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Resilience Assessment of Coral Reefs
Rapid assessment protocol for coral reefs, focusing on coral
bleaching and thermal stress
David Obura and Gabriel Grimsditch
IUCN Resilience Science Group Working Paper Series – No 4
i
IUCN Global Marine Programme
Founded in 1958, IUCN (the International Union for the Conservation of Nature) brings together
states, government agencies and a diverse range of non-governmental organizations in a unique
world partnership: over 100 members in all, spread across some 140 countries. As a Union, IUCN
seeks to influence, encourage and assist societies throughout the world to conserve the integrity and
diversity of nature and to ensure that any use of natural resources is equitable and ecologically
sustainable.
The IUCN Global Marine Programme provides vital linkages for the Union and its members to all the
IUCN activities that deal with marine issues, including projects and initiatives of the Regional offices
and the six IUCN Commissions. The IUCN Global Marine Programme works on issues such as
integrate coastal and marine management, fisheries, marine protected areas, large marine
ecosystems, coral reefs, marine invasives and protection of high and deep seas.
The Nature Conservancy
The mission of The Nature Conservancy is to preserve the plants, animals and natural communities
that represent the diversity of life on Earth by protecting the lands and waters they need to survive.
The Conservancy launched the Global Marine Initiative in 2002 to protect and restore the most
resilient examples of ocean and coastal ecosystems in ways that benefit marine life, local
communities and economies. The Conservancy operates over 100 marine conservation projects in
more than 21 countries and 22 US states; they work with partners across seascapes and landscapes
through transformative strategies and integrated planning and action. The focus is on: (1) Setting
priorities for marine conservation using ecoregional assessments and tools for ecosystem based
management; (2) Ensuring coral reef survival by creating resilient networks of marine protected areas;
(3) Restoring and conserving coastal habitats by utilizing innovative new methods; (4) Building
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Acknowledgements
We would like to acknowledge the following programmes that contributed to the development of the
protocol through their general work and supporting workshops and fieldwork: the International Union
for the Conservation of Nature (IUCN), The Nature Conservancy, the Great Barrier Reef Marine Park
Authority, the Coral Reef Targeted Research Programme for Management, World Wildlife Fund – US
and Tanzania Programme Office, Living Oceans Foundation, Island Conservation Society, D’Arros
Research Station, Seychelles Island Foundation, CORDIO and the Ministry of Foreign Affairs of
Finland.
Editors
David Obura & Gabriel Grimsditch
Contributors
Paul Marshall, Naneng Setiasih, Greta Aeby, Lizzie McLeod, Alison Green, David Bellwood, Howard
Choat, Haji Machano, Ameer Abdulla, Robert Steneck, Jerker Tamelander.
Cover Photography
Front cover: Bleached Acropora coral on the Great Barrier Reef, Queensland, Australia. Copyright:
Paul Marshall, Great Barrier Reef Marine Park Authority, GBRMPA.
Back cover: Coral reef and research diver, Misali Island, Pemba, Zanzibar. Copyright: Jerker
Tamelander, IUCN.
ii
Resilience Assessment of Coral Reefs
Assessment protocol for coral reefs, focusing on
coral bleaching and thermal stress
iii
The designation of geographical entities in this book, and the presentation of the material, do not imply
the expression of any opinion whatsoever on the part if IUCN or The Nature Conservancy concerning
the legal status of any country, territory, or area, or of its authorities, or concerning the delimitation of
its frontiers or boundaries. The views expressed in this publication do not necessarily reflect those of
IUCN or The Nature Conservancy, nor does citing of trade names or commercial processes constitute
endorsement.
Published by: IUCN, Gland, Switzerland
Copyright: © 2009 The International Union for the Conservation of Nature and Natural
Resources / The Nature Conservancy
Reproduction of this publication for educational or other non-commercial purposes is
authorized without prior written permission from the copyright holders provided the
source is fully acknowledged.
Reproduction of this publication for resale or other commercial purposes is prohibited
without prior written permission of the copyright holders.
Citation: Obura, D.O. and Grimsdith, G. (2009). Resilience Assessment of coral reefs
– Assessment protocol for coral reefs, focusing on coral bleaching and thermal stress.
IUCN working group on Climate Change and Coral Reefs. IUCN, Gland, Switzerland.
70 pages.
ISBN: 978-2-8317-1151-5
This is the official manual (2009 edition) of the Reef Resilience Assessment protocol
developed by the IUCN working group Climate Change and Coral Reefs. For queries
about the methods, please send them to the contacts below.
Available from:
IUCN Global Marine Programme, International Union for the Conservation of Nature,
Rue Mauverney 28, 1196 Gland, Switzerland.
Tel : +41 22 999 02 17 Fax: +41 22 999 00 25
E-mail: marine@iucn.org or Gabriel Grimsditch; ggrimsditch@iucnus.org
CORDIO East Africa (Coastal Oceans Research and Development – Indian Ocean)
# 9 Kibaki Flats, Kenyatta Beach
P.O.BOX 10135, Mombasa 80101, Kenya
Web: www.cordioea.org
David Obura; dobura@cordioea.org
This publication is available as a download from the IUCN Global Marine Programme
website at the following address: http://www.iucn.org/cccr/publications/
A catalogue of IUCN publications is also available.
Printed in Switzerland on chlorine-free paper from FSC-certified forests.
iv
Resilience Assessment of Coral Reefs
Assessment protocol for coral reefs, focusing on
coral bleaching and thermal stress
David Obura and Gabriel Grimsditch
IUCN Climate Change and Coral Reefs Marine Working Paper Series – No 4
v
About the IUCN Climate Change and Coral Reefs Marine Working Group
The IUCN Climate Change and Coral Reefs Marine Working Group (formerly the IUCN Resilience
Science Working Group), focused on coral bleaching, resilience and climate change, was established
in 2006 by the Global Marine Programme of IUCN on a 3-year grant from the John D. and Catherine
T. MacArthur Foundation. The goal of the working group is to draw on leading practitioners in coral
reef science and management to streamline the identification and testing of management interventions
to mitigate the impacts of climate change on coral reefs. The working group consults and engages
with experts in three key areas: climate change and coal bleaching research to incorporate the latest
knowledge; management to identify key needs and capabilities on the ground; and ecological
resilience to promote and develop the framework provided by resilience theory as a bridge between
bleaching research and management implementation.
One of the outputs of this group was the setting up of a website that provides links to projects, events,
partners and publications.
For more information, see http://www.iucn.org/cccr/publications/
This publication is the 4th in a series of publication on management tools to promote resilience in
marine ecosystems. The other three, also available from IUCN’s Global Marine Programme are listed
below:
Coral Reef Resilience and Resistance to Bleaching
Gabirel D. Grimsditch and Rodney V. Salm
© IUCN/TNC, October 2006
Managing Mangroves for Resilience to Climate Change
Elizabeth Mcleod and Rodney V. Salm
© IUCN/TNC, October 2006
Managing Seagrasses for Resilience to Climate Change
Mats Björk, Fred Short, Elizabeth Mcleod and Sven Beer
© IUCN/TNC, September 2008
Introduction
6
Table of Contents
1. Introduction ..................................................................................................................................... 8
1.1. Coral reefs, climate change, and reef resilience.................................................................... 8
1.2. Resilience definitions ............................................................................................................. 9
1.3. Justification ............................................................................................................................ 9
1.4. Using resilience in management............................................................................................ 9
1.5. Goal and objectives.............................................................................................................. 10
1.6. Scope of resilience assessment .......................................................................................... 10
1.6.1. Coral reef compartments............................................................................................. 10
1.6.2. Drivers of resilience ..................................................................................................... 11
1.7. The resilience assessment protocol..................................................................................... 13
2. Survey design ............................................................................................................................... 15
2.1. Site selection........................................................................................................................ 15
2.2. Sampling time ...................................................................................................................... 15
2.3. Safety ................................................................................................................................... 16
2.4. Overview of methods ........................................................................................................... 16
2.4.1. Visual estimation of indicators..................................................................................... 16
2.4.2. Quantitative methods .................................................................................................. 17
2.5. Team composition and skills ................................................................................................ 17
2.6. Equipment ............................................................................................................................ 18
2.7. Desk study/background information..................................................................................... 18
2.7.1. Environmental.............................................................................................................. 18
2.7.2. Reef status and history................................................................................................ 19
2.7.3. Anthropogenic threats ................................................................................................. 19
3. Field methods ............................................................................................................................... 20
3.1. Benthic cover ....................................................................................................................... 20
3.1.1. Objective...................................................................................................................... 20
3.1.2. Indicators ..................................................................................................................... 20
3.1.3. Methodology ................................................................................................................ 20
3.1.3.1. Photoquadrats ........................................................................................................ 20
3.1.3.2. Algal community ..................................................................................................... 22
3.1.4. Materials ...................................................................................................................... 22
3.1.5. Observer skills ............................................................................................................. 22
3.1.6. Background data ......................................................................................................... 22
3.2. Coral community composition .............................................................................................. 23
3.2.1. Objective...................................................................................................................... 23
3.2.2. Indicators ..................................................................................................................... 23
3.2.3. Methodology ................................................................................................................ 23
3.2.4. Materials ...................................................................................................................... 24
3.2.5. Observer skills ............................................................................................................. 24
3.2.6. Background data ......................................................................................................... 24
3.3. Coral size classes and population structure ........................................................................ 25
3.3.1. Objective...................................................................................................................... 25
3.3.2. Indicators ..................................................................................................................... 25
3.3.3. Methodology ................................................................................................................ 25
3.3.3.1. Size class and recruitment...................................................................................... 25
3.3.3.2. Maximum size of corals .......................................................................................... 27
3.3.4. Materials ...................................................................................................................... 27
3.3.5. Observer skills ............................................................................................................. 27
3.3.6. Background data ......................................................................................................... 27
3.4. Coral condition and threats .................................................................................................. 28
3.4.1. Objective...................................................................................................................... 28
3.4.2. Indicators ..................................................................................................................... 28
3.4.3. Methodology ................................................................................................................ 28
3.4.4. Bleaching and mortality ............................................................................................... 29
3.4.5. Coral diseases and other conditions ........................................................................... 30
3.4.6. Other threats................................................................................................................ 30
3.4.7. Materials ...................................................................................................................... 31
3.4.8. Observer skills ............................................................................................................. 31
3.4.9. Background data ......................................................................................................... 31
Introduction
7
3.5. Fish community structure and herbivory .............................................................................. 31
3.5.1. Objective...................................................................................................................... 31
3.5.2. Indicators ..................................................................................................................... 31
3.5.3. Methodology ................................................................................................................ 31
3.5.3.1. Functional groups ................................................................................................... 31
3.5.3.2. Herbivore functional groups.................................................................................... 33
3.5.4. Sampling...................................................................................................................... 35
3.5.4.1. Long swim............................................................................................................... 35
3.5.4.2. Transects/point counts............................................................................................ 36
3.5.5. Materials ...................................................................................................................... 36
3.5.6. Observer skills ............................................................................................................. 36
3.5.7. Background data ......................................................................................................... 37
3.6. Site resilience factors ........................................................................................................... 37
3.6.1. Objective...................................................................................................................... 37
3.6.2. Indicators ..................................................................................................................... 37
3.6.3. Methodology ................................................................................................................ 37
3.6.4. Data sources ............................................................................................................... 37
3.6.5. Approach ..................................................................................................................... 37
3.6.5.1. 5-point scale ........................................................................................................... 38
3.6.5.2. Spot vs. continuous measurements ....................................................................... 38
3.6.6. Resilience indicators.................................................................................................... 38
3.6.6.1. Benthic indicators ................................................................................................... 38
3.6.6.2. Substrate and reef morphology .............................................................................. 39
3.6.6.3. Cooling and flushing ............................................................................................... 40
3.6.6.4. Shading and screening ........................................................................................... 40
3.6.6.5. Extreme conditions and acclimatization ................................................................. 41
3.6.6.6. Coral condition........................................................................................................ 42
3.6.6.7. Coral population structure....................................................................................... 43
3.6.6.8. Coral associates ..................................................................................................... 44
3.6.6.9. Fish functional groups - herbivory .......................................................................... 45
3.6.6.10. Connectivity ............................................................................................................ 45
3.6.6.11. Anthropogenic factors - negative............................................................................ 46
3.6.6.12. Anthropogenic factors – positive (management).................................................... 47
3.6.7. Materials ...................................................................................................................... 48
3.6.8. Background data ......................................................................................................... 48
4. Data management and analysis ................................................................................................... 49
4.1. Archiving and storing data.................................................................................................... 49
4.2. Data analysis........................................................................................................................ 49
4.3. Reporting and publication .................................................................................................... 49
5. References.................................................................................................................................... 51
6. Resources..................................................................................................................................... 52
6.1. Benthic cover .........................................................................Error! Bookmark not defined.
6.2. Coral community structure (genera) ......................................Error! Bookmark not defined.
6.3. Coral size class distributions (selected genera)..................... Error! Bookmark not defined.
6.4. Coral condition .......................................................................Error! Bookmark not defined.
6.5. Fish community structure - herbivores...................................Error! Bookmark not defined.
6.6. Resistance and resilience indicators...................................... Error! Bookmark not defined.
6.7. Data entry and analysis..........................................................Error! Bookmark not defined.
7. Field Datasheets ........................................................................................................................... 53
7.1. Coral genera ........................................................................................................................ 53
7.2. Coral sizes............................................................................................................................ 54
7.3. Condition .............................................................................................................................. 55
7.4. Fish-herbivore functional groups.......................................................................................... 56
7.5. Fish-basic functional groups ................................................................................................ 57
7.6. Resistance/resilience factors ............................................................................................... 58
8. Resilience Indicators Table........................................................................................................... 59
Introduction
8
Good recovery on a solid reed framework (left) compared to no recovery on unconsolidated branching framework
(right) By Jerker Tamelander, IUCN
1. Introduction
1.1. Coral reefs, climate change, and reef resilience
Coral reefs and their associated seagrass beds and mangrove habitats support the highest marine
biodiversity in the world. More than 500 million people worldwide depend on them for food, storm
protection, jobs, and recreation. Their resources and services are worth an estimated 375 billion
dollars each year, yet they cover less than one percent of the Earth’s surface. Unfortunately, many of
the world’s coral reefs have been degraded, mainly due to human activities. According to the Status of
Coral Reefs of the World: 2004, 70% of the worlds’ coral reefs are threatened or destroyed, 20% of
those are damaged beyond repair, and within the Caribbean alone, many coral reefs have lost 80% of
coral species.
