Coral Reef Monitoring Protocol for Assessing Marine Protected Areas

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Coral Reef Monitoring for Assessing Management Effectiveness of

Marine Protected Areas

Version 1.0

Gabby Ahmadia, Joanne Wilson, & Alison Green

Coral Reef Monitoring Protocol for Assessing Marine Protected Areas

Gabby Ahmadia, Joanne Wilson, & Alison Green

A publication supporting the Coral Triangle Initiative on Coral Reefs, Fisheries and Food Security (CTI-CFF)

www.coraltriangleinitiative.org

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CORAL REEF MONITORING

PROTOCOL FOR ASSESSING MARINE PROTECTED AREAS

Gabby Ahmadia, Joanne Wilson, Alison Green

This publication was produced and printed with support from the United States Agency for International Development’s regional Asia program through the Coral Triangle Support Partnership

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Coral reef monitoring protocol for assessing marine protected areas Authors:

Gabby Ahmadia: Conservation Science Program, World Wildlife Fund, 1250 24th Street NW | Washington, DC 20037 USA

Email: [email protected]

Joanne Wilson: Sea Solutions, PO Box 285, Pottsville, NSW 2489 Email: [email protected]

Alison Green: The Nature Conservancy, South Brisbane, 245 Riverside Drive West End, Queensland 4101

Email: [email protected]

USAID Project Number: GCP LWA Award # LAG-00-99-00048-00

Citation: Ahmadia G.N, Wilson J.R. & Green A.L, 2013. Coral Reef Monitoring Protocol for Assessing Marine Protected Areas in the Coral Triangle. Coral Triangle Support Partnership.

This is a publication of the Coral Triangle Initiative on Corals, Fisheries and Food Security (CTI-CFF). Funding for the preparation of this document was provided by the USAID-funded Coral Triangle Support Partnership (CTSP). CTSP is a consortium led by the World Wildlife Fund, The Nature Conservancy and Conservation International.

For more information on the Coral Triangle Initiative, please contact:

Coral Triangle Initiative on Coral Reefs, Fisheries and Food Security Interim-Regional Secretariat

Ministry of Marine Affairs and Fisheries of the Republic of Indonesia Mina Bahari Building II, 17th Floor

Jalan Medan Merdeka Timur No. 16 Jakarta Pusat 10110, Indonesia www.coraltriangleinitiative.org

dissemination of material in this report for educational or other non-commercial purposes are authorized without any prior written permission from the copyright holders provided the source is fully acknowledged. Reproduction of material in this information product for resale or other commercial purposes is prohibited without written permission of the copyright holders.

Disclaimer: This document is made possible by the generous support of the American people through the United States Agency for International Development (USAID). The contents are the responsibility of Coral Triangle Support Partnership (CTSP) and do not necessarily reflect the views of USAID or the United States Government.

Front cover photos: Diver collecting data for coral reef monitoring in Eastern Indonesia (©

Joanne Wilson). Back cover photos: (© Gabby Ahmadia and Edy Setyawan).

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Table of Figures

Figure 1. Link between monitoring and management ... 3 Figure 2. Example sampling design for quantitative assessment of benthic and fish

communities on two reef types in a Marine Protected Area ... 10 Figure 3. Fish aggregation survey diagram view from above ... 24 Figure 4. Average percent cover (±SE) for main benthic categories within no take and use zones in an MPA 2009 – 2011 ... 32 Figure 5. Cover of hard coral showing cover of branching and tabulate forms at each site in no take and use zones in a) 2009; b) 2010 and c) 2011 ... 33 Figure 6. Average herbivore fish biomass (±SE) within sites in different management

zones in an MPA from 2009-2011 ... 34 Figure 7. Average carnivore fish biomass (±SE) across sites within in a No Take and a Use zones in an MPA from 2009-2011 ... 35 Figure 8. “Difference-in-Difference” graph showing another example of how data can be analyzed to illustrate management effectiveness.. ... 36

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Foreword

Marine protected areas (MPAs) are an integral component of the Coral Triangle Initiative on Coral Reefs, Fisheries, and Food Security (CTI-CFF) as one of the primary strategies for fisheries management and biodiversity conservation. To ensure MPAs are achieving their goals, it is important that well designed and effectively implemented monitoring programs are in place to monitor their performance and provide a basis for adaptive management. As the CTI-CFF seeks to conserve regional resources through design strategies articulated in the Coral Triangle Marine Protected Area System Framework and Action Plan¹, standardized protocols allow more accurate and informative comparisons as the geographic range of monitoring and evaluation is expanded. Therefore, we are pleased to announce the release of a new updated and expanded

“Coral Reef Monitoring Protocol for Assessing Marine Protected Areas” by Ahmadia, Wilson and Green. This protocol has been developed to provide one pathway to collect information on a subset of regional

indicators in the CTI-CFF Monitoring and Evaluation System Operations Manual². The Coral Reef Monitoring Protocol will provide information for basic indicators (specifically the first and second higher-level outcomes and impacts indicators of the CTI-CFF) for tracking progress towards the goals in the CTI-CFF Regional Plan of Action. This protocol also can contribute information to the resource management questions for MPA management effectiveness system endorsed by the government of Indonesia.³

The Coral Reef Monitoring Protocol for Assessing Marine Protected Areas is a revision and update of the manual “Biological Monitoring Methods for Assessing Coral Reef Health and Management Effectiveness of Marine Protected Areas in Indonesia,” which Wilson and Green released in 2009 to provide technical advice on this issue for field practitioners in Indonesia. While this protocol was developed and widely applied throughout Indonesia, it follows standard global protocols and applies them specifically to local coral reef ecosystems and species. Since many of these ecosystems and species are widely distributed throughout the Coral Triangle and other tropical marine ecosystems, these protocols may also be useful for field

practitioners elsewhere. Therefore, an update was required to broaden the geographic scope to include the entire Coral Triangle, and to incorporate lessons learned from applying this protocol in the field, feedback from users, and new scientific advances in the field.

This report addresses many of the refinements required and requested by field practitioners, and includes new sections on data analysis, processing and interpretation. We hope that this document will assist field practitioners to develop and implement effective monitoring programs for their MPAs.

