counter those arguments. You
can also download a free ‘Skeptical Science’ smart-phone app.
THERE IS A LINK TO REFERENCES FOR THIS TUTORIAL
ON LEARNJCU
(in the folder ‘Lectures and Tutorials’ – ‘Week 4’)
21
5.4 TUTORIAL 4 (COMPUTER WORKSHOP) - MARINE
RESERVES: DO THEY PROTECT
EXPLOITED SPECIES AND CORAL REEF HABITATS
(VIDEO SURVEY EXERCISE)
5.4.1 Introduction

Marine reserves or marine protected areas (MPAs) have become
one of the major tools for the
management of coastal marine habitats and exploited marine
organisms (Lubchenco et al. 2003).
There are essentially two main types of MPAs (Hastings &
Botsford 2003). The first and most
common is a “no-take” area that is specifically designed as a
fishery management tool for
exploited species or multi-species assemblages (Gell & Roberts
2003). The second type of MPA is
a “conservation” area set aside for the protection of marine
biodiversity (e.g., Fernandes et al.
2005). The evidence for local fishery benefits of MPAs is
overwhelming, with the vast majority of
exploited species increasing in abundance, biomass and
reproductive potential in no-take areas
(e.g., Gell & Roberts 2003, Russ 2003). The role of reserves in
fisheries management has been
questioned, particularly for mobile species, where open areas
become overfished or where there
are compliance problems (e.g., Agardy et al. 2003, McClanahan
et al. 2006). However, while many
questions remain unanswered, such as the degree to which
MPAs benefit adjacent fished areas

through larval connectivity (Sale et al. 2005), the case in
support of the benefits of MPAs for
fisheries is overwhelming.
The degree to which MPAs benefit the vast majority of
unexploited species is less clear. MPAs
continue to be established in the belief that they can protect a
“representative” range of species
and habitats, promote biodiversity by protecting rare species or
unique habitats, safeguard areas
in face of widespread habitat degradation, and contribute to
recovery of damaged areas
(Lubchenco et al 2003). There is surprisingly little evidence for
many of these claims. Many believe
MPAs are necessary, but by themselves insufficient to maintain
marine biodiversity. There is little
doubt that closing representative of complementary areas is the
most efficient way to include as
many species as possible in areas closed to fishing or collecting
(e.g., Fox & Beckley 2006).
However, such species are only “protected” if you assume that
fishing and collecting are the main
threats to these species. In coastal areas subject to terrestrial
run-off, pollution or in the context of

global warming, MPAs may do little to prevent the decline of
sensitive species (Boersma & Parrish
1999, Jones et al 2004, Cicin-Sain & Belfiore 2005). While
MPAs may still increase the abundance
and biomass of exploited species in degraded habitats (e.g.,
Hawkins et al. 2006), they may do
little to halt degradation (Jones et al. 2004). The reduced
fishing pressure and increase in the
abundance of large fishes in MPAs may itself be responsible for
a decline in many smaller species
(e.g., Graham et al. 2003).
It is important that we consider whether or not marine reserves
“work” in the way they are
intended. Not only can this tell us how we are impacting on
marine assemblages (if indeed we
are), but it can also increase our understanding of how marine
species respond to human
exploitation and to each other. Since some organisms increase
in abundance in reserve areas,
and others may decline, we need to sample a range of organisms
at different trophic levels to
determine whether MPAs are achieving the desired goals. While
establishing marine reserves is

probably not going to be harmful if they do not work, if they do
work, there can be no better
support than the biological knowledge that they are successful.
Much of this information can be
gained from examining what goes on inside and outside marine
reserves, before and after they are
established. They can be considered large-scale experiments in
which we are learning a great
deal about how to manage and protect marine biodiversity.
22
The aim of this exercise is to examine the effects of a marine
reserve network in Kimbe Bay,
Papua New Guinea on key coral reef organisms from different
trophic levels, including corals,
algae, urchins and herbivorous fish. Many argue that
maintaining healthy populations of herbivores
is crucial to maintaining reef biodiversity as a whole. GP Jones,
along with a number of
collaborators, has been monitoring MPA’s (small reefs closed to
fishing) and fished reefs in Kimbe