Climate change is now recognized as one of the greatest threats to coral reefs worldwide. While a
changing climate brings many challenges to coral reefs, one of the most serious and immediate
threats is from mass coral bleaching associated with unusually high sea temperatures. Coral
bleaching has lead to substantial damage to coral reefs on a global scale (16% of reefs suffered
lasting damage in 1998 alone), with some areas losing 50-90% of their coral cover (Wilkinson 2000).
Further degradation is predicted: severe coral bleaching events may be an annual occurrence by mid-
century, even under optimistic climate scenarios (Hoegh-Guldberg 1999, Hughes et al. 2003).
The amount of damage depends on not only the rate and extent of climate change, but also on the
ability of coral reefs to cope with change. Importantly, the natural resilience of reefs, that maintains
them in a coral dominated state, is being undermined by stresses associated with human activities on
the water and on the land. Unmanaged, these stresses have the potential to act in synergy with
climate change to functionally destroy many coral reefs and shift them to less diverse and productive
states dominated by algae or suspension feeding invertebrates. Coral reefs are under pressure from a
variety of human activities, including catchment uses that result in degraded water quality,
unsustainable and destructive fishing, and coastal development. These local pressures act to reduce
the resilience of the system, undermining its ability to cope with climate change, and lowering the
threshold for the shift from coral-dominated phase to other phases. Increasingly, policy-makers,
conservationists, scientists and the broader community are calling for management actions to restore
and maintain the resilience of coral reefs to climate change, and thus avoid worst-case scenarios.
Introduction
9
Two general properties determine the ability of coral communities to persist in the face of rising
temperatures: their sensitivity and their recovery potential. Sensitivity relates to the ability of individual
corals to experience exposure without bleaching, and if they bleach to survive. Recovery potential
relates to the community’s capacity to maintain or recover its structure and function in spite of coral
mortality. These properties at the coral colony and coral community level are termed ‘resistance’ and
‘resilience’, respectively (West and Salm 2003, Obura 2005, Grimsditch and Salm 2006). Together,
they determine the resilience of coral communities to rising sea temperatures.
1.2. Resilience definitions
Resistance – when exposed to high temperature and other mitigating factors, the ability of individual
corals to resist bleaching, and if bleached to survive.
Resilience – following mortality of corals, the ability of the reef community to maintain or restore
structure and function and remain in an equivalent ‘phase’ as before the coral mortality.
1.3. Justification
The need for rapid methodologies for measuring coral reef resilience and their application in assessing
the effectiveness of coral reef conservation management measures is becoming increasingly acute,
and especially so in the developing world. Earlier attempts have been limited to post-event
questionnaire assessments (Salm and Coles 2001, www.reefbase.org) with limited application and
problems of subjectivity and applying the findings to management (Obura and Mangubhai 2003). It is
therefore crucial to develop monitoring and assessment protocols to build an understanding of
bleaching resistance and resilience indicators for application in management, and to determine how
MPA management actions can influence resilience and resistance.
This document outlines a protocol that is one attempt at defining some basic resilience indicators that
can be quantified using rapid assessment methods. These will serve two primary purposes:
1) To provide simple methods that are applicable in a wide variety of developing country
settings. A large of percentage of the world’s coral reefs is located in developing countries with low
resources and capacity available for management and monitoring. Although monitoring of resistance
and resilience indicators can greatly improve coral reef management in the face of climate change,
these parameters are related to oceanographic phenomena and ecological community characteristics
that are relatively expensive and time-consuming to study in detail. Therefore it is of great importance
to develop rapid assessment methods for low-resource scenarios that can be used effectively in coral
reefs areas around the world.
2) To provide a first assessment of outcomes in coral reef conservation. Although Marine
Protected Areas (MPAs) cannot prevent the stresses that cause coral bleaching (increased
temperature and radiation), it is possible that they could improve resistance and resilience of coral
reefs by protecting them from other stresses (for example fishing pressure) and thus minimizing coral
mortality and/or allowing the community to recover from bleaching events. However, to date the
success of MPA management practices in influencing bleaching resistance and resilience has not
been systematically quantified on larger scales. To aid an assessment of the effectiveness of coral
reef conservation measures in the face of climate change it is necessary to develop easily-applicable
resilience indicators that can be monitored in MPAs around the world.
1.4. Using resilience in management
The ability of managers to adapt to climate change will be critical to the future of coral reefs, and also
for the social and economic services that they provide. While science is providing important insights
about the impacts of climate change on coral reef systems, strategies for managing them in a
changing climate are only just emerging (Marshall and Schuttenberg 2006). There is now an urgent
need to test and refine these ideas, and to accelerate learning through sharing management
experiences – successes and failures – in responding to the challenges of climate change.
Introduction
10
One of the major challenges for progressing resilience-based management lies in successful
application. While general resilience principles are influencing the way practitioners approach coral
reef management and conservation, there remains an urgent need for an operational tool for
assessing and mapping resilience in coral reef ecosystems. Drawing on current and emerging
resilience thinking, this document explores coral reef resilience in operational terms, and outlines a
suite of variables that are likely to be useful indicators of reef resilience in a management context, and
a protocol for measuring them.
1.5. Goal and objectives
The protocol is designed to provide a rapid assessment of coral bleaching resistance and resilience at
an individual site level. This is intended to facilitate assessment of any past management actions in
maintaining the resilience of coral reefs, and the making of new management decisions against local
MPA objectives.
Specifically, the protocol is intended to:
1) Assess the factors affecting coral bleaching during a bleaching event (resistance factors).
2) To assess the factors affecting coral and reef recovery following a bleaching event (resilience
factors).
3) Enable between-site comparisons at a local area/region/MPA (network) level.
4) Enable inter-regional comparisons at larger scales.
In a management context, the protocol should facilitate:
5) Building an understanding of bleaching resistance and resilience factors that can be addressed by
MPA design and management.
6) Assessing whether MPA design and management practices to date have addressed bleaching
resistance and resilience.
7) Designing networks of MPAs based on bleaching resistance/resilience characteristics.
8) Providing information to adaptively manage coral reefs in response to bleaching events and reef
resilience.
1.6. Scope of resilience assessment
Ecological resilience relates to the entire scope of positive and negative factors affecting a community,
such as resource extraction, pollution and invasive species. This assessment method focuses on
climate impacts, in order to focus manager’s efforts to limiting them, however these cannot be
assessed in isolation, and information on the other threats facing a reef is necessary to distinguish the
role of climate threats. To operationalize resilience for assessment, the scope of the concept, in
defining which components of the reef community to measure, and in identifying which processes are
the main drivers of community structure and health is necessary.
1.6.1. Coral reef compartments
There is a huge complexity of factors, species and compartments that make up a coral reef. The
primary ones for the assessment to focus on need to be identified, alongside considerations of ease of
measurement using visual reef assessment practices. We identify four levels at which to structure the
reef: (see Fig. 1 below)
1) the primary biotic compartments that
make up the reef community and have
been the focus of visual assessment of
reefs for three decades: corals, algae and
fish/consumer communities;
2) the ecological interactions that drive
dynamics within and among these
groups, including from members of the
coral reef community that are not within
the groups in (1) above;
3) habitat and environmental influences that
directly affect these compartments and
the interactions between them; and
4) external drivers of change, including
anthropogenic and climate factors.
Fig. 1. Resilience compartments model, coral reefs.
Introduction
11
In considering the above, it is important to note that both pattern (state) and process (function)
indicators and variables may be useful for measurement and interpretation. Both may be affected by
drivers of resilience.
1.6.2. Drivers of resilience
Balance in the coral reef community is affected by a vast array of processes, but these can be
differentiated into strong and weak drivers of change. In developing the resilience model that is the
basis for assessment, the strong drivers of resilience, or of shifts away from a resilient coral
community need to be identified. These drivers may act from one reef compartment to another (e.g.
fish to algae), or across different levels (e.g. anthropogenic factors to corals). The importance of
incorporating the latest science in identifying the strongest and most active drivers, and which may
change under different conditions and in different locations, is paramount.
A summary of the strong drivers, are the following:
Connectivity. Currents disperse coral larvae enabling re-seeding of impacted reefs from refuge
populations of hard corals. Connectivity provides many other functions as well, such as in the
provision of ecosystem services, such as ecological interactions between adjacent reefs (vagile
predators/herbivores). In the broader sense, connectivity includes factors such as available substrate
and successful settlement of larvae.
Physical/chemical factors. The physical/chemical environment is a key determinant of resilience by
determining the environmental envelope within which a reef community exists. In considering these,
however, it is important to understand the local environment, as reefs have thrived in very different
conditions (e.g. natural oligotraphic vs eutrophic areas). Of key concern here are proximity to
thresholds, and/or levels of variability that might convey vulnerability to changes considered under
anthropogenic effects. The complexity of interactions and compartments that relate to water quality,
nutrients and microbial activity (fig. 2) precludes simple explanations. Additionally, physical processes
affecting circulation around bays, headlands, etc may fundamentally affect other physical and
ecological processes, and these differences must be considered when establishing underlying
conditions.
Algal-coral dynamics, and therefore algal control through herbivory are both strong drivers of reef
state, as well as indicators of phase shifts from corals to algal dominance, or vice versa. Algal
populations have a strong influence on the recovery of coral communities following coral mortality, and
algal competition or microbial enhancement by algae may also affect the susceptibility of corals to
bleaching (Smith et al. 2006). A number of different herbivore functional groups are recognized that
mediate coral-algal dynamics in different ways, and the diversity of species and of their vulnerability to
stresses strongly affects how robustly each functional group contributes to reef resilience. Fish are the
primary taxonomic group controlling herbivory, though under degraded conditions, sea urchins
become important.
Anthropogenic factors may change any of the enclosed compartments in the figure, and drivers listed
above. For example, environmental factors may be altered by anthropogenic stresses such as coastal
development, and this may alter key drivers of resilience, such as circulation that affects thermal
stress. Similarly, fishing may affect the balance and actions of herbivore functional groups. Adding
complexity to the role of nutrients and physical/chemical processes, anthropogenic alterations of water
and substrate quality may have very complex impacts on reef processes.
Thermal stress. The assessment method is focused on climate change impacts, in particular coral
bleaching due to thermal stress. Thus greater focus in the methodology is given to this, and to factors
that affect it. Climate change-induced thermal stress is driven by large pools of warm surface waters,
driven by climate and oceanographic factors. The manifestation of these warm pools at the local level
is affected by regional to local environmental factors such as cooling and flushing that reduce the
temperature experienced locally. Synergistic stress by light is affected by shading and screening
factors that reduce the degree of stress. Biological factors are also important, such as the intrinsic
stress resistance of corals or zooxanthellae, and acclimatization driven by local patterns of variability
and warming/cooling trends over the coral lifetimes.
Introduction
12
The primary focus of this assessment protocol is on the effect of climate change on thermal stress on
corals, for which the strong drivers summarized above are added into the general model from Fig. 1
(see Fig. 2). Many other processes may affect this model and can be incorporated as needed for a
particular instance, the resilience framework providing a context to help identify the strong drivers that
maintain reef health and minimize vulnerability.
Fig. 2. Stron drivers for climate change impacts on coral reefs.
Many other drivers affect coral reefs, and these need to be considered for the local context when
customizing the method to a new area. For example, crown of thorns seastar outbreaks may play a
locally ‘strong‘ role, and the purpose of initial literature surveys and consultations is to ensure these
are catered for. There is also a difference between ‘slow‘ and ‘fast‘ drivers of resilience. Slow drivers
may cause small or near-zero increments of change over a long time but push the system to a
threshold beyond which change happens quickly and potentially irreversibly (e.g. pollution). Fast
drivers tend to cause large increments over a short time (e.g. mass bleaching event). These may play
different roles at different times, and particularly may affect phase shift reversals. Finally, drivers
important in phase shift reversals are poorly known, such as of rehabilitating algal communities to
coral reefs. These may be mediated by actors or processes relatively dormant or inactive under
normal conditions. The importance of an open approach to monitoring and assessment is therefore
essential.
Thus the model and methodology are first an application of general resilience principles in assessment
of the state of a reef community and the strong drivers affecting it, with a primary focus on thermal
stress as the climate change threat and key driver affecting reefs today. The methodology could be
adjusted to deal with other important threats as needed at individual sites.
Introduction
13
Fig. 3. Nested approach to monitoring resilience, building additional resilience indicators onto routine monitoring
approaches (step 1b). During a bleaching event (step 2b) a subset of resilience indicators would be included in
bleaching assessment protocols (Oliver et al. 2004).
1.7. The resilience assessment protocol
While the assessment protocol can be undertaken as an independent study, it is most useful in an
adaptive management structure that already incorporates annual or routine monitoring (see Figure 3
above). Thus routine monitoring (A in Fig 3) provides background time series information on a limited
set of variables that track coral reef status and function over time. Where the concern is about the
effects of coral bleaching, this resilience assessment is designed to be undertaken to increase
understanding of the resistance and resilience of reefs to bleaching, whether a bleaching event has
occurred in the past or not (B in Fig 3). This need be done only once, then again after a long period
(e.g. 5 years) or after a major event (e.g. bleaching, or other major pulse stress such as a cyclone,
COTs outbreak, etc.) to determine whether the reef has been shifted into another phase. During a
bleaching event, a separate monitoring approach is applied focused just on bleaching variables,
designed to be repeated over short periods of time (e.g. monthly) to track the actual event (C in Fig 3).
Fig. 4. The resilience assessment builds on a foundation from standard monitoring procedures, and other studies,
adding further detail on coral community and site-based resistance/resilience to bleaching.
Introduction
14
The main innovations of this resilience assessment are:
• More detailed measurements of coral populations (size classes, recruitment, etc), focused on
selected genera with different susceptibilities to bleaching, and linked with measurements of coral
health and condition
• More detailed measurements of algal height as a proxy for biomass
• Fish sampling focused on herbivorous fish, to estimate more precisely the potential controlling
effect of herbivory on the benthic community
• Estimation of potentially important resilience factors, as quantitative measurements of such a wide
variety of variables is not feasible in most reef monitoring situations
• Identification of indicators that affect thermal stress at a local site to assist in managing reefs
within different vulnerabilities to warm surface pools
For the most reliable interpretation of the above information, good knowledge of the current status and
recent history of the study reefs is necessary. Thus a literature review of local studies and monitoring
programmes, and consultation with scientists and managers familiar with the local setting, are
necessary.
