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Protocol For Coral Reef Mapping/Monitoring & FAD’s


  • To create a long term coral, reef fish, and benthic organism community/management monitoring programme in order to detect changes in % cover (coral) and abundances (fish/benthos) and to establish proper management plans for mitigation and conservation.
  • To research possible use of FAD’s as alternative fishing grounds for local people
    • Create an extensive data set of long term, bi-monthly fish sampling around FAD sites
    • Determine which sites are best suited for FAD’s
    • Draw conclusions from FAD usage to possible recovery of reef fish abundances


2.1. Sample Site

The Kisite-Mpunguti Marine National Park (coordinates) lies off Kenya’s south coast just south of Wasini Island, bordering Tanzania. The MPA covers approximately 11km2 while the Mpunguti marine reserve covers approximately 28km2. The area contains exceedingly high levels of biodiversity including approximately 64 genera of coral, 10 species of mangrove and 12 species of seagrass.

2.2. Coral Mapping

For mapping high quality remotely sensed photographs must first be taken. These may be satellite photographs, or aerial photographs taken from an aircraft. Ideally a spatial resolution of 10m or less is recommended. Before ground trothing it is advisable to pre-select points on the aerial photograph to represent different habitat types. Within these habitat types random points may be selected (random stratified approach).

2.2.1. Ground Trothing
The photographs will need to then be ground trothed via snorkel or SCUBA. The dive or snorkel teams will distinguish habitats by type and sub-type by filling in a basic protocol based on assessing by eye areas within 25m of a series of GPS reference points (Garmin now make a swimmers watch with underwater GPS capabilities).

The basic protocol for determining habitat types and sub-types are as follows:

  • Coral
  • Seagrass
  • Mangrove (if possible)
  • Sediment: coarse sand, medium sand, fine/mixed sand, mud, silt, rock (other than consolidated coral reef), or a mix of these

Sub-types are as follows:

  • Coral: fringing reef; patch reef; bottom reef; scattered coral community. Can also be classified by wave exposure: exposed; moderately exposed; semi wave exposed; sheltered
  • Seagrass: according to dominant species and density
  • Mangrove: according to dominant species and density
  • Rock (non-coral): non-reef intertidal rock (e.g. volcanic based rock); scalloped reef rock/karst; gravel/stones; coral rubble

For the coral communities cover can be calculated by recording coral cover using the DACFOR (dense; abundant; common; frequent; occasional; rare) scale which can then be converted into categories of % cover : D = 90 – 100%; A = 75 – 90%; C = 50 – 75%; F = 25 – 50%; O = 10 – 25%; R = 10 – less than 1%

Reefs should also be defined into the zones they are found as coral cover varies greatly between different zones. These are as follows: sublittoral (< 1m near shore); shallow (sediment) lagoon (1-5m deep); back-reef (reef lip facing the shore or lagoon); reef flat (mainly rock approx. 1m deep); reef edge; upper reef face/slope (approx. 3-10m deep); lower reef slope/face (>10m deep).

Volunteers will overestimate coral cover so best to have them tested prior by doing some underwater quadrats and use underwater dive slated with pictures that encompass all % coral cover proportions.

2.3. Coral Monitoring

To be able to establish a monitoring programme, one must first establish a baseline ‘health’ in order to be able to make comparisons after a period of time.

2.3.1. Transect Laying

Transects should ideally be placed along 2 or more standard depth contours (e.g. 10m, 7m, 5m, 3m) along the reef. These should be placed parallel to the beach and preferably be 50 metres long, although 25 metres will suffice. An advantage of laying a 50 metre line is that invertebrates and fish can also be sampled along the same transect. GPS points should be taken at the beginning and end of each transect. A surface buoy should also be placed at the start of each transect.

Transect lines must be weighted (braided rope wound round leaded pieces, often found around the bottom of fishing nets is best) so as they sit properly on the bottom. They should be secured with large elastic bands looped over the line and back through themselves, and hooked over a coral or other projection to keep them from moving. Leaded/weighted line is best as it rarely snags or breaks coral.

Once the line(s) are laid, coloured cable ties should be placed along the course of the line(s) around conspicuous corals or reef points every few metres in order to permanently mark the path of the transect(s).

Transects do not need to be straight. It can be better statistically for transect lines to zigzag in order for the line to stay in contact with the substrate (imagine a large coral structure in the way of a straight transect line would make it difficult to keep the line on the substrate, therefore difficult to sample accurately).

DO NOT USE MEASURING TAPE FOR TRANSECTS as it waves around and stretches, therefore it is difficult to lay in the first place, let alone repeat in the future.

2.3.2. Reef Monitoring

ALWAYS START WITH THE DEEPEST TRANSECT FIRST as this reduces the risk of decompression sickness and allows for maximum bottom time at each depth contour. The shallowest depth contour may also be done via snorkel.