1 Coral Triangle Initiative on Coral Reefs, Fisheries and Food Security (CTI-CFF). 2013. Coral Triangle Marine Protected Area System Framework and Action Plan. CTI-CFF, United States Agency for International Development Coral Triangle Support Partnership and US National Oceanic and Atmospheric Administration, Cebu City, Philippines.

75 pp.

2 Coral Triangle Initiative on Corals, Fisheries and Food Security (CTI-CFF) 2013. Monitoring and Evaluation System Operations Manual. U.S. Coral Triangle Initiative Support Program and CTI-CFF Monitoring and Evaluation Working Group.

3 Directorate for Conservation of Area and Fish Species (2012). Technical Guidelines for Evaluating the Management Effectiveness of Aquatic, Coasts and Small Islands Conservation Areas (E-KKP3K). Jakarta: Directorate for

Conservation of Area and Fish Species, Directorate General of Marine, Coasts and Small Islands, Ministry of Marine Affairs and Fisheries, ix + 61 pp.

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Acknowledgements

This “Coral Reef Monitoring Protocol for Assessing Marine Protected Areas” is the result of efforts of many monitoring and management staff from multiple institutions who contributed valuable information for developing the next version of this protocol. The authors would like to particularly thank the field staff from Conservation International (Nur “Ismu” Hidayat, Defy Pada, Edy Setyawan), The Nature Conservancy (Rizyha Ardiwijaya, Purwanto Muhajir) and World Wildlife Fund – Indonesia (Kartika Sumolang) who field tested the manual “Biological Monitoring Methods for Assessing Coral Reef Health and Management Effectiveness of Marine Protected Areas in Indonesia,” and provided excellent feedback. We would also like to thank Helen Fox (World Wildlife Fund – US), Sangeeta Mangubhai (International Union for Conservation of Nature), Andreas Muljadi (Coral Triangle Center) and Stuart Campbell (Wildlife Conservation Society) for their critical reviews of the protocol.

Others who provided helpful inputs about this protocol include Wawan Ridwan, Lida Pet-Soede, Estradivari, and Anton Wijonarno (all World Wildlife Fund – Indonesia), Luz Baskinas (World Wildlife Fund – Philippines), Louise Glew and Cathy Plume (Word Wildlife Fund – US), Tiene Gunawan, Mark Erdmann and Matt Fox (all Conservation International) and Alan White (The Nature Conservancy), Pahala Nainggolan and Payton Deeks (US Coral Triangle Support Partnership). Finally, we would like to thank Maurice Knight, Chief of Party for the Coral Triangle Support Partnership, for supporting this project. The authors apologize if we inadvertently missed mentioning others for their assistance with this protocol.

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Executive Summary

Marine Protected Areas (MPAs) can be an effective tool to protect biodiversity and sustainable fisheries on reefs from overfishing, destructive fishing practices, poaching and other harmful or illegal activities. MPAs are often managed through zoning and management plans to protect biodiversity, reef ecosystem health and populations of key fisheries species. Biological monitoring described in this protocol is designed to determine if MPA management or zoning plans have been successful in achieving these objectives and to provide a basis for adaptive management. This protocol provides an updated, refined and expanded version of the methods described in Wilson and Green (2009), “Biological Monitoring Methods for Assessing Coral Reef Health and Management Effectiveness of Marine Protected Areas in Indonesia,” taking into

consideration lessons learned from field application and feedback from users. A key modification is the inclusion of new components to provide advice regarding data analysis and reporting. While this protocol was developed in Indonesia, it would also be relevant for all six countries of the Coral Triangle since they share similar coral reef habitats and species.

Setting up a successful monitoring program requires a series of steps from setting objectives and survey design, field surveys, data entry and analysis, report writing and communication of final results. Monitoring teams must be proficient in all these skills, or seek additional assistance. While this monitoring protocol focuses on in-water activities for data collection, it also provides guidelines for developing the monitoring strategy, planning and coordination prior to data collection, data management, analyses, interpretation and reporting.

Benthic community structure (coral, other invertebrate and algal communities) and fish communities are used as a measure of the health of coral reefs. This document outlines methods for assessing benthic and fish communities on coral reefs which are simple, align with internationally recommended monitoring methods, are scientifically robust and can be undertaken by MPA management staff with some training.

Benthic communities are assessed using Point Intercept Transects where reef life forms are recorded every 0.5 m along 3 x 50 m transects at 10 m depth at each site. Fish communities are assessed using a

combination of belt transects and long swims. The number and size of all fish from selected taxa (in species or family groups) are recorded on 5 x 50 m transects at 10 m depth at each site. The list of fish taxa to be recorded can be tailored according to which species or groups are of local interest either for their commercial or ecological value but usually include key fisheries species and herbivores that play an important role in maintaining coral reef resilience. Large, highly mobile and vulnerable fish species such as sharks, large groupers, wrasses and parrotfishes are counted and measured on long swims of at least 400 m length at a depth of 3-5 m at the reef crest. The long swim method can be modified for monitoring fish communities at reef points or areas of high current that support high densities of fish.

Reef ecosystem monitoring results can be used as a baseline assessment of an area. If done repeatedly using the same or comparable methods, they can provide information on the performance of MPAs to:

 protect the health and biodiversity of benthic communities; and

 maintain or improve the abundance, size and biomass of reef fish especially those species which are targeted by subsistence, artisanal or commercial fishers.

Modifications and simplifications of the standard protocol are outlined to take into account environmental conditions (e.g. strong currents), resources available and skills of the monitoring team.

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1 MPAs in the Coral Triangle

Marine Protected Areas (MPAs) are widely accepted as a powerful tool to address threats to coral reefs and protect biodiversity, habitats and ecosystem services (Lubchenco et al. 2003). MPAs are one of the key strategies for conservation and sustainable fisheries in the Coral Triangle (CTI Secretariat 2009).

MPAs provide a focus for management to prevent illegal and unsustainable activities through enforcement activities, and increased education and awareness through outreach activities. MPAs may be managed as either:

1) fully protected no-take areas which prohibit any extractive activity including fishing. In areas of high population and use, these are usually small and managed by local communities often under traditional laws such as sasi in Indonesia; while in less populated areas they may be large and managed by

agreements between communities and tourism operators, or

2) multiple use MPAs which use a zoning plan to identify which areas of the MPA are suitable for different types of activities. Although terminology for each zone type varies widely, zoning plans usually include areas designated as ‘No Take Zones’ (NTZs) which do not allow fishing or other extractive activities as a key management tool.