This document is a product of the IUCN Working Group on Climate Change and Coral Reefs. It has
been produced to support a globally coordinated program that will test and further refine an approach
for assessing coral reef resilience as the basis for resilience-based management. The experience from
this program will underpin the development of a formal framework for assessing resilience in coral reef
ecosystems.
Survey Design
15
2. Survey design
The focus of the rapid assessment is on resistance and resilience of corals and the reef community to
climate change (thermal stress). The methodology takes the resilience principles and
compartmentalization of the coral reef community and strong drivers outlined earlier, and organizes
them into a practical set of field measurements.
2.1. Site selection
Site selection is essential in order to cover a broad range of sites in terms of health, reef habitat and
zone and potential influence of the factors that may affect coral bleaching and recovery.
The goal is to survey two depth contours, recognizing that strongest impacts of bleaching are in very
shallow water (< 8 m), with in many places a critical depth of 10-15 m below which levels of bleaching
and mortality are much less. Operationally, sites should be selected at approximately 3-5 m (or
shallower) and 10-12 m below the lowest low tide, the deepest samples also being bound by dive-time
restrictions and the need for sufficient sampling time to record all parts of the dataset. However, on
many reefs, the highest coral cover will not be found at these exact depths, and adjustments should
be documented and justified in the local site methodology.
The basic selection to criteria to consider should be:
1) Depth – include shallow (< 5 m) and deeper (operationally, 10-15 m, as deeper than that time
restrictions severely curtail sampling ability. With many divers, it might be feasible to do > 15 m).
This covers factors related to temperature and stratification, as well as to recovery speeds of
corals and growth rates of algae.
2) Habitat – include a mix of windward, leeward, channel and lagoon sites, or other relevant features
according to the area being studied.
3) Connectivity and currents – a transect along and across major currents and axes of water
movement.
4) Land - ocean influence – a transect from land-based influences to oceanic influences may affect
aspects of turbidity, water quality and access by resource users.
5) Management regime – to include differential effects of management on reef ecology.
6) Distance from human settlements – as a proxy for some human impact variables.
Site selection is assisted by having detailed coastal and bathymetric charts and recent high-resolution
remote sensing images, such as LandSat/SPOT, and preferably QuickBird and other similar
technologies, or aerial photographs. A hand-held or dive-boat based GPS and depth sounder help
finding appropriate sites in the field, and for recording location. All sites must be marked by GPS (in
degree units, not UTM), and backed by a site description and shore-based lines of sight if possible.
Where additional detail is possible and for local needs, beginning and end-points of sampling can also
be recorded by GPS.
A multivariate analysis is used to identify the factors that most strongly explain patterns in the dataset.
Accordingly the larger the number of sites, the better discrimination there will be. Thus aim at sampling
as many sites as possible, that is, completing all measurements of a single ‘site’ in one dive of the
sampling team. For example, deep and shallow sites sampled adjacent to each other can be done as
1st and 2nd dives of the survey team.
2.2. Sampling time
This will vary with different teams, however as a rule of thumb, 60-minutes of data collection has been
found to be necessary for a single site (ie. for the fish observer to record the swim and 3 transects,
and each coral size observer to record two transects). In practise, this may mean planning for dives of
approx. 70 minutes. With dive depths restricted to < 12 m, this is feasible and well within safe-diving
Survey Design
16
limits. With moderate boat/dive support two dives are possible each day. With excellent boat/dive
support it will be possible to sample three sites per day.
2.3. Safety
Safety of divers is the number one priority. No surveys should be undertaken when weather or sea
conditions are unsafe or if a diver does not feel well. In particular, teams should plan work to avoid
decompression dives during survey. Any diver who is not comfortable diving for any reason should
NOT participate in the diving aspects of the survey.
2.4. Overview of methods
The resilience assessment is designed to:
1) Provide an overarching semi-quantitative assessment of all components of reef resilience with
respect to climate change, through estimation of indicators grouped under key
compartments/drivers of reef resilience, and
2) For the key compartments and strongest drivers with respect to thermal stress and bleaching,
quantitative measures that enable more in-depth assessment of status and health.
A) Semi-quantitative Indicators
Habitat/environment
Physical site parameters
Substrate and reef morphology
Connectivity
B) Quantitative samples
Coral community
Population Cover, genera, size classes, recruitment
Individual condition Bleaching, mortality, disease, threats
Interactions/responses
Benthic interactions Algae community, competition
Coral interactions Competition
Fish functional groups Herbivory functional groups
Anthropogenic influences.
Climate/thermal stress
Cooling and flushing
Shading and screening
Extreme conditions and acclimatization
2.4.1. Visual estimation of indicators
A semi-quantitative scale (Likart) of 1-5 is used for estimation of all the resilience indicators, including
those for which more detailed quantitative data will be collected. The 5-point scale was selected to
facilitate estimation of minimum (1), maximum (5) and moderate (3) level for each indicator for the
region of application, and intermediate levels of low (2) and high (4). In general the direction of the
indicator is selected such that 1 designates low/poor/negative conditions for corals and 5
high/good/positive conditions. Indicators are grouped into clusters, as per the table above.
Because the indicators are semi-quantitative, there is considerable scope for subjective bias, and a
high level of experience is required in their estimation. Thus this component needs to be done by an
experienced scientist with considerable experience at the study location and in the region surrounding
it.
Survey Design
17
2.4.2. Quantitative methods
The focus of the quantitative methods is to build on past and current coral reef monitoring
programmes. This adds value to the information already collected by monitoring programmes, and
maximizes the interpretability of the new data on the basis of historic data. This approach also enables
capacity building of existing monitors/observers, so that staff, students and scientists that have been
the backbone of past monitoring activities can also be the primary implementers of this methodology.
For standardization of sampling among the components of the methodology, across locations and
teams that will apply it, and having considered the broad range of monitoring protocols currently being
applied, belt transects have been selected as the units of sampling – of 25*1 m for most benthic
variables, and 50*5 m for fish, and some variables are scored at the whole-site level. A summary of
the quantitative methods is given below:
Quantitative component Method/approach
Benthic cover
Compatible with main long term monitoring approach in the area. Preferred –
photo-quadrats analyzed using computer software. Alternatives – Line
Intercept transects, quadrats and other in situ methods.
Coral community structure
(genera)
Visual estimate of relative abundance of genera at the study site, in 5 classes
– dominant, abundant, common, uncommon, rare.
Coral size class distributions
(selected genera)
Belt transects (25 * 1 m) with subsampling using quadrats for small colonies <
10 cm. 15-20 selected genera, in doubling size classes (0-2.5, 2.6-5, 6-10, 11-
20 cm. etc)
Coral condition and threats
Incidence of coral condition and threats - bleaching, disease, predation, other
conditions and mortality. Sampled in the 25*1 m belt transects then in the
general study site.
Fish community structure –
focus on herbivores
Long swim (400* 20 m) or general site observation of large indicator fish, and
belt transects (50 * 5 m) recording the main functional groups at the lowest
taxonomic level possible, and focusing on herbivore functional groups.
2.5. Team composition and skills
The skills required for each component of the methodology are detailed in each relevant section, and
there is overlap in skills that might be good for different parts. In general, a team of 4 or 5 would be
ideal, though the work can be done with 2 or 3 with compromises. In the tables below, ‘X’ represents a
primary responsibility, and ‘-‘ represents an optional responsibility dependent on expertise. These are
given as guidance only, as the skills available in different team members may allow more optimal
allocation of duties. If this is done, then the field datasheets can be adjusted to best suit the team
members available.
Skill levels of ‘high’, ‘mid’ and ‘low’ are indicated. These are just indicative. In general there must be
one person very familiar with and who can lead the benthic work and score the resilience indicators,
and one very familiar with fish. Skills for the others on the team can be built up through on-site
training, and it may be necessary to assign 1-3 days for training to achieve a consistent level of data
collection.
Expertise Level 1) Resilience
indicators 2) Benthic
cover 3) Coral
genera 4) Coral
sizes 5) Coral
cond 6) Fish
1 Community/coral High X X
2 Coral Mid
X X
3 Coral Low X
X
4 Fish High X
5 Fish Low X
Survey Design
18
2.6. Equipment
The full list of equipment required for the surveys is summarized below. Details are given within each
section.
Underwater Specialized, dry
General Temperature loggers (see below) GPS, depth sounder
Charts, high-resolution remote
sensing images
1) benthic cover Digital camera with UW housing Computer
Software (Coral Point Count, or
Adobe Photoshop or equivalent)
2) coral diversity Datasheet
3) coral size class Transect line, 25 m (one per observer
or pair of observers) Genus guide for corals
1m ruler/stick marked at 10, 20, 40
and 80 cm to help guide size
estimates (3/4” PVC tube ideal for
this). One per observer.
Slate, marked along its top with 5, 10
and 20 cm to help guide size
estimates
Datasheet
4) coral condition - use line from coral size class Detailed ID resource of coral diseases
and lesions.
Datasheet, with checklist of
disease/condition codes
5) fish herbivore populations
Transect line, 50 m (may be useful to
have two, one for each buddy in a
team)
Detailed ID resource.
Datasheet, with ID sheet of main
groups
6) resilience indicators Datasheet Indicator/criterion table for constant
updates.
2.7. Desk study/background information
To interpret resilience variables and indicators, knowledge of their context is necessary, and this may
incorporate past, present and future aspects. These include environmental and human dimensions,
and a variety of sources will be needed.
2.7.1. Environmental
In the context of this study, temperature (thermal stress) is the key independent variable against which
resilience (of corals to bleaching) is being evaluated, and there are a number of other variables that
influence and co-vary with temperature and also influence resilience. Thus seawater temperature is
the primary indicator to quantify, followed by a number of oceanographic patterns that influence its
variability such as currents, upwelling, and periodic cycles. Because of the linkages between ocean
and atmosphere, atmospheric variables can provide useful proxies for variation in sea temperatures.
Air temperature and a number of other variables such as winds, rainfall and solar radiation can be
related to sea surface temperature patterns. And because they in many cases have longer historical
records and are used more commonly than ocean variables in long term projections, can serve as
proxies for variability and trends in seawater temperatures. Additionally, because radiation interacts
strongly with temperature in causing stress in corals, variables that affect solar radiation and heating
at the sea surface are also useful.
Survey Design
19
Background data for assessing reef resilience:
Area Purpose Datasets
Local climate –
seawater temperature
Variability and trends in sea
surface temperature In situ datasets on seawater temperature, light
penetration, etc.
Local climate -
meteorological and
oceanographic
Proxies for medium term patterns
in local climate - seasonal/annual
variability
Air temperature, rainfall, wind speed/direction,
radiation, sunhours/cloud cover, storms/cyclones,
waves, long term seawater temperatures
Regional climate –
long term trends
Long term trend indicators and
projections Available regional climate/sea change scenarios
The greater the scope of background data that can be collated is better. While primary data at the
local site are most desirable, in many cases datasets may only be available from nearby locations
(e.g. a city/airport) or at larger scales (e.g. climate variability/trends).
2.7.2. Reef status and history
Particularly if the area has already been the focus of conservation and protection actions, historical
data on reef status should be available, and ongoing monitoring may be underway. Historical research
on different aspects of reef ecology, and particularly any aspects related to variables recorded in the
assessment protocol should be compiled. If a long term monitoring programme is underway in the
area, or in nearby areas such that data sharing in a network is possible, then the protocol should be
customized to match the existing methods and/or the existing methods should be updated to be
consistent with the protocol – this allows more in-depth analysis of data recorded here against past
data.
2.7.3. Anthropogenic threats
Documentation of anthropogenic threats from the literature or in many cases government/official
statistics can be crucial in ensuring accuracy of the survey results. Thus demographic data can help
scale survey data on fisheries and pollution effects. Any past studies quantifying anthropogenic
impacts to the area, such as fishery catch data, or pollution monitoring, should be compiled.
Field methods
20
3. Field methods
The description of the field methods focuses on efficient application in the field, so does not linearly
follow the structure of sampling set out in “2.4 Overview of methods”.
The figure below indicates each of the detailed quantitative methods (B) – the part of the overall
dataset they provide and their order of presentation in the next sections. The semi-quantitative
resilience indicators (A) are described in detail in section 3.6.
3.1. Benthic cover
3.1.1. Objective
Benthic cover focusing on broad benthic categories and the algal community, important in assessing
phase shifts of coral reef communities to other forms.
3.1.2. Indicators
• Percent of overall benthic cover for benthic cover classes
• Percent of benthic cover by coral genus.
• Benthic algae abundance and composition
3.1.3. Methodology
3.1.3.1. Photoquadrats
Digital still photographs of the reef substrate are taken from a height of approximately 0.6-0.75 meters
above the substrate. Natural light is used in waters < 5 m deep with fill-in flash at deeper depths or on
overcast days. A red-shift can also be set within the camera, to enhance reds and help distinguish
classes such as coralline algae. Photographs can be taken haphazardly over a study site, counting 3-
4 between frames and ensuring successive images do not overlap. As a guide, photographs can be
taken of the coral size-class transects to ensure the photographs are representative of the other data
being collected. Alternatively, to minimize over-sampling of just one part of the study site, groups of 5
photos can be taken together with spaces of > 10 m between each group. Over 40 (about 45)
photographs should be collected, see below.
Photographs are downloaded onto a computer, and analysed for benthic composition and coral cover
using dedicated software such as Coral Point Count (Kohler and Gill 2006, see resources section 6).
Alternatively, generic software such as Adobe Photoshop can be used, where it is possible have
several layers in one image. 25 points are used for recording data from each photograph. In Adobe
Photoshop, this can be done by creating a new layer containing 25 circles (letter “o” in yellow shows
up best), evenly spaced over a sample photograph.
Field Method
21
To obtain results with sufficient accuracy and replication, the results for 4 images are combined
together to form one sample, or ‘transect’, of 100 points (this is easily done in CPCe). The images for
one transect can be sequential, but alternatively, to reduce sampling bias, can be randomly selected
from the available images using a random number generator. Not less than six of these transects (i.e.
24 images) are needed to calculate the mean and standard deviation of cover types, and preferably 10
‘transects’ (40 images) should be scored for each site. To ensure sufficient images are available, > 45
photographs should be captured for each site, to also allow for out-of-focus/problem photos.
The benthic substrate beneath each circle is identified according to the ability of the observers, with
Table 2.1 showing a hierarchy of levels useful for assessing resilience, adapted from English et al.