Bay since 1996 (MPAs established in 1999 - Jones et al. 2004).
For this exercise, video transects
for benthic organisms and fishes were carried out in June 2006
for 3 of the MPAs and 3 reefs open
to fishing and collecting. Your task is to compare the cover or
abundance of different organisms in
open and closed areas, and at the different sites, 7 years after
protection.
5.4.2 Kimbe Bay, Papua New Guinea
Kimbe Bay is a large bay on the northern coast of New Britain,
adjacent to the Bismarck Sea (Fig.
1). The small MPA network (Fig. 2) is located near two small
villages not far from the township of
Kimbe, the commercial centre for West New Britain Province.
Most of the fishing and collecting in
this area is at a subsistence level. Herbivorous fish are targeted
with nets in shallow water
habitats. Local fishers also use “poison rope” (vines containing
rotenone) to collect smaller fishes.
There is also intensive collecting of invertebrates such as
beche-de-mer at low tide. Although there
is not complete compliance with the reserve status, fishing

pressure is substantially reduced in the
MPAs. These reefs are also subject to coastal influences of
sedimentation and nutrient enrichment
from deforestation and cultivation of oil palm, and from
increased frequency of bleaching as a
result of ocean warming.
23
5.4.3 Sampling design
The goal is this exercise is to assess how a range of key
organisms, including habitat formers
(e.g., corals, algae) and potentially important consumers (e.g.,
sea urchins, herbivorous fish) have
responded to protection. Video transects were recorded for 6
sites in total, three MPAs (Lady Di,
Limuka, Gava Gava) and three reefs open to fishing (Malane
Huva, Garbuna, Luba Luba) in June

2006 (Fig. 2). Video footage is only provided for the shallow
reef crest habitat, which is subject to
the greatest fishing pressure and also the greatest wave motion.
Videos were made on snorkel,
sometimes in quite surgy conditions, so you should get a good
feeling for the practical difficulties in
obtaining data in this habitat. You might even get seasick!
Fig. 2: Satellite image showing open and closed (MPA) reefs
Two types of video are provided on the Marine Conservation
Biology YouTube channel:
(1) Benthic transects: There are 4 replicate 50m line transects
(called Coral 1-4 on the DVD)
for each site. For these transects, the diver pointed the video
camera downward and swam along
the transect line filming the substratum, keeping the transect
line in view. These transects can be
used to record two things: (a) the % cover of the main attached
organisms or substrate types, and
(b) the number of sea urchins Echinometra mathaei). You will

need to play the coral transects
twice, once to record the substratum types, and a second time to
count the sea urchins.
(2) Fish transects: There are also 5 replicate “timed swims” of 2
minutes each (called Fish 1-5
on the DVD) for each site. In these there is no transect line. The
diver swam slowly along the edge
of the reef crest pointing the video camera straight ahead. These
transects can be used to assess
the relative abundance of fishes in open and closed areas. Each
person will record the numbers of
two herbivorous surgeonfish, Ctenochaetus striatus and
Acanthurus lineatus. You will also need to
play each timed-swim twice, once to record each species.
On the MB3200 YouTube channel, there is a separate playlist
for each site
Click this link to view the playlists: Tutorial 4 playlists
When you click on a playlist title, you will get a list of the
videos for that site. Click on the name of a
video to play it, and you will get a list of all the videos for that
site on the right hand side.

N
Garbuna
open ( )
Gava Gava
( closed )
Limuka
( closed ) Lady Di
( ) closed
Malane Huva
) ( open
Luba Luba
( open )
24
Choose just 1 site and choose any 3 ‘Coral’ transects and any 3
‘Fish’ timed swims to survey.
Record benthic substrata, numbers of sea urchins and numbers
of the two fish species in the data
sheet provided, using the instructions below. Turn the volume
off while playing the videos.
There are some photos of the organisms you will be recording