When MPAs are effectively managed and zoning systems enforced, many of the ‘in water’ threats to coral reefs such as overfishing, destructive and illegal fishing, and poaching are significantly reduced. There are many examples from around the world which have shown that after protection and management, coral reefs and the associated fish populations can recover from these threats (e.g. McCook et al. 2010).

Therefore, with effective MPA management, the health of coral reefs and fish populations should improve assuming there are no additional environmental threats (such as sediment or nutrient run-off or major coral bleaching events, etc.). An MPA coral reef monitoring program is used to assess changes in reef health.

Therefore coral reef monitoring is one way to test the effectiveness of the design and implementation of an MPA zoning and management plan.

Coral reef monitoring can be combined with assessment of other factors such as MPA governance, progress towards implementation of zoning and management plans, and social and economic monitoring to assess the overall effectiveness of MPA management. There are many protocols advising how to do these broader types of assessments (e.g. Pomeroy et al. 2005, Glew et al. 2012).

This document focusses on how to design, implement and interpret a coral reef monitoring program for coral reefs to test the impacts of an MPA zoning plan.

2 Reef monitoring to assess MPA management performance

Many MPAs around the world have measured how much and how quickly reef health and fish populations improved after implementation of MPA zoning and management using standard reef monitoring methods (Halpern 2003, Russ et al. 2008, Aburto-Oropeza et al. 2011). This information has been of great value for managers and policy makers. For example in American Samoa, fish monitoring showed there was a dramatic decline in parrotfish abundance which led to a nation-wide ban on night-time scuba fishing (Wilkinson et al.

2003). In Wakatobi NP, monitoring showed that fish populations were better protected in No Take Zones where local communities were involved in management and identified where patrols should be increased (Purwanto et al. 2010). Monitoring in Belize revealed a large decline in parrotfish abundance, which led to a countrywide ban on the capture of parrotfish.

It is essential that monitoring is recognized as an integral part of the MPA management cycle. Monitoring will have the greatest value when managers and monitoring staff work together. There are some key steps in the monitoring program where it is important that managers and monitoring staff work together:

1) Planning – Before monitoring, identify the questions that are relevant to managers. It is a good idea to discuss what changes can be expected as a result of the MPA implementation and develop

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specific questions to be answered by the monitoring program.

For example: are fish populations increasing in the No Take Zones? Are fish species that are

important to local communities recovering? Are the fish getting bigger? Is the coral reef recovering?

2) Immediately after surveys – Discuss with managers the areas visited, key highlights, any threats or illegal activity seen, any major damage to reefs, any areas of excellent condition or other issues.

3) Reporting – Monitoring staff need to analyse and interpret monitoring data in a way that answers the original management questions. The monitoring results also need to be communicated in a way that non-scientists can understand. Scientific reports or papers should be prepared along with summaries or information sheets highlighting the main points and recommendations prepared in non-technical language.

Monitoring is an integral part of management. Monitoring results will be used as the basis of management decisions such as where and when patrolling resources should be allocated, recommendations for regulation of specific fishing gear and allow managers to report on the effectiveness of the MPA to stakeholders and communities. These decisions affect how scarce management resources are allocated and also affect local resource users. Therefore it is important that monitoring and data analysis is scientifically robust so that management decisions are based on the most accurate information. The key to ensuring a scientific monitoring program is used and supported by management is by:

1) designing a monitoring program which answers managers’ questions; and

2) communicating the results of monitoring in a way that managers can use (Figure 1 ).

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Figure 1. Link between monitoring and management

3 Choosing the right approach and protocol for monitoring your MPA?

Deciding on the best monitoring program and the best protocols to use for your MPA or MPA Network should take into consideration many factors. There is no ‘one’ perfect monitoring protocol that will answer all your questions and no matter which protocol you choose, there are always tradeoffs. One of the biggest questions that managers and monitoring teams face in choosing their monitoring strategy; is whether to:

(1) monitor intensively and quantitatively at a few sites and/or

(2) do broadscale, semi-quantitiative surveys across a large area

These decisions must be made for each MPA depending on objectives, resources, skills of monitoring team, funding etc. The following paragraphs provide some guidance to help you choose the best approach and protocol for your MPA (also see Box 1).

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4 Box 1. Monitoring definition and principles

The definition of monitoring (compared to resource assessment or applied research) is “A series of

measurements that are repeated on the same sites or individuals over a period of time and used to evaluate success and impacts of management strategies (Kenchington and Ch’ng 1994 in Day 2008).”

There are several fundamental approaches for monitoring:

1) identify your objective

2) examine options for monitoring

3) decide between intensive monitoring at a few sites OR less intensive monitoring across a larger area 4) choose a standard protocol and follow it

5) repeat your measurements at the same sites and month/s over time

Other types of underwater surveys in support of MPAs may include (modified from Kenchington and Ch'ng 1994 in Day 2008):

Resource assessments – one-off surveys for biodiversity, habitat mapping or reef condition to be used as the basis of MPA planning.

Applied research – targeted studies that are designed to understand underlying causes of observed changes in ecosystems

3.1 Identifying objectives for monitoring

Monitoring programs should be designed to measure progress towards achieving management objectives specified in management plans for the MPA or MPA network. To ensure that your monitoring program is designed to measure progress towards your management objectives, it is important to clearly articulate the objectives of the monitoring program. The objective/s should clearly define how monitoring data will be used.

The broad objective that could be fulfilled by this monitoring protocol is:

To provide a quantitative assessment of the effectiveness of MPA zoning plans in improving the condition of the benthic communities and the status of fish populations on coral reefs.

Therefore this protocol will allow you to quantitatively assess changes in benthic communities and fish populations on coral reefs over time in different types of zones within your MPA. The methods described here are consistent with currently recommended monitoring methods in the international scientific literature (English et al. 1997, Hill and Wilkinson 2004).

However, if your objective is to get information from large areas or to detect large scale disturbances (i.e.

crown of thorns, bleaching events, bomb fishing) in your MPA, then manta towing (English et al. 1997) may be a more appropriate method. Manta towing also requires observers to be less skilled as fewer benthic categories are recorded so communities can be involved in this type of monitoring. However, note that manta towing is not suitable for accurate fish surveys and it is not quantitative, since it relies on observer estimations rather than measurements.