(1996). In general, enter data in more detailed categories and subsequently analysis can be done at
more aggregated levels depending on the need.
Priority among the categories is weighted towards cover types that are important both because they
are indicators of the phase/state of the reef (hard and soft corals, other invertebrates and coralline, turf
and fleshy algae), and when abundant tend to exert a strong controlling influence on competitors.
Benthic categories for identification:
Basic Intermediate Detailed
Hard coral Growth form Genus
Soft coral Growth form Genus
Other inverts Corallimorpharia, sponge, other Major taxa (e.g. Tubipora, gorgonian, corallimorph,
zooanthid, hydroids, sponge, ascidian, other)
Fleshy algae Halimeda, brown macroalgae,
green macroalgae, calcareous
algae
Genera
Turf/algal assemblage Thickness classes
Coralline algae Encrusting, nodular, rubble
Recent dead coral - -
Rubble - Size
Microbial Mats, filaments -
Sand - -
Seagrass - Genera
Competition by fleshy algae prevents recruitment by new corals, and growth by existing corals
By – Peter Verhoog
Field methods
22
3.1.3.2. Algal community
Measurement of algal biomass is not possible in a rapid assessment approach, but it can be
approximated by measurement of algal canopy height (see AGGRA, Robert Steneck pers. comm.).
Fleshy algae is differentiated from turf algae by height (> 1 cm) and that the structures that
differentiate genera can begin to be seen.
This measurement is done in the same 1m2 quadrats as sampled for small corals see section 3.2.3)
as follows:
• Estimate the % cover of all the macroalgal components within the 1m2 quadrat;
• For each component for which cover is estimated, measure the average height of algal fronds.
This may require several measurements of vertical height – write the individual heights onto the
datasheet, and the average will be calculated during analysis.
Macroalgae components can be identified at different levels of resolution to suit the observer. Note
that if genera/finer scale taxa are identified, also estimate the cover at the broad scale to ensure that
the sum of genus % cover adds up to the same value as the broad categories.
Broadest groups Intermediate Fine (e.g. major genera)
Fleshy algae red …
brown
Sargassum, Dictyota, Stypopodium,
green
Ulva, Dictyosphaeria,
Calcareous algae Halimeda and oher calcareous genera
3.1.4. Materials
Wet Dry
Digital camera with UW housing Computer
1m2 quadrat – algae cover Software (Coral Point Count CPCe; Adobe Photoshop or equivalent that
can handle multiple layers in an image)
Ruler (cm) – algal canopy height
3.1.5. Observer skills
In-water - A single observer, comfortable with diving and handling a camera underwater. May be
familiar with benthic monitoring techniques. Must be able to make unbiased selection for
photoquadrats, ensure high-quality un-blurred focused photographs in the field.
Image analysis – one or more observers with ability to distinguish the required categories of benthic
cover, and past experience in coral monitoring and image analysis.
3.1.6. Background data
Compile the literature and results of past monitoring, surveys and research projects in the study are,
and build up a narrative of coral reef health and any changes over that time. Construct timelines for as
long as possible of the major benthic cover types in the table above (hard coral, soft coral, algal types,
etc.)
Field Method
23
Robust recovery, through recruitment and growth of branching and plating coral colonies, on a previously
impacted reef By – Jerker Tamelander, IUCN
3.2. Coral community composition
3.2.1. Objective
Coral community structure can give insight on current status, past threats and future changes, from
growth form to genus level.
3.2.2. Indicators
2.1 Rank abundance/diversity of coral community.
3.2.3. Methodology
Proportional abundance of all genera at a site is estimated on a five-point scale. This is done towards
the end of the dive when an overall impression of the sampling site has been made, and the relative
abundance of genera can be estimated. Additionally, it may be useful to update the numbers on the
boat immediately following the dive.
Codes Class Explanation Numerical (approximate)
D 5 Dominant Dominate the coral community and/ or
structure of the site
>30% of coral cover
A 4 Abundant Visually abundant and seen in large
numbers. Co-dominate the site
10-30% coral population by number or area
and/or large number of colonies (>100)
seen/inferred in the immediate area of the
site (2500 m2)
C 3 Common Easily found/seen on site, but not
dominant in any way
>1% of coral population by number or area
and/or >20 colonies seen/inferred in the
immediate area of the site (2500 m2)
U/O 2 Uncommon/
Occasional
Not easily found, but several
individuals seen or can be found by
dedicated searching.
<10 colonies seen/inferred in the immediate
area of the site (2500 m2)
R 1 Rare Found by chance occurrence or only
1 or 2 found by dedicated searching.
<2 colonies seen/inferred in the immediate
area of the site (2500 m2)
Field methods
24
Seventy seven coral genera are listed below with three-letter codes used in the datasheets and
illustrations. The 3-letter codes are based on the first 3 letters of the genus name when possible.
Where this leads to duplicates a combination of the dominant letters of the name is used that also
preserves the sort order of genera by full name and by the code.
Genus code Genus code Genus code Genus code
Acanthastrea aca Distichopora dis Leptoseris les Pocillopora poc
Acropora acr Echinophyllia eph Lobophyllia lob Podabacea pod
Alveopora alv Echinopora epo Madracis mad Porites por
Anacropora ana Favia fat Merulina mer Psammocora psa
Anomastrea ano Favites fav Micromussa mic Sandalolitha san
Astraeosmilia asm Fungia fun Millepora mil Scolymia sco
Astreopora ast Galaxea gal Montastrea mon Seriatopora ser
Australomussa aus Gardineroseris gar Montipora mtp Siderastrea sid
Barabattoia bar Goniastrea gon Moseleya mya Stylaster sta
Blastomussa bla Goniopora gop Mycedium myc Stylocoeniella stc
Caulastrea cau Gyrosmilia gyr Oulophyllia oul Stylophora sty
Coeloseris coe Halomitra hal Oxypora oxy Symphillia sym
Coscinaraea cos Heliofungia hef Pachyseris pac Trachyphyllia tra
Ctenactis cte Heliopora hep Parasimplastrea par Tubastrea tub
Culicia cul Herpolitha her Pavona pav Tubipora tup
Cycloseris cyc Heteropsammia het Pectinia pec Turbinaria tur
Cynarina cyn Horastrea hor Physogyra phy Zoopilus zoo
Cyphastrea cyp Hydnopohora hyd Platygyra pla
Diaseris dia Leptastrea lep Plerogyra plg
Diploastrea dip Leptoria leo Plesiastrea pls
Datasheet instructions – a datasheet with three-letter codes for each genus likely to be found in the
area is needed. For clarity, the datasheet should exclude genera DEFINITELY NOT expected to be
found in the region, but it is important to INCLUDE ALL LIKELY genera, so that after the dive, some
genera that were seen but might not have been recorded are entered as present. The datasheet
should have space for additional notes on any dominant/abundant/rare species.
Statistics from this dataset include:
• Genus richness, diversity and rank abundance
• Multivariate analysis and site association by coral genus composition
• Assessment of the target genera as representative of the site
• Diversity/dominance of coral genera at the site
3.2.4. Materials
Wet Dry
datasheet
3.2.5. Observer skills
A single observer, familiar with coral identification at least to the genus level and with broad
experience in observing corals in the field. Ability to identify >90 % of coral genera at a site with ability
to make notes/photographs and confirm identifications of unknown corals from ID guides.
3.2.6. Background data
Compile historical data on coral diversity and relative abundance for the study area and surrounding
region, noting any changes in composition from any cause.
Field Method
25
Large coral colonies may fall both in an outside the belt transect, requiring a decision by the observer to include
them or not. Further, the observer often has to decide when fragments clearly of the same genet function as one
single large colony (e.g. here) as opposed to separate individual smaller colonies.
By – Cheryl-Samantha Owen, Save Our Seas Foundation
3.3. Coral size classes and population structure
3.3.1. Objective
To colle ct data on coral community structure including recruitment and colony sizes of key genera
dominant in the local area and representing different functional groups of corals.
3.3.2. Indicators
• Size class distributions (graphic), median and maximum size (index) by genus and overall
• Size class structure (densities, diversity, histogram, curve, median, mode, breadth, etc)
• Recruitment and small-colony survivorship (densities, diversity, survivorship)
• Recruitment rate – number of colonies in size class 1
• Recruit survivorship – ratio of size class 2 to 1
• Ratio of susceptible: intermediate: resistant genera (groups above, and defined by data set)
• Comparison of maximum colony size among sites
3.3.3. Methodology
Data is collected within transects, for size class and recruitment, and at the overall site level, for
maximum sizes of corals.
3.3.3.1. Size class and recruitment
A belt transect 25 m long and 1 m wide is used to record the number of colonies in targeted genera,
for colonies larger than 10 cm. Sampling for corals smaller than 10 cm is done using six 1 m2 quadrats
located along the transect, either located haphazardly along the transect, or at fixed intervals (e.g. at
0, 5, 10, 15, 20, and 25 m).
Only colonies whose center lies WITHIN the transect are counted – large colonies with their center
outside the transect must be ignored. A 1 m stick can be used to help guide estimation of transect
Field methods
26
width, held out in front as the observer swims down the transect. It can also be placed on the bottom
at right angles to the transect line to mark the 1m2 quadrats.
Size classes are listed in Table 3.1. The 1 m stick can also be marked at 5, 10, 20, 40 and 80 cm to
help guide size estimation of large colonies in the transect, and the top of the slate at 2.5, 5 and 10 cm
to assist with small colonies in the quadrats.
Measuring coral recruits By – Cheryl-Samantha Owen, Save Our Seas Foundation
Size classes for coral measurements.
Size classes (cm) Sampling method Aids to sampling Observers
(1) 0-2.5
(2) 3-5
(3) 6-10
Recorded in six 1 m2
quadrats per transect, at 0,
5, 10, 15, 20 and 25 m.
2.5, 5 and 10 cm marks at
top of slate; 5 and 10 cm
marks on 1 m stick
(4) 11-20
(5) 21-40
(6) 41-80
(7) 81-160
(8) 161-320
(9) > 320
Recorded in 25*1 m belt
transects
10, 20, 40 and 80 cm marks
on 1 m stick. For larger, use
multiples of 1 m stick, or
divisions on transect line.
A single individual can do
both. If a paired buddy
team, one can do the
quadrats the other the
transect.
Selected general are recorded, as sampling all genera requires significantly greater time, and
increases errors in identification particularly for small and rare colonies, and for inexperienced
observers. Selected genera should number about 15-20 and cover a range of bleaching resistance
from low to high, and may differ from one study region to another due to different relative abundance
of corals. However within one region (e.g. western Indian Ocean) or under one institution it is helpful to
use the same set of genera to enable detailed comparisons among sites. Selected genera must be
abundant/typical ones to ensure a reasonable number of colonies are sampled – scoring many genera
with only few colonies will not be useful for constructing size class distributions. If the abundance of
corals locally is not well known, then some preliminary surveys to identify the abundant/common
genera is necessary to select appropriately
Coral genera selected for Western Indian Ocean locations:
Low Intermediate - faviids Intermediate - other High
Acropora
Montipora Echinopora
Favia Fungia
Galaxea Porites (massives, non-
branching)
Field Method
27
Pocillopora
Seriatopora
Stylophora
Favites
Platygyra
Hydnophora
AcanthastreaLobophyllia
Porites (branching)
Coscinaraea
Pavona
Astreopora
The length (area) of transect sampled will be dependent on the complexity of the benthic community.
Ideally, four 25 m transects should be collected from each site, though less 2 might be possible,
depending on observer experience. Once practised, a diver should be able to record two full transects
in one dive, so two observers can record 4 transects.
Because of variability in site characteristics and observer efficiency, a full transect or all 6 quadrats
may not completed. The total distance surveyed, and number of quadrats, must be recorded to allow
for this so that partial transects/quadrats can be analyzed.
3.3.3.2. Maximum size of corals
For each site, the maximum size of coral colonies is recorded in two ways:
1) For the selected genera – completion of the replicate transects, record the maximum size of
colony seen ANYWHERE in the site, by writing an “L” into the appropriate table cell in the
datasheet (e.g. if the largest Acropora is a table 2.5 m in diameter, write an “L” into the 1.6-3.2 m
size class cell).
2) For all corals – in the site as a whole, record the 3 largest colonies at the site, of any
genus/species, estimating the size, and identity (genus/species) as possible).
Datasheet instructions – this datasheet has space for two transects on each side of the paper. Large
colonies are entered in the top section, and small colonies in the bottom. A scoring system, e.g. in
groups of 5 ( IIII ), is most efficient in the field, and the number of colonies in each table cell added up
during transfer to the computer. Genera are not pre-listed for small colonies as there is high variability
in occurence so enter these as they are seen. A space is given at the top of the transect and quadrat
fields for the length of transect and number of quadrats – if a transect cannot be completed it is still
worthwhile to collect a partial dataset, and the length of the transect used to standardize to a fixed
area. The largest colony at the site for each genus (not necessarily inside the transects) is indicated
by an “L” in the relevant table cell (for only one transect, if two are recorded at each site).
3.3.4. Materials
Wet Dry
transect line, 25 m (one per data collector)
1m ruler/stick marked at 10, 20 , 40 and 80 cm to help guide size estimates
slate, marked along its top with 5, 10 and 20 cm to help guide size estimates
datasheet
3.3.5. Observer skills
Two observers, familiar with coral identification at least to the genus level for common taxa. Should be
able to distinguish known from unknown genera, and to identify genera down to small sizes of 2-3 cm
and if possible less. Experienced with benthic monitoring, such as LIT or using photographs.
3.3.6. Background data
Compile any past data on coral recruitment and sizes, though it is likely to be limited. Also, compile
information on any extreme events (e.g. cyclones, floods) that may have caused high mortality to all or
specific size classes or taxa of corals, to help interpret size class distributions.
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3.4. Coral condition and threats
3.4.1. Objective
To collect data on coral threats including bleaching, disease, predation and other factors directly
affecting corals.
3.4.2. Indicators
• Bleaching prevalence
• Disease prevalence
• Predation prevalence
• Urchins, COTs and other threats
3.4.3. Methodology
Using the same belt transect as the size class samples, the incidence of threats is noted for all
colonies, including those not in the targeted genus list.
The coral threat observer should work the transect either following the size class observer or from the
other end, to ensure not getting in each other’s way. If the incidence of threats is low enough that the
observer is finished with the transect before the size classes are completed, then collect the same
data in a random swim area around the transects, the data being separated from that from within the
transects.