on LearnJCU, so have a look at
these before you start.
5.4.4 Playing the videos and recording your data
(1) Benthic transects:
(a) In this exercise we will divide the substratum into 9 simple
categories:
(1) Complex corals - branching, plate, digitate, foliose
(2) Massive, encrusting & solitary corals
(3) Soft corals, sponges, encrusting invertebrates
(4) Bare rock, coralline paint
(5) Turf algae on coral rock
(6) Turf algae on rubble
(7) Macroalgae
(8) Sand, gravel, or rubble.
(9) Others, including unidentified substrata.
The transect line has 100 random points marked with a black
pen and numbered (1-100). Pause

the video when the random point is close to the middle of the
screen and record the main
substratum underlying the point. Continue until you have
recorded the substratum for all the
random points, marking the substratum on the data sheet
provided as you go.
(b) Run each coral transect again to count the sea urchin
Echinometra mathaei, including all
individuals seen on screen. Individuals of this species are very
patchy and often deep in
grooves that they have created (see Figs. 10 and 11). You will
need to be quite vigilant to see
them, and may need to pause or rewind the video to confirm
their presence. Don’t be surprised
if you get none on some transects! To calculate urchin densities
we will assume each transect
is 0.2m wide by 50m long (10m2).
(2) Fish transects:
Play each fish transect twice, once to count Ctenochaetus
striatus (relatively common) and a
second time to count Acanthurus lineatus (relatively rare).
Record your counts on the data sheet

provided. Fish are mobile and hard to see in the distance, which
makes counting them difficult. It is
best to count them only when they come into the lower half of
the screen where they are close
enough to identify. Count each individual only once. If a fish
swims through your view and then
offscreen, and you see what you think is the same fish reappear,
count this as a new individual.
Our counts of these two species will be expressed as mean
numbers seen in 2 min of observation.
That is, they will not be expressed as a density or numbers per
m2.
5.4.5 Class data set
Submit your data sheet via the drop box on LearnJCU (in the
Week 5 folder) by the end of Week 5.
We will compile a class data set and upload this on LearnJCU
(under ‘Assessment’) at the
beginning of Week 6.
25

5.5 TUTORIAL 5 (Information Session): HOW TO WRITE UP
THE MARINE RESERVES
REPORT
In this tutorial we will run through how to graph, analyse and
interpret your results. This is an
online tutorial, with a recording provided on LearnJCU for you
to view in your own time, i.e. there is
no face-to-face tutorial in Week 6. There is also a screen
recording on LearnJCU on how to
calculate means and standard errors, and plot graphs with
custom error bars in Excel.
5.5.1 Graphing your data
You will need to download the Excel file containing the class
data set from LearnJCU (in the folder
‘Assessment’ – ‘Assignment 1’). In this workbook there are
three worksheets titled “Data Benthic”,
“Data Urchins” and “Data Fish”. In each sheet there is a data set
that resembles the following
table,

Open_Closed Reef Transect X Y Z
Closed Limuka 1 - - -
Open Luba Luba 1 - - -
Closed Lady Di 1 - - -
Closed Gava Gava 1 - - -
Open Garbuna 1 - - -

26
Open Malane Huva 1 - - -
and which provides you with the counts (fish, urchins) or
percentage cover (benthic categories) in
each transect at each reef (represented by XYZ above).
Remember that for benthic composition
and urchins there were four transects, but for fish there were
five transects at each reef. You will
need to calculate and plot the mean for each variable (fish,
urchins, benthos) for each reef. In
excel you can calculate the mean using the formula “ =
average(D2:D5)”, for example, to calculate

the average of the values in cells D2 through D5. Once you have
calculated the means you can
use these to create a chart.
You will also need to plot the standard errors on your chart of
means. Standard error is the
standard deviation divided by the square root of the number of
transects used to calculate the
mean. In Excel you can calculate the standard error for each
mean using the formula “ =
stdev(D2:D5)/sqrt(4). Don’t forget to use sqrt(5) for the fish
data. Those of you who have learned
how to use pivot tables in other courses can use this as an
opportunity to practise your pivoting
skills! Once you have the standard errors you need to add them
to your graph as custom error
bars.
Don’t forget to code your reefs as open or closed as well as
providing their names. You should end
up with a figure for each fish species, urchins and for branching
corals and the rock/algae category
(don’t worry about the other benthic categories) that roughly
resemble the template provided

below.
Figure X. Mean abundance of Ctenochaetus striatus at three
reefs open to fishing and three reefs
closed to fishing in Kimbe Bay, Papua New Guinea. This graph
is an example only… not your data.
0
10
20
30
40
50
60
70
80
90
Luba Luba
) ( Open