The data collected using this protocol can be used to address many specific management questions about how MPA zoning is affecting benthic and fish communities. For example, the following objectives can be assessed in different MPA zones:

 trends in populations of key fisheries species;

 trends in size and biomass of fish;

 changes in coral cover and composition of benthic communities.

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3.2 Checklist

If you have identified that your objective for MPA monitoring aligns with the objective of this protocol, the next step is to determine if you have the necessary resources to carry out this protocol. Table 1 is provided as a checklist to test if it is suitable for your purposes. If this protocol is not conducted in the manner in which it is intended, then you may compromise the usefulness of the data. For example, if you are unable to sample the minimum number of sites to compare multiple sites within different zone types, data analysis options will be limited and interpretation of any trends less certain.

If adequate access to equipment/operations, funding, and a team with the necessary skills are not available, then this protocol should not be used because this compromises data analyses and limits your ability to determine if there are any changes due to the implementation of the zoning plan. There are many other monitoring approaches that can be used for different objectives or to match available resources and skills (reviewed in Hill and Wilkinson 2004).

Table 1: Checklist of criteria to determine if this is the best protocol for your MPA

Criteria Question Why important? Yes/No

1. Objective Is your objective to test the effectiveness of an MPA management plan (or community based area)?

It is important to align your monitoring to your management objective/s. This protocol is specifically designed to examine changes in environmental conditions over time and between different types of MPA regimes (i.e. No Take vs. Use Zones or inside/outside small MPAs)

2. Equipment

& Operations

Do you have the equipment (i.e.

transects, GPS, boat or ship time, dive gear) to carry out the protocol?

It is essential that the team obtain all the necessary equipment for

monitoring and have been trained in how to use it.

3. Skill set of team

Do you have a team that has the necessary skills to complete all aspects of the

monitoring protocol?

Team must be experienced divers and trained in GPS, fish or benthic

identification, fish length estimation, and must meet the standards of this monitoring protocol (see Training your team, Section 4.7)

4. Time Does your team have enough time to complete the field survey, analyze and interpret results, write reports and

communicate results to key stakeholders?

If you don’t have time or commitment to analyze and present the results to key stakeholders (e.g. managers, community members), then it will be difficult to communicate results in a timely manner to adaptively manage the MPA

5. Funding Do you have necessary funding to support sufficient sampling of the MPA?

It is important to ensure that there is enough funding to adequately sample the MPA and ensure there is sufficient replication of sites in the different MPA zones, and to cover time required for data analysis and reporting.

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3.3 Using and adapting these protocols

The monitoring protocol outline below is recommended as a standard basic coral reef monitoring protocol to assess the performance of a management plan and management actions to achieve the objectives of the MPA.

It is important to recognize that there may be many reasons, such as, specific skills in the monitoring team or specific environmental conditions at each MPA site, which may justify some modification or adaptation of these methods. For example, modifications may be required for sites with strong currents or where coral reefs are limited to shallow depths. In addition, at some MPAs there may be additional capacity and resources to allow for additional monitoring at more sites, depths, or reef types or to collect data on a specific theme. For example, you may have an expert join your team and record coral disease, coral recruitment or a broader range of fish species. If this is possible, it is important that these additions align with your monitoring objectives. Where possible, modifications of the standard protocol have been provided throughout this document to allow for a range of environmental conditions and logistical situations (see Frequently Asked Questions (FAQ)Section 7).

4 Designing your coral reef monitoring

After you have gone through the checklist to ensure that you have all the necessary resources to carry out this monitoring protocol, the next step is to design your coral reef monitoring plan. An MPA monitoring plan must include information on where, when and how frequently the monitoring teams should sample the MPA. The team must make decisions about:

 what reef habitat type to sample (see 4.2.1 below),

 how many sites to sample,

 where sites are located,

 how frequently to sample (e.g. annually, every 2-5 years), and

 what time of year to sample (e.g. season, month).

The design of the MPA monitoring plan is one of the most difficult and the most important part of the monitoring program and substantial time and effort must be dedicated to developing your sampling design.

It is critical that the MPA monitoring plan is designed carefully so the results of the monitoring can be analyzed correctly and will be able to answer the managers’ questions accurately. The following section provides guidelines to help in the design of an effective MPA monitoring plan.

Individual sampling plans should be developed for each MPA (See Section 4.8) that take into account the unique reef types and environmental conditions, and the human and financial resources available at each site.

4.1 Start with your objective and management questions for your MPA

The design of the MPA monitoring plan needs to reflect both your monitoring objective and management questions. The overall monitoring objective for this protocol is to assess the effectiveness of the MPA management plan on coral reef health and the status of fish populations. In order to test differences among zones within an MPA it is necessary to survey multiple sites of similar reef habitat type in each different MPA

Because of the importance of this step, the MPA monitoring plan must

be checked by at least one expert with advanced skills in coral reef

monitoring design and statistical analyses.

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zone type. For this protocol, it is recommended that surveys are done on the most common reef type at your MPA which is usually continuous reef slopes. However it can be modified for steep slopes and sheltered habitats including patch reefs.

If there are specific management questions about changes at special or strategic sites (i.e. popular dive sites, areas where large fish aggregate or areas which have experienced or are vulnerable to bleaching or other disturbance etc.) then these sites can also be added to the MPA sampling plan.

Box 2: Identify and take natural patterns of variation into account

All biological data will vary from place to place and over time due to natural variation in the environment.

This type of natural variation must be understood and should be taken into account in the design of your monitoring program. Such variation occurs as a result of:

Natural Variability

●Seasonal patterns ● Tidal influence ●Reef type ●Reef Exposure ●Reef Slope Observer Variability

●Differences between observers

●Accuracy and precision of the data e.g. measurements vs. estimations

The aim of a monitoring program is to detect variation caused by differences due to management – in this case between MPA zones. If the data are highly variable we may not be able to detect differences due to management. Therefore the monitoring program should ensure that all other sources of variation are taken into account, reduced or removed in the survey design. For example, if season or tidal currents affect fish abundance, monitoring should always be done at the same season or tidal state.

Differences between observers can be reduced by ensuring the same person collects the data or that all observers are well trained and ‘calibrate’ their observations regularly. One of the biggest potential sources of error in this method is in counting and estimating the lengths of fish so fish observers should be very experienced and calibrate their observations before each monitoring expedition.