Data to be recorded in coral condition surveys.
Related to: Taxa Data
Coral Genus/species and size
class
Percentage of colony pale (colour card level 2) and/or bleached
(colour card level 1) and/or dead. All colour card (levels 3 and
greater are classed as “normal”.
Presence of disease or other clear condition affecting the colony
Threat Eroding sea urchins, crown
of thorns, Drupella, other
threats.
Number of individuals in belt transect (subsample if density is high)
and number in general swim over study site.
Crown-of-thorns seastars, Acanthaster plancii, devouring an Echinipora colony. By – Jerker Tamelander, IUCN
Field Method
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3.4.4. Bleaching and mortality
Bleaching and mortality levels by colony can be recorded at different levels of precision. The most
basic level is summarized in the table below, from Oliver et al. (2004), below but if observers are
experienced researchers, more detailed data can be collected. CoralWatch colour cards can be used
to standardize among observers(Siebeck et al. 2006) can be used to standardize among observers.
However it may only be useful to record colour shades 1 and 2, which represent bleached and pale
respectively; in many instances colour shades 3- may be considered as “normal“ for the corals, so not
useful in this case to record them individually.
Colour categories from Oliver et al. 2004.
Category Description Colour cards
0 No bleaching evident All shades 3-6
B1 Partially bleached (surface/tips); or pale but not white; Shade 2
B2 White Shade 1
B3 Bleached + partly dead Shade 1
D Recently dead
Examples:
• for a Porites massive colony 30 cm in diameter, with 50% of the colony pale, the record would be
Por(mas) B1. A more experienced data collector could record this as Por(mas) C5 p50%. (C5 for
size class 4).
• for a Stylophora pistillata colony 15 cm in diameter, 60 % bleached, 40% dead), the record would
be stypis B3. A more experienced data collector could record this as stypis C4 bl60 d40.
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3.4.5. Coral diseases and other conditions
Disease and other conditions to be recorded; need to be confirmed for each site, may include the list
below (sources: Disease Working Group (CRTR), McLeod(2007):
DISEASES:
• TUM-Growth anomalies/tumours
• SEB-Skeletal eroding band/skeletal eroding disease – powdery/eroded skeleton
• BBD-Black Band Disease (BBD)
• BrD - Brown/other colour bands,
• WBD - White Band Disease
• WP - White Plagues/Syndromes
• WS - Spots – white spots (Porites),
• PS - pink/purple spots/lines (Porites),
• BP - Blotch/spot disease – large dark spots/patches
OTHER:
• Possible other conditions for identification to be confirmed for each site, may include:
• Predation scar – parrotfish/other excavating grazer
• Predation scar - COTS
• Tubeworm infestations
• etc.
Where more detailed disease work is possible, or the team has a collaboration with external groups,
then follow established/more detailed protocols for photographing/document/collecting disease
conditions observed.
For the same two examples as listed above, with the Porites colony showing parrotfish scars and the
Stylophora colony black band disease, the records would be:
• Por(mas) B1 COTs, or Por(mas) C5 p50% COTs
• stypis B3, BBD, or stypis C4 bl60 d40 BBD
3.4.6. Other threats
This area primarily focuses on invertebrate predators and threats to corals, that can have an impact on
community structure when at moderate to high abundances. These include:
Crown of thorns seastars (COTs), Acanthaster planci. At levels of > 1-2 individuals per transect
predation impact is significant, and both individuals and predation scars should be counted.
• Cushion star, Culcita. Can also have an impact on corals through predation, though not as
high as COTs.
• Drupella – predatory snail, often found on branching corals. Generally not possible to count,
but can be recorded as number of colonies infested and range of density.
• Eroding sea urchins – large-bodied sea urchins, in particular the genera Diadema, Echinothrix
and Echinometra (the latter may be at very high densities and cryptic, so subsampling may be
necessary).
Datasheet instructions – a blank datasheet is given, as the presence of any condition may be low at
any one site, so the same sheet might be used over multiple sites. Make sure to clearly label the site,
date and transect # for each set of data. Alternatively, using a disease/condition datasheet already
developed for the area will ensure compatibility with broader datasets. For transects with no
disease/bleaching/condition noted, indicate this with a blank, to document the site was surveyed, but
no condition seen.
Statistics from this dataset include:
• For targeted coral genera/species, prevalence of bleaching/disease (ie. ratio of affected : total
population)
• For non-targeted coral genera/species, incidence of bleaching/diseased (ie. number affected)
• Number of colonies showing each condition, and total recorded
• Prevalence of each condition - proportion of colonies recorded with a condition compared to
number of colonies in the transect.
• Overall levels of each condition recorded as a number and prevalence.
Field Method
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3.4.7. Materials
Wet Dry
transect line, 25 m (use existing from coral size class observer)
Datasheet
checklist of disease/condition codes (on datasheet)
3.4.8. Observer skills
A single observer, familiar with coral identification at least to the genus level and with broad
experience in observing corals in the field. Ability to distinguish conditions such as scars from different
sources, bleaching and ‘disease’ conditions.
3.4.9. Background data
Compile any past data on coral bleaching or diseases, as well as on land- or sea-based stresses or
vectors for bleaching or disease.
3.5. Fish community structure and herbivory
This section improves on standard underwater visual census (UVC) of fish by focusing on herbivore
functional groups, adapted from Green et al. (2009) to include other functional groups of fish.
3.5.1. Objective
To collect data on herbivore and other functional groups of fish that exert top-down control on phase
shift dynamics on coral reefs.
3.5.2. Indicators
• Number of fish species, overall and by functional groups.
• Abundance/density of fish overall, by functional groups and species.
• Composition of fish population by functional/trophic groups.
3.5.3. Methodology
The method focuses on censusing fish at sufficient resolution to allow analysis of biomass and by
functional group. The level of detail needed for different functional groups various from species to
family level, and equations for calculating biomass from length can vary by species. If possible
therefore, species-level sampling of fish is ideal. However, this is rarely possible, so several
compromises are presented below.
3.5.3.1. Functional groups
With a focus on assessment of the resilience of reef communities, fish sampling should be focused on
the major functional groups that we currently understand to exert top-down control on reef dynamics
and may be indicators of resilience (in the coral community). These are:
• Herbivores – exert the primary control on coral-algal dynamics and are implicated in determining
phase shifts from coral to algal dominance especially in response to other pressures such as
eutrophication, mass coral mortality, etc. E.g. parrotfish (Scaridae), surgeonfish (Acanthuridae).
• Piscivores/carnivores – top level predators, they exert top-down control on lower trophic levels of
fish, are very vulnerable to overfishing, and good indicators of the level of anthropogenic
disturbance (fishing) on a reef. E.g. sharks, groupers (Serranidae), jacks (Carangidae).
• Scavengers/generalists – second-level predators with highly mixed diets including small fish,
invertebrates and dead animals, their presence/absend is a good indicator of anthoropogenic
disturbance (fishing). E.g. snappers (Lutjanidae), emperors (Lethrinidae), sweetlips (Haemulidae).
• Obligate and facultative coral feeders – the relative abundance of these groups are a secondary
indicator of coral community health. E.g. butteflyfish (Chaetodontidae) and some filefish
(Monacanthidae).
Field methods
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• Sessile invertebrate feeders – feed on coral competitors such as soft corals and sponges, their
relative abundance may be a secondary indicator of abundance/stability of these groups and of a
phase shift. E.g. angelfish (Pomacanthidae).
• Planktivores – resident on reef surfaces, but feed in the water column. Their presence/absence
may be related to habitat for shelter and water column conditions. E.g. some triggerfish
(Balistidae), fusiliers (Caesionidae).
• Detritivores – feed on organic matter in sediment and on reef surfaces, their relative abundance
may be an indicator of eutrophication and conditions unsuitable for corals. E.g. goatfish (Mullidae).
For each application, the history of fish surveys in the area should be considered, and adjusted to
enable construction of functional groups for analysis here. For example, if family level surveys have
been done, then some families have to be split into genus/species sub-groups to distinguish different
functional/trophic groups – e.g. triggerfish split into planktivores and benthic invertebrate feeders, etc.
See below for how this is done for herbivore functional groups.
An indicative list of families, some of them with multiple functional groups (e.g. Balistidae), is given
below, to be combined with the list of herbivore functional groups for surveys.
Group/family English Notes
Piscivores/scavengers
Carangidae Jacks/trevallies
Haemulidae Sweetlips
Lethrinidae Emperors
Lutjanidae Snappers
Mullidae Goatfish
Serranidae Groupers
Invertivores
Balistidae Triggerfish Invertivores, all on the benthos
Pomacanthidae Angelfish Invertivores/sessile
Labridae Wrasses Invertivores
Obligate coral feeders
Monacanthidae Filefish Oxymonacanthus only
Chaetodontidae Butterflyfish Coral obligates/indicators, by species
Detritivores
Acanthuridae Detritivores - Ctenochaetus
Planktivores
Caesionidae Fusiliers Planktivores
Balistidae Triggerfish Planktivores, all in the water column
Acanthuridae Unicornfish Some > 20 cm; by behaviour in water column
Field Method
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3.5.3.2. Herbivore functional groups
Green et al. (2009) distinguish 6 herbivore functional groups: large excavators, small excavators,
scrapers, grazers, browsers and grazers/detritivores. Each plays an ecological role in coral reef
resilience. The composition of these functional groups varies across taxonomic scales; in some cases
whole fish families belong to one group but in many cases genera and even species within the same
family can fall into different groups. In some cases functional group changes with size or age of the
fish. Fish families that are herbivores include the Acanthuridae (surgeonfish), Ephippidae (batfish),
Kyphosidae (chubs), Pomacanthidae (angelfish), Scaridae (parrotfish) and Siganidae (rabbitfish).
Functional groups of herbivorous fishes.
Functional group Taxonomic groups Function and notes
Large excavators
Humpheaded parrotfish
– large individuals (>35
cm)
Bolbometopon, Chlorurus
microrhinos, C. frontalis and
Cetoscarus bicolour. All
humpheads > 35 cm
Bioerosion. They take fewer, larger, deeper bites,
remove more of the substratum with each bite, and
play a key role in bioerosion.
Small excavators
Humpheaded parrotfish
– small individuals (<35
cm)
As above and other Chlorurus
species (C. bleekeri and C.
sordidus; All humpheads <35
cm)
Bioerosion. Take more, smaller, shallower bites, and
remove less of the substratum with each bite.
Scrapers
Other parrotfish Scarus and Hipposcarus Bioerosion, colonization surfaces. Remove algae,
sediment and other material by closely cropping or
scraping the substrate.
Grazers
Small rabbits, many
surgeons
Small rabbitfish (<20cm), all
Centropyge, all Zebrasoma,
most Acanthurus (excl.
planktivores/ringtails).
Algal control. Remove epilithic algal turf from the reef
substratum, but do not scrape the surface, prevent
coral overgrowth and shading by macroalgae.
Browsers
Unicorns, chub, batfish,
large rabbits, Calotomus
Chub, batfish, large siganids
(> 20cm), and parrotfish of
genus Calotomus,
Leptoscarus.
Unicornfish - all sizes of N.
brachycentron, N. elegans, N.
lituratus, N. tonganus and N.
unicornis,
Unicornfish - <20cm of N.
annulatus, N. brevirostris, N.
maculatus, N. mcdadei, and
N. vlamingii
Algal control. Feed on macroalgal fronds, reduce
coral overgrowth and shading by macroalgae.
Grazers/detritivores
Ringtail surgeons
Ringtail surgeonfish -
Acanthurus blochii,
dussumieri , leucocheilus,
maculiceps, nigricauda,
olivaceus, pyroferus, A tristis
and A xanthopterus.
Algal/sediment control. feed on a combination of
algal turf, sediment and some animal material similar
role to grazers, remove macroalgae before it can
become established.
The two families that are the most complex in monitoring heribovrious fish are the Scarids (parrotfish)
and the Acanthurids (surgeonfish). All Scarids are herbivores, though they are split between four
functional groups – excavators (large and small), scrapers and browsers. Acanthurids are more
complex, as they are split between three functional groups (browers, grazers and grazers/detritivores),
and some Acanthurids fall into other functional groups, namely planktivores and detritivores as follows:
• Planktivores: unicornfish (Naso) larger than 20 cm (N. annulatus, N. brevirostris, N. maculatus, N.
mcdadei, and N. vlamingii), some Acanthurus species (A. albipectoralis, A.mata, A. nubilus and A.
thompsoni) and the monospecific genus Paracanthurus. Planktivorous surgeonfish can be
excluded by behaviour (surgeons swimming/schooling in the water column not on the benthos),
rather than by taxonomy, so can be relatively easily excluded visually.
• Detritivores: Ctenochaetus. This is only common in shallows, where it may be in large schools.
Field methods
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A number of other families of herbivorous fishes are not included in the list above for the following
reasons:
• Small, cryptic families (blennies and gobies) - not amenable to visual census techniques, and low
contribution to ecosystem resilience.
• Damselfishes - small, and hard to identify, and wide variety of diets.
• Monacanthidae and Balistidae – some may also be herbivores, but unconfirmed.
For logistical reasons, Green et al. (2009) recommend simplifying the range of herbivore functional
groups. Considering that some functional groups are distinguished on the basis of size (thus can be
assigned during analysis, not in the field), and the relative importance of parrotfish and surgeonfish
and their different functional groups. Two levels of resolution are suggested for surveys, depending on
the expertise of the observer.
Bumphead parrotfish, Bolbometopon, the large excavators on the reef. By – Jerker Tamelander, IUCN
Field Method
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Recommended level of identification for fish herbivore functional groups.
Family English Functional grp Level of identification Notes
Scaridae Parrotfish Excavators Humpheads - Bolbometopon,
Cetoscarus, Chlorurus
Scrapers Scarus, Hipposcarus
Browsers Calotomus, Leptoscarus
If these cannot be
distinguished, then all >35 cm
are excavators, and all < 35
cm are scrapers
Acanthuridae Surgeonfish Browsers Unicorns (Naso)
Grazers/
detritivores
Most Acanthurus, Zebrasoma
Some Naso excluded by size,
all planktivores could be
excluded by behaviour/
location in water column
Siganidae Rabbitfish Browsers/Grazers
-detritivores
Whole family Differentiated by size
Kyphosidae Chub Browsers Whole family
Ephippidae Batfish Browsers Whole family
Centropyge Angelfish Grazers-
detritivores
Whole family
Simplest level of identification for fish herbivore functional groups.