Malane
Huva
( Open )
Garbuna
( Open )
Gava Gava
Closed ( )
Lady Di
( Closed )
Limuka
( Closed )
27
5.5.2 Analysing your data
The data should be analysed for significant differences in the
abundance of fish and urchins and in
the percentage cover of benthic categories using a two-level
nested ANOVA, where Reefs are
nested in Open v Closed status. If you know how to perform this
analysis you may carry out this
procedure yourself using the data provided. For those students

who are unsure we have included
the following for your information.
In these analyses, Open v Closed status is a fixed factor, while
Reef is a random factor. This is
because reefs can only be Open or Closed, there is no other
option. In contrast, we chose six
reefs from a network of reefs, in which there were a number of
other reefs we could have chosen,
therefore, they are random.
Our dependent variables in these analyses are each species of
fish, urchins, and each benthic
category, and we need to do a separate ANOVA for each
variable. For the two species of fish and
the urchins, testing of the assumptions of ANOVA revealed that
the variances were heterogenous.
These can be greatly improved by a square-root transformation.
Since the benthic categories were
percentage cover, we needed to do an arcsine transformation.
Examples of how the ANOVAs
might look for the transformed data are as follows (your data
will be different):

Branching/plate/digitate/foliose corals
Source SS df MS F p
Open Vs Closed 0.047
Reefs (Open Vs Closed) 0.888
Error 0.162
1 0.047 0.213 0.668 4 0.222
24.713 < 0.000 18 0.009
Bare rock/turf algae/coralline paint
Source SS df MS F p
Open Vs Closed
Reefs (Open Vs Closed)
Error
0.000
0.614
0.064
1 0.000 0.001 0.9768 4 0.153
43.210 < 0.000 18 0.004
Echinometra mathaei
Source SS df MS F p

Open Vs Closed
Reefs (Open Vs Closed)
Error
6.484
187.184
22.152
1 6.484 4
46.796 18
1.231
0.139 0.729
38.025 < 0.000
Ctenochaetus striatus
Source SS df MS F p
Open Vs Closed 129.656 1 129.656 14.319 0.019
Reefs (Open Vs Closed) 36.219 4 9.055 9.033 < 0.000
Error 24.058 24 1.002
28
Acanthurus lineatus

Source SS df MS F p
Open Vs Closed 10.990 1 10.990 6.415 0.064
Reefs (Open Vs Closed) 6.853 4 1.713 3.560 0.020
Error 11.551 24 0.481
You will need to include your ANOVA results in your report
either as Tables to which you refer in
the text e.g. “Mean abundances of Ctenochaetus striatus were
approximately two to eight times
greater at closed reefs compared with open reefs in Kimbe Bay
(Figure X) and this difference was
significant (Table X)”. If you do this don’t forget to create table
headings to go under or above each
table, for example, “Table X. Two-level nested ANOVA for
variation in abundance of Ctenochaetus
striatus according to reefs and open vs closed status”.
Alternatively you can simply provide the
ANOVA results as follows (ANOVA: MS = 129.6, d.f. = 1, p =
0.019) when referring to differences
in Ctenochaetus abundance according to reserve status.
5.5.3 Writing your assignment