4.2 Choosing your sites – standard monitoring

4.2.1 Coral reef habitat types

The first step in choosing the best sites to survey is to select the coral reef habitat type(s) you are going to sample. In order to detect differences between No Take and Use Zones, it is important to compare sites with similar coral reef habitat types i.e. reef zones (e.g. crests, forereef slopes, lagoon patch reefs etc.) with similar environmental conditions and characteristics such as exposure, angle of the slope and sediment loads. This is because different coral reef habitat types will have different types of coral and fish

communities. Therefore it is important to measure the difference between MPA No Take and Use Zones, not just the natural differences between different reef types.

It is recommended that you choose 1 or 2 reef habitat types which are common in your MPA. To make an informed decision about which habitat types to use, gather as much preliminary data about the coral reefs in your MPA as you can such as exposure (exposed, semi-exposed, sheltered), reef type (i.e. atoll, fringing, barrier), reef zone (crest, forereef slope, patch reef etc.), reef slope (i.e. wall, slope).

Methods to collect preliminary information about reefs in the MPA include:

1. Coarse sampling of that habitat within your MPA which can be done by snorkeling or manta tows (English et al. 1997)

2. Taking a look at available maps and imagery (i.e. from remote sensing) that delineate the coral reefs

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3. Referencing past reports and publications including rapid ecological assessments (REAs)

4. Consultation with dive operators, local communities, scientists, or any other stakeholders familiar with the coral reefs in the MPA

Where possible, monitoring should be standardized on one or two main reef habitat types where it is possible to sample (considering weather conditions, currents, etc.) and which are represented in both No Take and Use Zones.

Box 3. Selection of habitat type is not always straightforward

Selecting which reef habitat type to sample is not always straightforward and requires both knowledge of the coral reefs in the MPA and expert judgment to determine which reef habitats are suitable replicates. For example, categorizing the different exposure types can be difficult. It is relatively easy to distinguish

between highly exposed reefs and sheltered (lagoonal) reef sites, but reefs vary in exposure between these two extremes. To determine which sites to use requires knowledge of the area (as some coral reef sites may be exposed at different times of year), and familiarity with coral reefs and the communities they support.

Sometimes, preliminary data collection is required to determine differences between reefs, and the range of reefs within and outside of an MPA. Thus, consultation with an expert is recommended in choosing what reef habitats to use and where they are located.

4.2.2 How many sites should I survey?

For the standard monitoring plan, once the coral reef habitat types have been selected, the next step is to decide on the number and location of survey sites in each reef habitat type.

Calculating the number of sites to monitor in your MPA will depend on

 the objective

 size of your MPA

 the number and diversity of reef habitat types, and

 available resources.

Careful planning and discussions amongst the entire MPA team are needed to decide on a monitoring plan which includes enough sites to detect changes in the conditions of the coral reefs over time in different management zones, surveys enough sites to cover most areas of the MPA, while working within available resources. On coral reefs, natural variation between sites is high especially in fish populations (see Box 2).

This means that it is important to sample sufficient replicate sites in each zone to be able to detect differences due to management rather than simply natural variation.

As the objective is to compare the effectiveness of the management of MPA zoning (No Take vs. Use Zones) on the benthic and fish communities, replicate sites are needed within each zone type and reef habitat type.

If only one reef habitat type is dominant in the MPA and therefore it is the only habitat type being sampled, then it is recommended to sample a minimum of 8-12 sites in each management zone. This should ensure sufficient spatial coverage of the MPA but if your MPA is very large then more sites can be added. If you are including two or more reef types, then the minimum recommended number is 5-8 sites in each reef habitat type selected within each management zone.

If there are additional resources and/or if the MPA is large, adding additional sites beyond the minimum recommended number would increase the ‘power’ or ability of the statistical test to detect changes between management zones.

The following sampling design allows for assessment of differences between fully protected (no take) and use (traditional use or general use) zones for two common habitat types in an MPA.

 In reef habitat type A, choose at least 5-8 replicate sites inside No Take Zones and 5-8 replicate sites within areas outside No Take Zones (control sites – see below) = sub total of 10-16 sites

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 In reef type B, choose at least 5-8 replicate sites inside No Take Zones and 5-8 replicate sites within areas outside No Take Zones = subtotal of 10-16 sites

This design will result in a total of 20-32 sites per MPA for the standard monitoring plus special and strategic sites (see Section 5.2.3). With a team of 5 people, doing 3 dives per day, the standard

monitoring of 20-32 sites can be done in 7-11 days. Additional time for special and strategic sites should be allocated and to allow for gear breakage/bad weather as appropriate for each site.

4.2.3 Control Sites

By monitoring control sites outside of the MPAs, this will allow for comparisons to reefs that are in a marine protected area. If the control sites are measured before the conservation intervention (MPA) is

implemented (control-baseline) and these control sites are then monitored after the MPA was implemented you can compare the differences in the changes of the reef ecosystems in and out of the MPAs and can directly measure the impact of the conservation intervention (the MPA). This approach is referred to as Impact Evaluation (see Box 4).

In some situations we may wish to compare areas within the MPA with control sites outside that have no or little management regime. Alternatively, we may wish to compare zones within an MPA that provide different management regimes, e.g. comparing No Take Zones with Use Zones where fishing is allowed (in this case, the Use Zones will act as controls for measuring the effectiveness of No Take Zones).

Control sites are matched up to sites within the MPA based on similar characteristics. Similar replication of sites is needed to ensure there is enough statistical power. One control site can actually serves as a match for sites within multiple MPA’s. There are many methods for “matching” of control sites which can be read in Rosenbaum (2010) and Callendo & Kopieing (2008).

Box 4. Impact Evaluation

Impact evaluation deals with questions of causality. In other words, it seeks to understand how a particular conservation or management intervention (e.g., marine protected area) causally affects variables of interest, known as outcomes. The outcomes being evaluated may be ecological or social, and include both the intended and unintended effects of the intervention. Put simply, impact evaluation asks ‘What is the impact of a conservation intervention on an outcome of interest? (Glew, 2013).