Functional group Level of Identification Notes
Excavators Bumpheads/parrotfish > 35 cm
Scrapers All parrotfish < 35 cm Combines scrapers with small excavators –
their function is most similar than other
groups.
Browsers Rabbitfish, Chub, Batfish, small unicornfish Combines small rabbitfish from grazers, and
loses some parrotfish. Large unicornfish can
be excluded by size, and planktivorous
unicornfish by behaviour.
Grazers/detritivores All surgeonfish except unicornfish Combines grazers with grazers/detritivores.
Strongly simplifies surgeonfish identifiction.
As a first exercise for each region, a full listing of herbivorous species and their allocation to each
functional group must be done, as in the annexes at the end of this section, and if possible checked by
an expert before starting the surveys. Underwater, some unlisted species may be seen, which need to
be added to the list and verified.
3.5.4. Sampling
Sampling combines one long swim, to maximise sampling of the large mobile fish (e.g. bumphead
parrots) with 3 replicate transects for density estimates of fish.
3.5.4.1. Long swim
The long swim consists of a 20 minute timed swim at a standardised swimming speed parallel to the reef
axis. The length of the swim should be standardized as far as possible to 400 m, though in some
conditions it may not be possible to go this far. Record the approximate length of each swim, and take into
account currents, etc in estimating the distance swum. The area sampled should be approximately 20 m
wide, or 10 m on either side of the observer, though it might be less due to visibility constraints. Document
any departures from the standard length and width.
Only the largest size classes of key species in the different functional groups should be recorded, i.e. from
30 or 35 cm and up, and the size of each fish (or size class in 10 cm bins if many fish are encountered),
recorded. A sample list of key species is indicated here, though this should be tailored to the local
situation.
Field methods
36
Functional group Fish
Predators Sharks
Large groupers:
Epinephelus tukula
E. caeruleopunctatus
E. multinotatus
Other Epiniphelidae
Cephalopholis sp.
Scavengers Lutjanus bohar
Herbivores Bolbometopon spp.
Chlororus spp.
Scarus spp.
3.5.4.2. Transects/point counts
Transects are undertaken using standard 50*5 m belt transects for the remainder of target species (the
transect length should always be 50 m, with fewer replicates if restricted by time). If they occur in the
transects, include the larger individuals previously counted in the long swims. Lay transects consecutively
along the depth contour parallel to the reef axis, separated by at least 5 to 10m from the end of the
previous transect. Swim along the transect counting and estimating the size (TL in cm) of all species.
The transect laying technique may depend on the number of observers. With a single observer fish can
be sample in the first pass WHILE the transect is being laid, and small fish in the second pass while it is
being taken up. Adapt the technique to the observers’ experience.
Where point counts have been used historically, it may be more useful for analysis to continue their use
here, rather than applying transects. Point counts of 7 m radius (150 m2) are the easiest to implement.
With two divers sampling separate circles, up to 10 can be recorded following the end of the long swim, or
in some cases can be conducted intermittently during the long swim. Local conditions will determine the
time to spend on each point count (5-10 minutes), and taxa may have to be counted in individual ‘sweeps’
of the circle to minimize increasing numbers of fish during longer counts when new fish may swim into the
circle.
A minimum size for inclusion of 10 cm should be used, except for Centropyge, where 5 cm should be
used. 5 cm size classes should be used (i.e. 5-10, 10-15, 15-20 cm, etc).
If two depth zones are sampled (e.g. 5 and 10-12 m), these may be very close together where the reef
slope is steep. In this case the long swim counts for BOTH depths together. Alternatively, if the reef is
homogeneous, then shift the deep and shallow samples along the reef to ensure the long swim samples
do not overlap.
Datasheet instructions – some additional space is given for genera/species note written on the
datasheet.
3.5.5. Materials
Wet Dry
transect line, 50 m (may be useful to have two, one for each buddy
in a team)
point count – central marker and 7 m radial line
Datasheet
3.5.6. Observer skills
One or two observers, familiar with UVC of fish and ability to distinguish major genera and key species
of fish in the field. Ability to recognize targeted species of fish from a list and with prior preparation
from field ID materials. Size and distance estimation.
Field Method
37
3.5.7. Background data
Compile past data from UVC of fish and any herbivory studies. Additionally, fisheries data that shows
effort levels, catch trends and composition, particularly if target species have changed over time and
moved down the food chain.
3.6. Site resilience factors
3.6.1. Objective
To collect data on site-level factors influencing the resistance and resilience of corals to thermal
stress.
3.6.2. Indicators
• Estimated level of each resistance/resilience indicator (5-point scale)
3.6.3. Methodology
Resilience indicators are estimated using two approaches – in situ estimation based on recognition of
key features, and desk-study, based on reference material (including the literature, maps, charts,
reports, etc), local knowledge and available data. Some indicators are quantified using one approach,
some may be by both, where information from one approach may modify that from the other. The
underwater datasheets include spaces for each factor, though some may be quantified only by desk
study.
3.6.4. Data sources
In situ observation – during a field survey, levels are scored based on a detailed criterion table. The
criterion table must be customized to each area of application, and be held consistent for an entire
survey. A 5-point scale is used (1-low, 5-high) for each indicator, and scored for each sample
site/zone. Indicators are scored after the mid-point of the dive to allow time for familiarization with the
site. Levels may be adjusted during or after the dive, and through discussion with other team
members. In the water, the observer should go through each group of indicators, spending up to 5
minutes on each group, as necessary. A comments field for each indicator is given to facilitate
documentation of the indicator level chosen.
Reference sources – where information from ongoing datasets (e.g. of temperature), the literature,
reports, maps, charts, local knowledge or key informants can be used, parameters related to each
indicator should be quantified. As far as possible this should be done in real units, to be converted to a
5-point scale during preliminary stages of analysis. For example, fishing pressure may be obtainable
from catch data, underwater monitoring data, local knowledge (particularly on individual-site basis), or
by proxy by distance from the nearest fishing village. Likewise, distance to deep water can be
measured directly from charts, either by straight-line distance, or where known by upstream-
downstream distance.
3.6.5. Approach
Indicators are grouped into several clusters, reflecting major ecological components shown by
research to date to be important in resistance/resilience of coral reefs to climate change:
• benthic cover, principally of hard and soft corals, algal types and substrate condition (rubble);
• physical/environmental parameters conferring resistance or resilience, relating to cooling/flushing,
shading/screening and acclimatization of corals;
• coral population and community indicators of resistance or resilience, relating to coral condition
and population structure;
• coral associates with positive or negative impacts on corals;
• fish community structure, particularly herbivores;
• anthropogenic factors that affect resistance or resilience, relating to water quality, substrate
condition and fish/herbivore populations.
• connectivity and genetic relatedness, affecting recolonization and risk-spreading across multiple
locations.
Field methods
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3.6.5.1. 5-point scale
A semi-quantiative scale (Likart) of 1-5 is used for estimation of all the indicators. Where an indicator
can be quantified directly (e.g. visibility in meters, slope in degrees) it is recorded directly, and
converted to a 5–point scale during analysis. The 5-point scale was selected to facilitate estimation of
minimum (1), maximum (5) and moderate (3) level for each indicator for the region of application, and
intermediate levels of low (2) and high (4).
Note that two separate approaches can be taken when scoring indicators from 1 to 5:
• where 1 designates low/poor/negative conditions for the variable itself, and 5 designates
high/good/positive conditions. In this case, high macroalgal abundance would be scored as ‘5’ and
low abundance as ‘1’.
• where 1 designates low/poor/negative conditions for corals and 5 high/good/positive conditions. In
this case, high macroalgal abundance would be scored as ‘1’ and low abundance as ‘5’.
For final analysis, all indicators will be converted to a common scale to enable simple addition (i.e.
option b), but during fieldwork, the most direct and simple approach is to score using option a. This
must be explicitly noted for ALL indicators.
It is essential for the observer recording resilience indicator levels to be fully comfortable with the
rationale behind the scaling. A detailed description of each level of the 5-point scale for each indicator
is included as background material, and must be reviewed and customized for each region of
application. For example the location in a region with maximum wave energy should be designated as
5 on the scale – in one region this might be a reef front that experiences 2 m wind-waves during
storms, in another region this might be a reef front that experiences 4 m ocean swells during a
particular season. Scaling for between-region comparisons will be dealt with based on the levels set in
each region’s definition table, at a later date.
3.6.5.2. Spot vs. continuous measurements
Variables like temperature and visibility are estimated during the dive, however because of seasonal
and annual variability must be analyzed cautiously and in the context of background data. Where
possible, continuous measurements, such as in situ temperature recorders, should also be used. This
is unlikely to be possible for all site, but a representative selection of sites should be selected
according to local conditions and priorities. Spot measurements give some insight as to short-term
differences between sites, such as in exposure to upwelling water, influence of storms and mixing
events, etc.
3.6.6. Resilience indicators
The resilience indicators are presented in groups, which are maintained during analysis to relate to the
key drivers of reef resilience. Further illustration of this rationale can be found in Obura and Grimsditch
(2008).
3.6.6.1. Benthic indicators
These can be estimated on-site and/or be derived from more quantitative methods such as those used
in monitoring and assessment programmes, e.g. line intercept transects, photo quadrats, etc. The
advantages of estimating them with the other indicators is to ensure values are available for all sites.
Estimated values can be replaced by more quantitative values where/when these are available. The
disadvantage of estimated values relate to observer error in estimating percentages, however this is
somewhat ameliorated by conversion to a 5-point scale for analysis with other indicators.
Field Method
39
Variable Relevance Quantification Data source
Hard coral A primary indicator of reef health, hard corals are the main
reef-building taxonomic group on coral reefs
estimate %
cover
in situ
Soft coral Common competitor to hard corals, and can indicate
nutrient and wave energy conditions
estimate %
cover
in situ
Fleshy
Algae
A primary competitor and inhibitor of corals, and indicator of
nutrient/bottom-up and herbivory/top-down controls.
estimate %
cover
in situ
Turf Algae A primary competitor and inhibitor of corals, and indicator of
nutrient/bottom-up and herbivory/top-down controls.
estimate %
cover
in situ
CCA An indicator of suitable habitat for coral recruitment, and
consolidation of reef framework.
estimate %
cover
in situ
Rubble An indicator of substratum integrity and suitability for coral
recruitment and growth.
estimate %
cover
in situ
3.6.6.2. Substrate and reef morphology
Stress to corals and recovery (i.e. recruitment, growth, etc) are strongly affected by substrate quality.
The amount of rubble, measured under benthic cover estimates gives an indicator on the
consolidation of the reef. Topographic complexity is important as it determines the amount of space
available for fauna and flora to attach to, and the complexity of interaction between substratum and
the water column. Sediment quality and quantity strongly affect the survival of benthic organisms, and
in particular recruitment of larvae to benthic life stages.
Variable Relevance Quantification Data source
Topographic
complexity –
micro
The surface
roughness and small-
crevice space on
reefs affects
recruitment of corals.
Estimation on 5 point scale of surface roughness, from
smooth to complex 3-D spaces allowing light
penetration but shelter from predators and
sedimentation (e.g. in complex branching
frameworks), Approx. 1-10 cm scale.
In situ
Topographic
complexity –
macro
The large scale
structure of a reef,
providing habitats for
large and higher-
trophic level mobile
organisms (e.g. fish)
Estimation on 5 point scale of structure, from a flat
pavement to complex 3-D reef slopes with
spur/grooves, pillars, caves and large internal reef
spaces. Approx. 1-5 m scale.
In situ
Sediment layer
texture
Sediment grain size
and sorting affects
benthic organisms.
Estimation on 5 point scale, from large-size/carbonate
sand grains at one end (good) to fine silty sediment
with high terrigenous content at the bad end.
In situ,
reference
Sediment layer
depth
Depth of sediment
layers on hard
substrata, particularly
in association with
algal filaments/turf.
Estimation on 5 point scale, from no sediment on hard
substrata to drifts of sediment and/or entrapment of
sediment in algal filaments/turf that inhibit settlement.
In situ,
reference
Field methods
40
3.6.6.3. Cooling and flushing
The temperature of the surface skin of seawater that heats up and causes stress to corals may be
reduced by a number of physical processes causing mixing with deeper cooler waters and/or by
evaporative cooling. These factors may provide protection from and enhance resistance/tolerance of
corals to thermal stress.
Variable Relevance Quantification Data source
Temperature Primary stressor for bleaching
related to climate change.
Spot measurements with a thermometer allow
basic comparisons among sites, but ideally need
long term in situ records, and satellite data to
infer differences among sites.
In situ,
reference
Currents Currents cause vertical mixing
that may reduce surface
temperatures, and can reduce
coral stress by reducing
boundary layer effects on coral
metabolism.
Estimation on 5 point scale, informed by local
knowledge and/or by ‘typical’ expectations of
particular reef structures such as linear reef
fronts, channels, etc.
In situ,
reference
Waves
(Exposure)
Wave energy causes vertical
mixing, can reduce boundary
layer effects on coral
metabolism and increases
oxygenation of water,
enhancing coral metabolism.
Exposure to weather events is
expressed as wave energy to
corals.
Estimation on 5 point scale, from minimum
waves on sheltered/leeward reefs to maximum
waves on reef crests. Increasing depth reduces
the influence of wave energy, so is quantified
under ‘depth’ not in this indicator. Exposure and
wave energy are related, so one may be
sufficient for estimation.
In situ,
reference
Deep water Proximity to deep water
enables mixing with cold water
by upwelling and waves,
currents and exposure.
Estimation on 5 point scale, from immediate
proximity at a vertical wall, to distant.
Alternatively, distance to a deep contour (30/50
m) may be measured from charts.
In situ,
reference
Depth of reef
base
The depth of the base of a reef
slope affects the potential for
mixing of deep cool waters.
Actual depth of base of main reef slope. Along
with “deep water” gives an indication of potential
for upwelling/mixing of cooler water.
In situ,
reference
3.6.6.4. Shading and screening
Thermal stress in corals is exacerbated by light stress, so factors that reduce light reaching corals can
provide protection and/or enhance resistance/tolerance during coral bleaching events.
Variable Relevance Quantification Data source
Depth Basic zonation variable for coral reef
and community structure, and for
attenuation of temperature, light and
other variables
In situ measurement, usually samples
done in standard depth zones for
analysis. Tidal variation important to be
factored out, particularly where range >
2 m.