The report should be written as a short paper of 2,500 words,
formatted for the journal
“Ecological Applications”. Get a copy of a recent paper from
this journal and follow the format
as closely as possible. It should include a title, author, address,
abstract, key words, introduction,
methods, results, discussion and literature cited. Each figure
and table should be numbered and
have a clear legend that fully describes all axes and symbols.
Do not use colour for a scientific
paper. Cite each figure and table in the text where it is first
necessary.
TITLE: This should indicate the full scope of your study, while
also being as succinct as possible.
ABSTRACT: In a single paragraph, briefly describe your aim,
summarise all your main results and
highlight the significance of your findings. The major part of
this paragraph should be your most
important results.
KEY WORDS: List 7-8 words that might be useful to index your
work. You want to pick words that

would lead people to your paper in a literature search.
INTRODUCTION: This should not be more than 600 words and
should not have subheadings. It
should start with general concepts, which highlight the need for
your study. Refer to key papers to
make your case. Towards the end of the introduction you should
address an overall aim, which
outlines the hypothesis or hypotheses being tested. For example,
“The aim of this study was to
examine the hypothesis that the distribution and abundance of
coral-dwelling gobies is determined
by the availability of preferred coral species”. This could be
followed by a specific set of related
questions. At this stage you can introduce your study system
and why it was selected to examine
these questions. All basic issues examined in the paper should
be addressed in the introduction.
METHODS: State where and when the study was carried out,
describe your sampling design(s)
and any analytical methods used. Use sub-headings where
necessary. Include all methods that
are necessary to interpret the results in a logical sequence. Do
not include methods that did not

work or no data is presented for. Do not include any results in
this section.
29
RESULTS: Present your results in a logical sequence, again
using sub-headings where
necessary. In each paragraph, describe the main result first,
citing the appropriate figure or table.
E.g. “The abundance of Gobiodon micropus was strongly
correlated with the abundance of
Acropora loripes (Fig. 1)”. It is not necessary to introduce
figures. That is, statements like “The
relationship between Gobiodon micropus and Acropora loripes
is shown in figure 1” are
unnecessary. Follow main points by bringing out results of
lesser importance or giving more detail.
All figures and tables that are presented should be described in
the text. Do not interpret or
discuss results in the results section or state why you did not get
what you expected.
DISCUSSION: The discussion should begin by addressing your

most important result and should
follow directly from your aim. For example, “This study
confirmed that the distribution and
abundance of coral-dwelling gobies at Orpheus Island is largely
determined by the abundance of
preferred corals” or “This study challenges the widely held
generalisation that the distribution and
abundance of reef fishes is determined by habitat availability”.
After this you could progress
towards findings of lesser importance. In each case, compare
and contrast your findings to any
relevant published papers, without repeating your introduction.
If your results conflict with the
literature, put forward alternative explanations for your results.
Discuss how your study could be
extended to help resolve issues that arise from your preliminary
findings. You should have a
concluding paragraph that highlights the significance of your
contribution. You should not cite
figures and tables again in your discussion.
LITERATURE CITED: Follow the format of the journal. You
should cite papers more broadly than
your particular study group. All papers in this list should be

cited in the text and all papers cited in
the text should appear in this list.
5.5.4 Marking criteria
Our marking sheet will be as follows:
Marking category
Maximum
mark
Your
mark Comments
Title and key words 1.0
Descriptive title (not taken directly from the
report instructions provided on LearnJCU)
and at least 7 keywords.
Abstract 2.5
Brief summary of report (including aims of
study), including key results and their
significance

Introduction 3.5
Introduce topic starting with general
concepts; end with a statement of specific
aims/questions to be addressed
Methods 2.5
Describe study site. sampling design,
methods for both field and lab data collection
as well as analyses
Results 4.5
Good presentation of figures and ANOVA
tables (i.e. axis labels, legends, error bars,
captions/headings). Describe patterns from
figures and ANOVA results.
30
Discussion 4.5
Discussion of results for all organisms
included. Compare and contrast findings with

other studies and offer explanations for why
results may differ from other studies. Cite
references to back up arguments put forth to
explain results (i.e. no blatant speculation!).
References 1.5
Include at least 15 references. Format of
intext citations and reference list should be
consistent throughout and must follow the
format of the journal Ecological Applications.
Total 20.0
5.4.6 References
You will find the following references useful in writing your
introduction and discussion.
Agardy T et al. (2003) Dangerous targets? Unresolved issues
and ideological clashes around marine
protected areas. Aquatic Conservation Marine and Freshwater
Ecosystems 13: 353-367

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