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Reef type A e.g. exposed fringing

reef slopes

Reef type B e.g. sheltered fringing

reef slopes

No Take Zones Use Zones No Take Zones Use Zones

S1 S2 S3 S4 S5 S6 ……. S10 S1 S2 S3 S4 S5 S6 ……. S10

T1 T2 T3 T4 T5

S1 S2 S3 S4 S5 S6 ……. S10

T1 T2 T3 T4 T5

S1 S2 S3 S4 S5 S6 ……. S10

T1 T2 T3 T4 T5

Marine Protected Area

Figure 2. Example sampling design for quantitative assessment of benthic and fish communities on two reef types in a Marine Protected Area. S = Site, T = Transect. Please note that three transects are used for benthic communities and five transects plus a long swim are used for fish communities

10

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4.2.4 Selecting the location of sampling sites

Monitoring teams should work together to decide on the exact locations for monitoring. It is a good idea to consult with other members of the MPA team and with MPA science experts.

Below is a list of key things you should consider when selecting your location:

 Monitoring should be undertaken at multiple sites within an MPA and spread widely to ensure a good geographic cover of the study area.

 Within each reef habitat type and MPA zone type, sites should be selected which have similar characteristics and where there is adequate reef to enable you to replicate your transects and/or replicate sites.

 Fish and benthic surveys will be done at the same sites. Fish surveys need the largest area – at least 700 m of similar habitat is needed – 300 m for belt transects and 400 m for timed swims.

 Where possible, sites should be separated from each other by a reasonable distance (at least several hundred meters, preferably 500 m).

 Try to choose sites which are similar to each other. For example, in the middle of the No Take Zone, or similar distances from villages/other activities where possible (i.e.

avoid the edge of No Take Zones where fishing may occur).

 The site is safe to dive on and will not pose a safety risk for divers (e.g. strong currents making it challenging to lay down transect tapes)

Box 5. Randomizing sampling design

To reduce bias in the sampling design, site selection should be random when possible. This does not mean you should randomly point to a coral reef on a map, and choose it as a site. It does mean that once homogeneous (i.e. similar) areas of each habitat type have been identified, the location of the sites can be chosen at random within these areas. After the coarse surveys have provided an indication of the distribution of reef habitat types, suitable sites should be

randomly selected from within this area. This is called “stratified haphazard selection”.

However, once the sites have been selected, the teams should monitor these same sites on subsequent surveys.

4.3 Special and strategic sites

In any MPA, it is highly likely that there are a number of sites of special interest to stakeholders, managers or users of the MPA which are not included in the standard sampling plan to assess the effectiveness of zoning plans as described above. For example, dive sites on points or pinnacles where fish aggregate in large numbers at certain times, sites which experience or are more vulnerable to coral bleaching or other disturbance such as lagoons, sheltered areas which host unusual assemblages of corals and fish. Coral reefs in lagoons or in channels have very different characteristics to those on exposed reef slopes and so cannot be considered replicates as part of the standard monitoring. Strategic sites might include those reefs that are placed at different distances from a land-based impact so that changes can be tracked over time as to the influence of the land-based impacts on the reef ecosystems.

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Special and strategic sites are usually not selected as the basis for the standard monitoring program in an MPA for a number of reasons

1) there are usually not enough similar locations (replicates) in both No Take and Use Zones to test the implementation of zones in a scientifically rigorous way

2) conditions such as strong currents or the need to survey at greater depths means that the full methods (transects plus long swim) cannot be undertaken due to logistic or safety reasons

3) fish populations are highly variable and need to be sampled on the correct tide, time of day and more frequently than once a year to detect true differences.

Where there are either sites of interest (related to management objectives) or there are extra resources available, special and strategic sites should be included in the sampling plan. Changes at these individual sites can be tested over time and can tell managers something about

important changes or processes on these habitats.

4.3.1 Points, pinnacles and channels

Points, pinnacles and channels frequently experience strong currents, and thus often support much higher densities of large fishes as compared to other coral reef habitats. These sites are often popular dive sites and sightings from dive operators may suggest that these areas are improving because of MPA management. It is also important to test whether this is true scientifically. Some of these are also fish spawning aggregation sites that require specialized monitoring protocols (see below).

The presence of large fish is naturally highly variable due to time of day, currents, spawning season and the long range movements of these species. These sites experience much more variability, thus detecting changes will likely require either more frequent sampling throughout the year, or a long duration of monitoring spanning several years. The number and location of sites should reflect the objective of the monitoring and management questions you are trying to answer. These are often sites of interest for management and other stakeholders, so choosing these sites and determining how often they should be sampled, needs to carefully consider resources and how much information can be extrapolated from monitoring these sites. Another important consideration in sampling these sites is safety especially as some areas experience very strong currents. For example, monitoring these extremely variable sites, just once every two years, would not be sufficient sampling to reflect on the environmental conditions of the site. It is likely more frequent sampling would be needed in order to capture the variability and detect changes due to management rather than natural variability (see Frequently Asked Questions (FAQ)Section 7).

Due to the stronger currents and the difference in fish communities, slightly modified methods should be used to survey these sites and are provided within this protocol (see Section 4.3.1).

Data from special and strategic sites should be analyzed

separately from the standard monitoring sites

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4.3.2 Fish Spawning Aggregation Sites

Many fishes form aggregations for reproduction or feeding (for more information see the Society for Conservation of Reef Fish Aggregations at http://www.scrfa.org/). For most species, spawning aggregations provide ample opportunities to reproduce and many have a long history of commercial importance. It is now widely acknowledged that unmanaged fishing on

aggregations, especially spawning aggregations, can rapidly deplete fish populations with undesirable impacts on the species and the livelihoods of those who depend on them. Thus it is important to identify and monitor these areas, and to measure the success of MPA zones to protect them. Given their importance, specialised monitoring protocols are available to monitor fish spawning aggregation sites (see http://www.scrfa.org/get-involved/methods-manual- home.html).

4.3.3 Other coral reef types

Coral reefs include a diverse range of different reef types and only one or two main reefs will be sampled in the standard monitoring plan. Managers may also be interested in surveying some examples of different types of coral reefs, for example, reefs which experience extremely high temperatures in lagoons, or reefs which are very sheltered and contain unusual species of coral or fish, or reefs which are recovering from previous damage from bleaching, crown of thorns starfish or destructive fishing. Alternatively, managers may wish to also examine the impact of other disturbance such as sedimentation or coastal development and include some additional sites for comparison. Again, in these conditions, the protocol may need to be modified to suit local conditions, for example the surveys may be best done in shallow depths, and shorter transects (30 m) may be needed if reefs do not extend more than 150 m. Modifications of the method should be discussed with an expert to ensure the methods and the monitoring design and match the management question.