In situ
Visibility Proxy for turbidity and attenuation of
light levels at a site, a primary and
synergistic stressor with temperature.
Horizontal visibility at the sampling
depth, or improved with use of secchi
disc (though not possible in shallow
water). Where possible suspended
particulates/ turbidity can be measured.
In situ,
reference
Compass
direction/
Aspect
The aspect of a reef slope affects the
angle of incidence of the sun on the
reef surface, and therefore radiation per
area of reef/colony surface.
Compass direction of the reef slope.
The 5 point scale will be determined
based on compass direction and
latitude, during analysis.
In situ
Slope The angle of a reef slope affects the
angle of incidence of the sun.
Estimated slope angle, in degrees. The
5 point scale will be determined based
on the range of values, during analysis.
In situ
Physical
shading
Shading of corals by reef slopes, pillars
or above-water features (hills/cliffs/
rocks) can protect corals from stress.
Estimation on 5 point scale, with the
maximum for full shading at noon by
vertical wall/overhang.
In situ
Canopy corals Shading of understory corals by canopy
corals (tables, staghorn, plates, etc)
can protect them from stress.
Estimation on 5 point scale, with the
maximum for cover by canopy corals.
In situ
Field Method
41
Partially bleached Acropora colony By – Jerker Tammerlander, IUCN
3.6.6.5. Extreme conditions and acclimatization
Resistance and tolerance to thermal stress is enhanced by acclimatization of adult colonies to their
environment. Typically, acclimatization is most strongly expressed in varying and/or severe
environmental conditions, and variation in one stress factor may enhance generalized resistance to
multiple stresses.
Variable Relevance Quantification Data source
Low tide
exposure
Shallow corals exposed to the air
at low tide experience frequent
stress, and may be more resistant
to thermal stress.
Estimation on 5 point scale, relevant
only to very shallow corals.
In situ,
reference
Ponding/pooling Restricted bodies of water heat
up more due to less mixing and
greater residence times, and also
enhance metabolic stress.
Estimation on 5 point scale,
maximum for enclosed shallow
bodies of water
In situ,
reference
Field methods
42
3.6.6.6. Coral condition
The current status of a coral community depends on past events and current conditions. This
component estimates as best as possible the extent of past thermal stress/bleaching events (or other
major mortality events), recovery to date and current bleaching, disease and mortality.
Variable Relevance Quantification Data source
Bleaching Current levels of coral
bleaching.
Percentage of corals bleached. In situ
Mortality-
recent
Current levels of coral
mortality.
Percentage of corals showing partial/full mortality. In situ
Mortality-old Levels of mortality
from the past.
Degree of historic mortality evidenced by appearance of
dead coral skeletons. Directly quantified, or as 5 point
scale depending on ease of estimation.
In situ,
reference
Recovery-old Levels of recovery
from the past mortality
events.
Degree of recovery from old mortality, appearance of
dead coral skeletons and regrowth/recolonization of
corals since then, and knowledge on past mortality.
Directly quantified, or as 5 point scale depending on
ease of estimation.
In situ,
reference
Disease Levels of coral
disease
Percentage of corals showing disease conditions. In situ
Porites colonies exposed at low tide survive under extreme environmental fluctuations
By – Jerker Tamelander, IUCN
Field Method
43
Acropora coral recruit By – Gabriel Grimsditch, IUCN
3.6.6.7. Coral population structure
The size class structure of coral populations can reveal evidence of past events and current recovery
patterns. More detailed data on coral recruitment and size class distributions are collected in other
components of the assessment method, however these estimates might provide useful information
when these are not possible.
Variable Relevance Quantification Data source
Recruitment Recruitment of new corals
is necessary for population
recovery and injection of
genetic variability.
Estimated number and genus of
recruits/new corals < 2-3 cm, per m2 of
substrate.
In situ
Fragmentation Asexual reproduction by
fragmentation is an
important strategy of
propagation for many
corals.
Estimated contribution of fragmentation
in generating new colonies, and primary
genera affected. 5 point scale based on
evidence for partial
mortality/fragmentation producing
significant number of small to mid-sized
corals (e.g. 5 – 20 cm)
In situ
Dominant size
classes
The dominant size classes,
by area, indicate the
maturity and ecological
stage of a community.
Estimation of dominance in the coral
community by size class and genus of
coral, indicating successional stage of
the community.
In situ
Largest corals The largest corals at a site
indicate how long conditions
have been suitable at the
site, and the degree of
environmental stability/
community persistence
The size in meters, and genus/species of
the three largest colonies at the site.
In situ
Field methods
44
3.6.6.8. Coral associates
The presence and number of coral associates are indicative of the health and maturity of the coral
community, and influence of external factors. These variables are not primary indicators of reef
resilience, so lower priority than others.
Positive associates
Variable Relevance Quantification Data source
Obligate feeders The abundance and diversity of obligate coral
feeders are indicative of the health of coral
colonies and complexity of interactions at a site.
Estimation on 5 point
scale, from absent to high
abundance/ diversity.
In situ
Branching
residents
The abundance and diversity of fish and
invertebrate residents in branching coral
colonies are indicative of the health of coral
colonies and complexity of interactions at a site.
Estimation on 5 point
scale, from absent to high
abundance/ diversity.
In situ
Negative associates
Variable Relevance Quantification Data source
Competitors The abundance and diversity of coral
competitors are indicative of inhibiting
factors to coral growth and recovery.
Estimation on 5 point scale, from
absent to high abundance/
diversity
In situ
Bioeroders – external
(urchins, nonfish)
The abundance and diversity of
nonfish exernal bioeroders are
indicative of inhibiting factors to coral
growth and recovery
From transect/ quadrat counts or
by estimation on 5 point scale,
from absent to high abundance/
diversity.
In situ
Bioeroders – internal
(sponges, worms, etc)
The abundance and diversity of
internal bioeroders are indicative of
inhibiting factors to coral growth and
recovery
Estimation on 5 point scale, from
absent to high abundance/
diversity
In situ
Corallivores (negative
impact)
The abundance and diversity of
corallivores (eg. COTs, Drupella) are
indicative of additional mortality to
coral colonies.
From transect/ quadrat counts or
by estimation on 5 point scale,
from absent to high abundance/
diversity.
In situ
Tube worms on Lobophyllia coral. At low densities these are seldom harmful but at high densities may impede
coral growth and/or indicate poor conditions for corals By – Jerker Tamelander, IUCN
Field Method
45
3.6.6.9. Fish functional groups - herbivory
Fish exert important top-down controls on benthic communities, and in the case of ecological recovery
and resilience, herbivory has been shown to be particularly important. More detailed data on fish and
herbivore groups should ideally be collected in other components of the assessment method, however
these estimates might provide useful information when these are not possible.
Variable Relevance Quantification Data source
Abundance &
diversity of
herbivores
Overall herbivore populations are
critical for suppressing algal
growth and its inhibiting effects on
corals
Visual estimate of abundance/ diversity of
herbivores
In situ,
reference,
long term
Eroders Excavating/eroding herbivores
exert strongest control on algal
growth
Visual estimate of abundance/ diversity of
excavators - Bolbometopon, Chlorurus
In situ
Scrapers Excavating/eroding herbivores
exert control on algal growth
Visual estimate of abundance/ diversity of
smaller parrotfish.
In situ
Browsing Browsing herbivores exert control
on macroalgal fronds
Visual estimate of abundance/diversity of
unicornfish/chubs/batfish/large rabbitfish
In situ
Grazing Grazing herbivores exert control
on epilithic turf algae
Visual estimate of abundance/ diversity of
parrotfish and surgeonfish that crop algae
In situ
3.6.6.10. Connectivity
The degree of connectivity among reef sites is important in the recolonization by new
corals/individuals after mass mortality, as well as in how it affects genetic mixing, diversity and
relatedness. These indicators are highly tentative and require consultation with charts and knowing
regional reef and current distribution patterns, and underwater observation.
Variable Relevance Quantification Data source
Capacity for self-
seeding
(autochthony)
Recruitment of new corals appears to be
more strongly driven by self-seeding than
previously thought.
Patchiness of coral communities
up to 1 km scale,
robustness/diversity of adult
populations for reproduction.
In situ,
reference
Capacity for
external seeding
(allochthony) –
small scale
Larval density decreases with distance
from the source, thus inter-reef distances
important for allochthonous larval
seeding.
Connectedness of reef systems
on 10 km scale, combined
shapes, upstream/downstream
and inter-reefal habitat
considerations.
In situ,
reference
Capacity for
external seeding
(allochthony) –
large scale
Larval density decreases with distance
from the source, thus distances between
major reef tracts important for
allochthonous larval seeding.
Distance from nearest reef
system/complexity in regional
reef biome, scale of 100s of km.
In situ,
reference
Suitability of
currents in
maintaining
connectivity
among reefs
Locations within direct current flows will
have enhanced capacity for external
seeding of larvae, current systems
maximizing flow among reefs and
locations will maximize connectivity
among sites.
From no connection (cross-flow)
to strong connection (linear
flows, eddies, reversing flows).
In situ,
reference
Natural larval
dispersal barrier
Natural dispersal barriers reduce the
degree of external seeding of larvae
Distance to, size and nature of
nearest natural dispersal barrier.
In situ,
reference
Anthropogenic
larval dispersal
barrier
Anthropogenic factors that enhance
natural barriers or create new barriers to
external seeding of larvae
Distance to, size and nature of
nearest anthropogenic dispersal
barrier and/or enhancement of
natural barriers.
In situ,
reference
Field methods
46
3.6.6.11. Anthropogenic factors - negative
Anthropogenic factors influence many different ecological processes on coral reefs. Of principal
interest to this assessment method is how they alter the range of natural factors addressed above, in
general in negative directions. Estimation of the influence of anthropogenic factors focuses on the
degree to which they might shift natural factors.
Factor Variable Relevance Quantification Data
source
Water
quality
Nutrient input Nutrient enhancement or
eutrophication alters many reef
processes, in particular enhancing
algal and microbial growth, and
metabolically stressing corals.
Estimate degree of effect of
anthropogenically derived
nutrients on site, from zero to
extreme.
In situ,
reference,
long term
Pollution
(chemical)
Chemical pollution causes metabolic
stress to reef organisms, either
causing mortality, or reducing their
ability to withstand other stresses
Estimate degree of effect of
anthropogenic pollutants on
site, from zero to extreme.
Distance to pollution sources
can be an alternative.
In situ,
reference,
long term
Substrate
quality
Pollution
(solid)
Solid wastes foul the substrate and
may make it unsuitable for coral
recruitment and growth.
Presence of solid waste on site
and/or distance to sources.
In situ,
reference,
long term
Turbidity/
Sedimentation
Anthropogenically enhanced turbidity
and sedimentation in general
negatively affects corals, though see
turbidity factor.
Estimate degree of effect of
anthropogenic factors on
turbidity/sedimentation at site
In situ,
reference,
long term
Physical
damage
Physical damage to the site, or to
corals results in mortality and/or
inhibits recovery.
Estimate degree of effect of
physical damage on site
In situ,
reference,
long term
Fishing Fishing
pressure
Overfishing causes reef degradation
by changing trophic web structures,
altering top-down ecological controls
and leading to phase shifts.
Estimate degree of fishing by
observation underwater and/or
using catch monitoring data,
local knowledge and other
sources.
In situ,
reference,
long term
Destructive
fishing
Destructive fishing causes physical
damage to the site, and/or alters the
balance of fish population dynamics.
Estimate destructive fishing by
observation underwater and/or
using catch monitoring data,
local knowledge and other
sources
In situ,
reference,
long term
Field Method
47
Fishing pressure, on high-value top predators By – Cheryl-Samantha Owen, Save Our Seas Foundation
3.6.6.12. Anthropogenic factors – positive (management)
Anthropogenic factors that positively influence ecological processes on coral reefs are generally
implemented through explicit management frameworks. Three principal classes of management are
identified here, as these act differently on the various resilience factors already listed.
Factor Variable Relevance Quantification Data
source
Management Biodiversity
protection/
MPA
Protection of biodiversity from
degrading anthropogenic factors
using MP’s and other tools
focused on protecting sites from
degrading influences
Presence and effectiveness of
protected area-based
management
In situ,
reference
Resource
extraction/
fishing
Protection from extraction of
resources by fishing or other
activities, focused on
regulations that affect extraction
and offtake.
Presence and effectiveness of
resource management
measures limiting extraction
In situ,
reference
Environmental/
water quality
Limitation of human activities
that degrade environmental
quality, such as pollution
Presence and effectiveness of
e.g. ICZM or municipal/waste-
water management
In situ,
reference
Field methods
48
3.6.7. Materials
Wet Dry
Datasheet Indicator/criterion table for constant updates.
Temperature loggers – as needed
light/radiation meters – as needed
3.6.8. Background data
Background data required for this section is intensive, and the primary need for the information from
section 2.7. Each resilience factor and constituent indicator, above (or from the datasheet) should be
the subject of a literature/information search, and in each case develop a case history of the study site
and cite references that can be sourced for more detail. The background data should then be
interpreted together with the field-based indicator to obtain a final indicator level for each factor. In
some cases, only the field observation can be used, in other cases where information is available (e.g.
distance to 50 m contour from charts, or fishing effort and physical impacts from fisheries data), the
field observation can be replaced by harder data, with the justification written out.
Data Management and Analysis
49
4. Data management and analysis
4.1. Archiving and storing data
Primary data storage is Microsoft Excel spreadsheets, as these are generally more accessible to the
researchers and managers who will participate in this project. Data entry worksheets and procedures
are provided for each dataset in section 3.
Each project should maintain a higher-level folder that will contain all the data and analysis files, with
each dataset held in its own folders. A convention for folder and file naming is essential to maintain
order, and each filename should include its methodology/data type, site and date of surveys, followed
by any relevant version numbers/analyst initials to track different versions.
Parent folder Data folders Data files
Data-Site name 1-benthic
2-coralcomm
3-coralsiz
4-coralcond
5-fish
6-resilindic
a-Original raw file (Excel)
b-Clean data file (Excel)
c-Main analysis worksheets (Excel)
d-Subsidiary analysis sheets (Excel)
e-Multivariate analysis files (Primer)
f-other analyses …
During data entry and once the full datasets are entered, backup copies of all files must be kept.
Participating sites will be joined in a network for analyses with the following obligations:
• Sites funded by CCCR – full dataset provided to CCCR as a completed output of the surveys, with
joint analysis and publication of findings. These full datasets will then be accessible to the partners
in the network that are funded by CCCR and that contribute their data. A standard right of
publication period of 2 years for data from an individual site will be held by the field team for stand-
alone detailed publication of that data, however regional/combined analyses will be permitted
during this period.