Using modern digital underwater camera’s, photographs should ideally be 50cm x 50cm (0.25m2) quadrats taken on each side of the transect line (1m x 1m may also be used, but can be hard to distinguish coral genera as they are less clear). Quadrats will be sub-divided into 25 smaller squares each measuring 5cm x 5cm with string (see Fig. 1). One 5cm x 5cm sub-division will represent 4% cover (If 1m x 1m quadrats are used then sub-divisions will be 10cm x 10cm with each square representing 1% cover). The sizes of the sub-divisions are not important so long as it is clear what % cover 1 square represents.

Notes should also be taken on an underwater dive slate per quadrat, noting any
unusual observations or comments.

Example of sub-divided photo-quadrat

Once all photographs have been taken they will be analysed back in the lab, whereby percentage cover of coral genera will be recorded per quadrat. All photographs will be labelled and filed for future reference as permanent, visual evidence in support of quantitative data in order to accurately monitor any significant change over time.

In addition to coral genera, evidence of coral diseases such as black band or white band disease should also be recorded and monitored along with coral bleaching (If any visible).

As stated previously (section 2.3.1) transects will be placed on the exact course (marked by coloured cable ties) and re-sampled after a period of time (approx. 12 months) and compared for significant differences (Paired t-tests).

2.3.3. Fish and Invertebrate Monitoring

Again transect lines should be laid for monitoring and should each be 50m long (the same lines for corals can be used). Dive teams will swim along the transects at a constant speed counting and recording what they see at set distances either side of the transect.

Recommended band widths:

  • Small invertebrates such as molluscs should be counted 1 metre either side of the line
  • Big invertebrates such as sea urchins and star fish should counted at 2.5 metres either side of the line
  • Small reef fish such as clownfish, butterfly fish, angel fish etc should be counted at 2.5 metres either side of the line
  • Large fish such as Snappers & Groupers etc should be counted at 5 metres either side of the line

These should all be recorded on an underwater dive slate and if possible size estimations should also be calculated (practice will be required on land and underwater). For large species such as groupers, estimates should be made to the nearest 5 or 10cm. Medium/small spp. classify them as j (juveniles) and estimate to nearest 0.5cm – 1cm if possible. Size estimations greatly increase the value of a fish survey, providing good information on the status of fish stocks. Training using models or sticks on land and underwater generates a dramatic improvement of size estimates.

Note: Less experienced divers tend to over-estimate size, with experienced divers tending to underestimate size especially for large fish. Remember objects appear 25% larger/closer underwater.

For the small invertebrates, a 2 metre weighted pole can be used to swim along the transect (1m either side of line) to check the distance of animals from the line.

For the larger distances either side of the line, distances will have to be estimated by
eye, however it is best practice to lay a 10m (5m each side of transect) line at the beginning and end of each transect (possibly also in the middle). Divers can use side to side sweeping.

Species identification is paramount and thorough training and testing of volunteers and staff is critical to achieve good data. Training can be done using books, slides, videos and in the field. Underwater ID cards are essential.

Volunteers should be tested on their identification ability to assess their reliability in the field. Doubtful data, from those who do not pass the tests, should be rejected (no need to tell them).

2.4. Fish Aggregating Devices (FAD’s)

Initially 3 FAD’s will be placed in the deeper channels outside the marine park (done by professionals ). Ideally they should be over 1 kilometre apart from each other and the bases should be placed onto rocky substrate at around 200m. The fronds should sit at around 10m below the surface.

Sampling will be done every 2 weeks where fish species and size estimations will be recorded. Size estimation will be done as per the fish transect surveys in section 2.3.3. with volunteers and staff trained prior to sampling. Additionally photographs should be taken as permanent record to support data.

A circular boundary of around 20m diameter and approximately 30m deep (this may change) from the FAD should be estimated. Fish should then only be counted if they swim into or within this boundary for the duration of the dive (30mins). This allows for better quantification of data therefore more concrete statistics. Additional parameters such as visibility, water temperature, date and time should also be recorded.

In the short term:

  • Primarily the goal should be to establish a time frame of fish aggregation over a 3 year period which can be monitored bi-monthly. These can also be done for target species such as tuna etc
  • Compare effectiveness of each FAD and link effectiveness to physical parameters such as position in the channel etc
  • Compare effectiveness and species composition of FAD’s at different times of year (linked with water temperature)

In the long term:

  • Removing the fishing pressures from local people off the marine parks and onto FAD sites
  • Monitor changes in reef health and reef fish abundances
  • Monitor catches by local fishermen from FAD sites (Quota’s?)


DPSIR Framework

In order to make management decisions as a result from potential detectable change, protocol should follow the DPSIR framework approach to conservation.

DPSIR stands for: Driver; Pressure; State; Impact; Response. See Fig. 2 for examples and explanation.

The DPSIR framework approach for conservation

The DPSIR framework allows for an easy way to identify where problems/threats lie within an ecosystem. Therefore allowing for easier ways to present findings to people in authority.

For example government officials, game departments etc so as to make informed decisions and policies based on good scientific data.