4.4 Timing and Frequency of Monitoring

Time of year of sampling should take into consideration both the availability of resources and the team, and weather conditions. Sampling should take place at the same time of year, whether the MPA is being monitored every year or three years.

It is recommended that when possible, sampling should be done around the same time as peak sea water temperatures are predicted in the region. This is when coral reefs are most ‘stressed’

and will give the best indication of reef health. Teams will be able to assess and report any coral bleaching and note the presence of coral disease or other disturbances.

Monitoring of fish spawning aggregations will require dedicated surveys when target species are aggregating (see http://www.scrfa.org/get-involved/methods-manual-home.html).

This monitoring program is designed for sampling every 1-3 years, and the frequency will depend on the management questions and resources available. It is recommended that initially (for the first 3-5 years), teams undertake the surveys annually as this will ensure that the team is familiar with the methods and any can identify any sources of variation such as observer error, and train all team members to a high standard.

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4.5 Additional Resources

If there are additional resources available, then there needs to be careful consideration of where these should be used to maximize the benefits of monitoring. For example, if you have two different MPAs that are substantially different in size, then it would be wise to expend more resources to sample additional habitats in the larger MPA to have a broader understanding of the range of environmental conditions within the MPA.

4.6 Creating a coral reef monitoring plan for your MPA

An MPA coral reef monitoring plan should be prepared for each MPA. This document need only be 1-3 pages long and should outline (see Appendix 1):

 The monitoring objective and management questions

 The location and number of sampling sites as a map and list of GIS points

 Identify which sites are for the standard monitoring and for special and strategic sites

 How methods are modified for special and strategic sites

 Timing of the monitoring including time of year, time of day and any specific tidal stages as relevant

 Target fish species for your sites

 Any other specific information or details needed to ensure your monitoring is repeatable or may potentially influence outcomes.

4.7 Training your team

Before undertaking monitoring using this method, the monitoring team must be trained, pass competency tests, and calibrate their observations so differences in data between observers are minimized. *If different observers are used for different monitoring periods or for different sites within the same period, it is important to record what these differences are in your methods and in your database. This is because it is important to know that if a fish species was not found in one year, that it was a real absence and was not a result of the observer not knowing or recording that species.

Training should be done separately to monitoring. If trainers are trying to teach while collecting data, the data will not be good quality. The best approach is to train the team members both above and below water until they reach minimum competency levels (Table 2) and then do the monitoring soon after.

4.7.1 Estimating lengths of fish

Estimating the length of each individual fish seen on transects or long swims as accurately as possible is a critical component of this protocol. These data are needed to estimate the biomass of that family or species of fish, and are the greatest source of potential error in fish monitoring programs. It is important that all fish observers are provided with adequate training so they can estimate the lengths of fish accurately while swimming underwater. All fish are estimated using Total Length (TL), measured from the tip of the snout of the fish to the end of the tail. Usually observers are assigned one of two fish size classes to count - either small to medium fish (10-35 cm) or large fish (>35 cm) - but they should be competent to count all size classes.

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The level of accuracy of all fish observers should be recorded at the start of the monitoring so the degree of error of their estimates is known. Ideally, fish observers should be able to estimate the lengths of fish to within 5 cm accuracy and should aim to achieve that level of accuracy through training and practice. However it is likely that some fish observers who

participate in monitoring assessments will be able to estimate the lengths of fish to within 10 cm accuracy.

The following guidelines should be followed when deciding how to record the lengths of fish.

A. Observers should be trained using fish models of all size ranges both above and below water and by working with experienced fish observers to compare their results on real fish during underwater surveys.

B. Ideally all fish observers should be trained to accurately measure fish at 5 cm intervals for a range of different size fish larger than 10 cm. A minimum size of 10cm TL should be used to exclude juveniles as this method is not suitable for accurately recording

juveniles which can be difficult to see and are often hiding among the substrate. Fish lengths should be recorded in 5 cm intervals i.e. 10-15 cm (midpoint 12.5 cm), 15-20 cm (midpoint 17.5 cm) etc.

C. If fish observers have not achieved high accuracy at 5 cm intervals, they should record their estimate of the fish size i.e. 13, 24, 31 cm and also record their level of accuracy underwater i.e. 10 cm.

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Table 2. Skills and minimum competency requirements for members of the coral reef monitoring teams

Skill Requirements

Diving All members of the monitoring team must be experienced divers with a diving certification and training in reef monitoring methods.

Divers must have logged a minimum of 10 dives and can work underwater for 60 minutes at 10 m depth without running out of air. They must be comfortable working in moderate currents and be willing to follow all safety procedures.

GPS All members of the monitoring team must be able to operate and use a GPS – enter waypoints, search for the next site, find the position for each site. It is important each member of the team is familiar with the specific GPS unit/s used during the expedition. At least two people must be able to use the GPS to calculate the distance between two points so the length of the long swim is recorded accurately. Reading and adjusting position according the format used (between GPS and location map).

Laying transects At least three people on the team must be experienced in laying transect tapes so they are well laid out for the benthic team observations.

Benthic community observations (PIT)

At least two people on the team must be able to identify all life forms listed in Appendix 5 with 100% accuracy and they must be able to recognize bleached corals.

Fish observers At least two people on the team must be able to

1. Identify all fish families, genera and species listed in agreed targeted fish species.

2. Record fish length to 5 cm with 75 % accuracy (see section below).

3. Accurately estimate transect widths of 5 m and 20 m.

4.8 Preparing for your monitoring expedition

Once you have designed your monitoring plan and trained the monitoring team, there are a few important tasks to include in the planning for your monitoring expedition.

1) Order any necessary equipment and underwater paper for data sheets. Ensure data sheets are printed at least one week before the monitoring surveys. Sometimes it is difficult to access specialized equipment in remote areas so planning ahead is important.

2) Check with other field teams or enforcement patrols about any conditions or activities which may affect the sites you have chosen for example has there been any recent reports of bombing or crown of thorns starfish etc.