• Independently funded sites – will be invited to join the network by contributing data, with the same
rights and responsibilities of others in the network. For partners that will share only
analyzed/summarized data, joint publications will be possible, but not full access to the entire
datasets.
4.2. Data analysis
Analysis modules for each dataset are under constant preparation and revision and will be shared as
and when necessary. Analysis currently consists of:
• Basic statistics – mean, variance, ranges, frequencies – in Microsoft Excel
• Basic analysis of variance – nonparametric and parametric – Microsoft Excel or other
statistical packages as available to the sites.
• Multivariate analyses – Multi-Dimensional Scaling, cluster analyes and others – Primer,
funded sites to be provided with a licensed copy (Clarke & Gorley 2006, Clarke & Warwick
2001).
4.3. Reporting and publication
Reporting will be done at three levels:
1) A technical report of findings at each project area of implementation. Model reports from past
projects will be provided, but each report should be tailored to local interests and needs as well
(see Rufiji-Mafia-Kilwa seascape assessment, Tanzania. Obura et al. 2008a). The reporting model
should emphasize an executive summary/management guidance format in which the first pages
summarize the main findings with enough technical detail to explain recommendations, but limited
data presentation to ensure accessibility to a broad range of readers. Detailed results and
discussions follow this section and can easily be referred to when needed.
2) A regional analysis of completed sites will be done led by the CCCR, with the first one targeted for
June 2009 in conjunction with an analysis workshop for partners. This will result in a technical
Data Management and Analysis
50
report following the same model as above, and using the individual site reports as primary
references.
3) Peer review publications will be developed as follows:
• For each project site, focused on the primary resilience indicators for the site and the key
scientific implications of the finding (e.g. Obura et al. 2008b).
• For the global dataset, on regional variability and interactions among resilience indicators.
• Full participants in data sharing can suggest specific questions to test from the datasets to be
written up as peer-review publications.
References
51
5. References
Bellwood, D, Hughes, TR, Hoey, AS 2006 - Sleeping Functional Group Drives Coral-Reef Recovery.
Current Biology 16, 2434–2439
Clarke KR, Gorley, RN 2006. Primer v6: user manual/tutorial. Primer-E: Plymouth.
Clarke KR, Warwick, RM. 2001. Change in marine communities: an approach to statistical analysis
and interpretation. 2nd edition. Primer-E: Plymouth.
Disease Working Group, Coral Reef Targeted Rsearch for Management Project. Coral Disease
booklet.
English S, Wilkinson C, Baker V (1996) Survey Manual for Tropical Marine Resources. Australian
Institute of Marine Science, Townsville
Green, AS, Bellwood, D, and Choat, H (2009.). Monitoring functional groups of herbivorous reef fishes
as indicators of coral reef resilience.
Grimsditch, G. D. and Salm, R. V. (2006). Coral Reef Resilience and Resistance to Bleaching. IUCN,
Gland, Switzerland. 52pp.
Hoegh-Guldberg, O. (1999) Climate change, coral bleaching and the future of the world’s coral reefs.
Greenpeace: Sydney (Australia), 28 pp.
Kohler, K.E. & Gill, S.M. (2006) Coral Point Count with Excel extensions (CPCe): A Visual Basic
program for the determination of coral and substrate coverage using random point count
methodology. Computers & Geosciences 32:1259–1269
Marshall P, Schuttenberg H (2006) A Reef Manager's Guide to Coral Bleaching. Great Barrier Reef
Marine Park Authority, Townnsville, Australia.McLeod(2007
Obura, DO (2005) Resilience, coral bleaching and MPA design. Estuarine Coastal and Shelf Science
603, 353-372.
Obura, DO, Grimsditch, GG (2008) – Resilience-Integrating Science and Management in Coral Reefs
Relevant to Climate Change. In: Obura, D.O., Tamelander, J., & Linden, O. (Eds) (2008) Ten
years after bleaching – facing the consequences of climate change in the Indian Ocean.
CORDIO Status Report 2007. CORDIO (Coastal Oceans Research and Development, Indian
Ocean)/Sida-SAREC. Mombasa. http//:www.cordioea.org pp.
Obura D, Mangubhai S (2003) An Initial Assessment Of Environmental And Ecological Factors And
Their Contributions To Coral Bleaching Resistance And Resilience Of Reefs In The Western
Indian Ocean. In: Obura D, Payet R, Tamelander J (eds.) Proceedings of the International
Coral Reef Initiatve (ICRI) Regional Workshop for the Indian Ocean, 2001.
ICRI/UNEP/ICRAN/CORDIO, Nairobi (pp 97-112)
Obura, D.O., Machano, H., Ndagala, J., Zavagli, M. (2008) Opposing effects of water quality on coral
bleaching resistance and recovery. Proceedings of the 11th International Coral Reef
Symposium, Ft. Lauderdale, Florida, 7-11 July 2008
Oliver J, Marshall P, Setiasih N, Hansen L (2004) A global protocol for assessment and monitoring of
coral bleaching. ReefBase. ICRAN, Penang (Malaysia) (35)West, JM and Salm, RV. (2003)
Resistance and resilience to coral bleaching: implications for coral reef conservation and
management. Conservation Biology 17(4), 956-967.
Siebeck UE, Marshall NJ, Kluter A, Hoegh-Guldberg O (2006) Monitoring coral bleaching using a
colour reference card. Coral Reefs 25:453-460
Smith JE, Shaw M, Edwards, RA, Obura, D, Pantos, O, Sala, E,. Sandin,SA, Smriga, S, Hatay, M and
Rohwer, FL l. (2006) Indirect effects of algae on coral: algae-mediated, microbe-induced coral
mortality. Ecology Letters 9, doi: 10.1111/j.1461-0248.2006.00937.x.
West J, Salm R (2003) Environmental determinants of resistance and resilience to coral bleaching:
implications for marine protected area management. Conservation Biology 17: 956-967
Wilkinson C (2000) Status of Coral Reefs of the World: 2000. Australian Institute of Marine Science,
Townsville, Australia
Resources
52
6. Resources
6.1. Benthic cover
• Coral Point Count software http://www.nova.edu/ocean/cpce/index.html
• Kohler, KE and Gill, SM (2006) Coral Point Count with Excel extensions (CPCe): A Visual Basic
program for the determination of coral and substrate coverage using random point count methodology.
Computers and Geosciences 32: 1259-1269.
6.2. Coral community structure (genera)
• Veron, C. (2000) Corals of the world Version 3. Australian Institute of Marine Sciences.
6.3. Coral size class distributions (selected genera)
• Veron, C. (2000) Corals of the world Version 3. Australian Institute of Marine Sciences.
6.4. Coral condition
• CoralWatch colour cards – Siebeck, UE, Marshall, NJ, Kluter, A and Hoegh-Guldberg, O. (2006) Fine
scale monitoring of coral bleaching using a reference card.
• Coral disease guide – Disease Working Group (2008) - www.gefcoral.org/
• Aeby, G. (2007) Coral diseases. NOAA and Hawai’i Institute of Marine Biology
• McLeod (2007) Coral lesions from multiple sources. TNC
6.5. Fish community structure - herbivores
• Green, A, Bellwood, D and Choat, H. (2009) Monitoring functional groups of herbivorous reef fishes
as indicators of coral reef resilience. The Nature Conservancy and James Cook University.
6.6. Resistance and resilience indicators
• Resilience indicator table – pages 59 to 70 of this manual
• West, J and Salm, R. (2003) Resistance and resilience to coral bleaching: Implications for coral reef
conservation and management. Conservation Biology 17: 956-967.
• Obura, D. (2005) Resilience and climate change: Lessons learnt from coral reefs and bleaching in
the Western Indian Ocean. Estuarine, Coastal and Shelf Science 63: 353-372.
• Grimsditch, G and Salm, R. (2006) Coral reef resilience and resistance to bleaching. IUCN.
6.7. Data entry and analysis
• Datasheets and basic analysis sheets provided as appendices to this manual
• Primer software manual and teaching resources. Clarke KR and Gorley, RN (2006) and Clarke KR,
Warwick, RM (2001)
Resources
53
7. Field Datasheets
7.1. Coral genera
IUCN-CCCR Resilience Assessment model datasheets – March 2009
Coral genera
Date: Site: Collector:
Notes: Dominance: Rare species:
Abundant:
aca cau dis gyr les oul poc sty
acr coe eph hal lob oxy pod sym
alv cos epo hef mad pac por tra
ana cte fat hep mer par psa tub
ano cul fav her mic pav san tup
asm cyc fun het mil pec sco tur
ast cyn gal hor mon phy ser zoo
aus cyp gar hyd mtp pla sid
bar dia gon lep mya plg sta
bla dip gop leo myc pls stc
Date: Site: Collector:
Notes: Dominance: Rare species:
Abundant:
aca cau dis gyr les oul poc sty
acr coe eph hal lob oxy pod sym
alv cos epo hef mad pac por tra
ana cte fat hep mer par psa tub
ano cul fav her mic pav san tup
asm cyc fun het mil pec sco tur
ast cyn gal hor mon phy ser zoo
aus cyp gar hyd mtp pla sid
bar dia gon lep mya plg sta
bla dip gop leo myc pls stc
Resources
54
7.2. Coral sizes
IUCN-CCCR Resilience Assessment model datasheets – March 2009
Coral size
Date: Site: Collector:
A) Large
corals Transect 1 Transect 2
Genus '11-20 '21-40 '41-
80
80 -
'160
'160
-320
>> '11-20 '21-40 '41-
80
'160 '320 >>
Acropora
Pocillopora
Stylophora
Seriatopora
Montipora
Porites
(mass)
Pavona
Porites(bra)
Galaxea
Echinopora
Platygyra
Favia
Favites
Goniastrea
Leptastrea
Lobophyllia
Fungia
Hydnophora
Coscinaraea
B) Small
corals
Resources
55
7.3. Condition
IUCN-CCCR Resilience Assessment model datasheets – March 2009
Coral condition
Date: Site: Collector::
C) Coral condition
Time and associated coral size transects Coral Size
Genus/species and size class Classes (cm)
BLEACHING (BASIC): B2 - Bleached ; C1 1-2.5
0 - No bleaching evident;
B3 - Bleached + partly
dead ; C2 3-5
B1 - Partially bleached (surface/tips) or pale but not white; D - Recently dead C3 6-10
DISEASES: LESIONS/OTHER C4 11-20
TUM-Growth anomalies/tumours Drupella C5 21-40
SEB-Skeletal eroding band/skeletal eroding disease –
powdery/eroded skeleton COTS C6 41-80
BBD-Black Band Disease (BBD) Competition C7 81-160
BrD - Brown/other colour bands, Bioeroders C8
161-
320
WBD - White Band Disease Feeding scars C9 > 320
WP - White Plagues/Syndromes Human damage (var)
WS - Spots –white spots (Porites), Dynamite crater
PS - pink/purple spots/lines (Porites),
BP - Blotch/spot disease – large dark spots/patches
Resources
56
7.4. Fish-herbivore functional groups
IUCN-CCCR Resilience Assessment model datasheets – March 2009
Fish-herbivore functional groups
Date: Site: Collector::
LONGSWIM‐HerbivoresGroupers:
Bolbometopon sp.
Chlororus sp.
Scarus sp.
Cheilinus undulatus Emperors/Snappers
Sharks
Point Counts 1 2 3 4 5 6
Bolbometopon Excavators
Chlorurus Excavators
Cetoscarus Excavators
Scarus Scrapers
Hipposcarus Scrapers
Calotomus Browsers
Scarids
Leptoscarus Browsers
Ringtail:
blochii,
dussumieri ,
leucocheilus,
xanthopterus,
nigricauda,
olivaceus
Grazer
Acanthurus
(excl. ringtails)
Graz/Detr
Zebrasoma Grazer
Naso -
brachycentron,
lituratus, unicornis
Graz/Brows
Naso - annulatus,
brevirostris,
vlamingii
Graz/Brows
Naso - other
species
Planktivores
Acanthurids
Ctenochaetus Detritivores
Siganids Graz/Brows
Centropyge Grazer
Chub/Kyphosus Browsers
Others
Batfish Browsers
Resources
57
7.5. Fish-basic functional groups
IUCN-CCCR Resilience Assessment model datasheets – March 2009
Fish-basic functional groups
Date: Site: Transect: Collector::
3-10 10-
20 20-
30 30-
40 40-
50 50-
60 60-
70 70-
80 >>80
Carangidae Piscivores/
scavengers
Haemulidae Piscivores/
scavengers
Lethrinidae Piscivores/
scavengers
Lutjanidae Piscivores/
scavengers
Mullidae Piscivores/
scavengers
Serranidae Piscivores/
scavengers
Labridae Invertivores
Chaetodontidae Coral obligat/
indicators
Siganidae Herbivore
Kyphosidae Browsers
Ephippidae Browsers
Pomacentridae in water column
on benthos
Balistidae Invertivores
planktivores
Pomacanthidae Invertivore
Centropyge Herbivore
Scaridae Excavators -
Bumpheads
Scrapers -
Scarus
Browsers -
Calotomus,
Leptoscarus
Acanthuridae Unicorn
Acanthurus,
Zebrasoma
Others-
Detritivore,
Ctenochaetus
Planktivore/water
column
Resources
58
7.6. Resistance/resilience factors
IUCN-CCCR Resilience Assessment model datasheets – March 2009
Resistance/resilience factors
Date: Site: Collector
Factor Variable Comments
Hard Coral Coral
Soft Coral
Fleshy Algae
Turf Algae
Algae
CCA
1. Benthic
Substrate Rubble
Top.Compl. -
micro
Top. Compl. -
macro
Sediment
texture
Substrate &
Morphology
Sediment
layer
Site
Description, sketch, etc.
Temperature Factor Comments
Currents Bleaching
Wave energy/
exposure
Mortality-recent
Deep water
(30-50m)
Coral disease
Cooling &flushing
Depth of reef
base
Mortality-old
Depth
3-Coral Condition
Recovery-old
Visibility (m) Recruitment
Compass
direction/
aspect
Fragmentation
Slope
(degrees)
Dominant size
class
Physical
shading
4-Coral
Population
Largest corals
(3)
Shade & screen
Canopy corals Obligate feeders
Exposed low
tide
Branching
residents