Marine Conservation Biology

Please look at the attached word document.

POTENTIALLY THREATENED MARINE SPECIES: STATUS REPORTS

Don't use plagiarized sources. Get Your Custom Essay on

Just from $13/Page

Order Essay

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 species selected is the

Patagonian Toothfish.

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.

_NOTE_

I would be extremely grateful if you could follow the following ‘skeleton’:

Table of Contents
Introduction 3
General Information 3
Biological Characteristics 3
Ecological importance 3
Distribution 3
Current Status of Patagonian Toothfish 3
Management 3
Recommended Management 4
Prognosis and Conclusion 4

The marking rubric is as follows:

image1

MB 3200

201 9

Marine
Conservation

Biology

MB3200

Marine Conservation Biology

Marine Biology and Aquaculture,

Australia’s endangered handfish

College of Science and Engineering,
James Cook University

2019 Subject Manual

SUBJECT CO-ORDINATOR

Geoff Jones (142-225)

Consulting hours: Thursday 9:30am – 2:00pm

Email: geoffrey.jones@jcu.edu.au

LECTURER, ENQUIRIES & WEB MANAGER

Prof. Jeff OBBARD

Email: jeffrey.obbard@jcu.edu.au

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)

CONTENTS

1. ABOUT THIS SUBJECT ……………………………………………………………………………………………… 4

2. CLASS ORGANIZATION AND TIMETABLE ………………………………………………………………… 1

3. LECTURE TOPICS AND RECOMMENDED READING …………….. ………………………………… 0

4. THREATENED MARINE SPECIES: STATUS REPORTS ………….… ………………………………. 9

5. TUTORIALS ……………..….………………………………………..……… 28

6. EXAMINATION INFORMATION AND STUDY QUESTIONS ………….. 63

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.

• 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.

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)

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?”

Section 5.4 and LearnJCU.

5. Information session: How to write-up the Marine Reserves Report”

Section 5.5 and LearnJCU

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.

Section 5.6 and LearnJCU

7. Computer-based tutorial: “World Map: approaches to selecting sites for marine reserves”

Section 5.6 and LearnJCU.

8. Paper critique: “Marine reserves have rapid and long-lasting effects”

Section 5.7 and LearnJCU

9. Computer workshop: “Classifying threatened marine species using RAMAS Red List”

10-11. Student poster presentations: “Threatened marine species”

Section 4.2 and LearnJCU

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.

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 jeffrey.obbard@jcu.edu.au

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,

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:

Week 1

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

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

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

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

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

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

Section 5.5 and LearnJCU

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.
Section 5.9 and LearnJCU

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”

Section 5.6 and LearnJCU

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

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

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.

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

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.

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

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

Ecology and Evolution 20:74-80

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

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

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

Ecology and Evolution 22:652-659

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

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

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)

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.

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.

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.

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.

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’)

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?

(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.

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]