3) All team members no matter how experienced need refresher training within 1 week prior to data collection to test their accuracy and calibrate among observers for both benthic

communities (benthic team) and fish identification and length estimation (fish team). This should be done over at least 4 dives or until observers are calibrated to collect the same data from the same site.

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4) Clearly identify the monitoring team and assign roles and responsibilities for all tasks such as recharging batteries for cameras, maintaining and repairing transect tapes, operating GPS units, data entry and storage, checking fuel, filling dive tanks, discussing the route and anchoring sites with the captain of the vessel (if necessary) etc. Many of these additional tasks are critical to the success and smooth running of the survey.

5) Prepare a large laminated map of the coral reefs in the MPA with all the sampling sites and numbers identified and the zoning plan shown. You will also need a separate list of the site numbers, names, location (GPS points), type of site (standard or special/strategic) and coral habitat type.

6) There needs to be an emergency plan in place with a procedure if an emergency situation may occur. There should be a checklist of emergency equipment (oxygen kits, first aid kit, radio communication/mobile phone, etc.) and all equipment needs to be on the boat in working order. There should also be a list of contacts for a decompression chamber/office and SAR office with different options. Everyone who is part of the monitoring team (including boat crew) needs to be familiar with the emergency plan. It is also highly recommended that monitoring team and boat crew receive training on first aid, CPR, and oxygen administration.

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5 Field survey method

Field surveys will encompass underwater surveys of both benthic and fish communities on coral reefs. The methods described here are based on standard coral reef monitoring methods used in other MPAs around the world including developing countries. These are quantitative methods and this means that careful measurements are taken at a limited number of sites. However, when undertaken according to the protocol, these methods should be able to detect if there are any changes in benthic and fish communities due to management compared to natural

variability.

5.1 Recording site characteristics and sampling event details

Site characteristics and sampling event details should be recorded during and shortly after conducting your monitoring.

 Site descriptions or characteristics should provide information regarding the coral reef and location of the survey (things that will not change from year to year).

 Sampling event details describe the conditions of the site on that particular day.

o Benthic monitoring and fish monitoring conducted at one site on one occasion at the same depth are considered one sample event and should be given the same sample event identification number.

o If two different depths are sampled at the same site, then this is considered two different sampling events.

Site characteristics will not change over time, so they only need to be recorded on the first visit to the site. Because sampling event details are related to the environmental conditions and monitoring team for the particular time of monitoring, they need to be recorded every time the team is monitoring a site.

5.1.1 Site Characteristics

Recording site characteristics is important not only so the monitoring team has the relevant information to return to the same monitoring site but also because some of the information regarding the sites are needed for data analyses. Therefore it is important to be consistent in the way in which the data is recorded. The following are the recommended site characteristics that should be recorded:

(1) Reef type: atoll, fringing, lagoon, barrier, patch (2) Reef slope: wall, flat, slope

(3) Reef zone: crest, fore reef, back reef

(4) Exposure: exposed, semi exposed, sheltered, very sheltered (5) Latitude and longitude of starting point

(6) Reef direction (which shoulder is the reef on when swimming along the transect): right or left

(7) Notes: Anything else that might influence the reef communities or aid in finding the location of the site (e.g. nearby island or feature on land or sea).

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5.1.2 Sampling Event Details

The following sampling event details should be recorded during each survey at a site:

(1) Site (2) Date (3) Depth

(4) Latitude and longitude at start and end of long swim (track if possible) (5) Agency/organization

(6) Observers for both benthic and fish: use the same set of names or initials (7) Underwater visibility (in meters)

(8) Currents: high, moderate, low

(9) Notes: anything else that might influence the reef communities or any mishaps or conditions that did not allow data to be collected

5.2 Fish communities

Underwater visual census methods are the most effective methods for monitoring coral reef fishes, particularly in remote locations (Choat and Pears 2003). Coral reef fish populations (focusing on key fisheries species) will be surveyed using underwater visual census methods described by English et al. (1997), Wilkinson et al. (2003), Choat and Pears (2003), Hill and Wilkinson (2004), Sweatman et al. (2005) and Green and Bellwood (2009).

Belt transects are used as they provide a high degree of precision for most fisheries species and herbivores, and are suitable for monitoring for multiple objectives (fisheries and resilience) and because they allow for multiple passes of the transect to count different species (Green and Bellwood 2009). This method provides the most effective technique for monitoring medium to large coral reef fishes that are amenable to visual census techniques. However, if possible, transects should be combined with a long swim method, which provides more precise estimates of the abundance and biomass of large, highly mobile and vulnerable species that tend to be rare, patchy or clumped in distribution (particularly sharks, large groupers, wrasses and parrotfishes) (Choat and Pears 2003).

In this protocol we recommend undertaking fish and benthic surveys at two depths: 2-3 m (reef crests) and 10 m (reef slopes). These depths are recommended for a number of reasons:

1) Depending on the reef profile, the area between 3-8 m is often an ‘intermediate’ area and so the sampling is designed to sample representative areas of reef crests and reef slopes.

2) A maximum depth of 10 m is recommended to minimize the risks that divers will run out of air before completing the surveys or suffer decompression sickness.

3) If you just want to measure one depth (based on resource limitations or are opting to monitor more sites), then it is recommended to monitor between 8-10 m as this depth is generally considered to be the most representative of a coral reef.

5.2.1 Belt transects

Reef fishes will be surveyed using 5 x 50 m transects at each site. Each survey will consist of two observers swimming along transects placed parallel to the reef crest at a depth of 10 m.

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Observers will count and estimate the size (total length (TL)) of individual fish of the target fish species.

Each observer will record different size groups of fish and use different transect widths as follows:

 Observer #1 will swim 1-2 m above the substratum, counting and estimating the size of small to medium sized individuals (10 - 35 cm TL) of the target species using a transect width of 5 m (2.5 m either side of the observer). Care should be taken to accurately estimate the width of the transect and fish found outside this range should not be counted. If a fish is on the edge of the survey area, the observer should count it if more than half its body is inside the area. Since this observer has to count the most individuals and species, he/she should be an experienced fish observer.

 Observer #2 will swim slightly behind and above Observer #1 to provide a better view of the larger area and to minimize disturbance to small fishes by the passage of the divers.

This observer will swim 3 m above the substratum, counting and estimating the size of all large individuals (>35 cm TL) of targeted species using a wider transect width of 20 m (10 m either side of the observer). Care should be taken to accurat