mozambique channel coral reef habitat map product -...

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Earth Observation Information Products/Services for the World Bank projects

Project A: Mozambique Channel Mapping

Contract: ESRIN/Contract No. 4000103101/11/I-IW

Between COLLECTE LOCALISATION SATELLITES (CLS)

and

INSTITUT de RECHERCHE pour le DEVELOPPEMENT (IRD)

Final Report

January 2012

Mozambique Channel Coral Reef Habitat Mapping

Principal Investigator: Serge Andréfouët

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This report can be referred as:

Andréfouët S, 2012, Mozambique Channel Coral Reef Habitat Mapping. Report to Collecte

Localisation Satellites, IRD, Nouméa, January 2012. 56 pages.

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TABLE OF CONTENTS

INTRODUCTION

Principles for habitat mapping and change detection ______________________________ 5

Bibliography on habitat mapping and change detection ____________________________ 6

Material and Methods _______________________________________________________ 8

Study site _____________________________________________________________________ 8

Imagery ______________________________________________________________________ 9

Processing ___________________________________________________________________ 11

Results ___________________________________________________________________ 11

Habitat classification scheme and habitat map _____________________________________ 11

Change detection ______________________________________________________________ 16

Discussion and perspectives __________________________________________________ 16

Bibliography on Aldabra Atoll ________________________________________________ 18

Acknowledgments __________________________________________________________ 18

Material and Methods ______________________________________________________ 19

Study site ____________________________________________________________________ 19

Imagery _____________________________________________________________________ 20

Processing ___________________________________________________________________ 21

Results ___________________________________________________________________ 22




Bibliography on the Grand Récif de Toliara _____________________________________ 28



Study site ____________________________________________________________________ 31

Imagery _____________________________________________________________________ 32

Processing ___________________________________________________________________ 34

Results ___________________________________________________________________ 35





Bibliography on Mayotte Island ______________________________________________ 39


Study site ____________________________________________________________________ 41

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Imagery _____________________________________________________________________ 42

Processing ___________________________________________________________________ 44

Results ___________________________________________________________________ 44




Bibliography on Rodrigues Island _____________________________________________ 49

Habitat mapping ___________________________________________________________ 54

Change detection __________________________________________________________ 54

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INTRODUCTION

Principles for habitat mapping and change detection

This report presents for 4 sites of the Indian Ocean habitat maps achieved using recent high

resolution imagery, and a change detection analysis by comparing with historical images.

The creation of the habitat map product follows the guidelines published in Andréfouët (2008)

(Coral reef habitat mapping using remote sensing: a user vs producer perspective.

Implications for research, management and capacity building. Journal of Spatial Science

53:113-129). As such, the maps are created with a general application in mind on biodiversity,

conservation and fishery management, using simple remote sensing techniques. The objective

is thus to produce a map showing the actual complexity and remarkable features of a site, and

with a high thematic accuracy, yet using methods that could be easily transferred to non-

specialists. The habitat classification scheme is dependant on the site, in order to represent all

the specificities of this site. There is no pre-established habitat classification scheme, which

often induces a simplified view of the actual diversity present on a site.

In contrast with habitat mapping, the change detection analysis does not follow a pre-

established methodology. There are various appropriate methods used in change detection and

several publications offer examples (see bibliography below). We focus here on the changes

that may show a disturbance, and not on changes due to normal seasonal variation (algal

biomass for instance) or normal changes in water quality. Specificities here include the use of

a multi-sensor approach (Quickbird vs WorldView for instance) when doing the comparison.

Licensed historical images, if provided by other institutions, were shared on a collaborative

basis for research. Images remained the property of the image provider and license owner.

In a remote sensing context, coral reef habitats are defined in a hierarchical fashion. Four suite

of attributes are needed to fully resolve a habitat: attributes on geomorphology, cover,

architecture, and key species. Without ground-truthing, only the fist level (“geomorphology”)

can be interpreted from a remote sensing image with good accuracy (>90%). All other levels

require ancillary data acquisition through specific field work to train and validate the product.

When describing habitats at a more detailed hierarchical level, accuracy is decreasing. Since

this project aims to produce maps without resources for ground truthing, the level of choice is

the geomorphological level.

Geomorphological information, despite being the first level of habitat representation, is a rich

level from which many ecological and physical information can be derived. Geomorphology

is the result of geological, eustatic (i.e. sea-level variation), climate forcing and ecological

dominance of a site. Often, specific communities of living organisms are found on different

geomorphological zones. When using very high resolution images, fine structures can be

mapped within the main geomorphologic zones typically present in a coral reef complex:

forereefs, reef flats, passes, sedimentary terraces, lagoons.

The subsequent sections of this report present the images and methods used for each case

study, the classification scheme inferred from the images, and selected illustrations of the

products.

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Bibliography on habitat mapping and change detection

Andréfouët S (2008) Coral reef habitat mapping using remote sensing: a user vs producer

perspective. Implications for research, management and capacity building. Journal of

Spatial Science 53:113-129

Andréfouët S, Roux L, Chancerelle Y, Bonneville A (2000) A fuzzy possibilistic scheme of

study for objects with indeterminate boundaries: application to french polynesian

reefscapes. IEEE Trans Geoscience and Remote Sensing 38:257-270

Andréfouët S, Muller-Karger F, Hochberg E, Hu C, Carder K (2001) Change detection in

shallow coral reef environments using Landsat 7 ETM+ data. Remote Sensing of

Environment 79:150-162

Andréfouët S, Chagnaud N, Kranenburg C (2009) Atlas des récifs coralliens de l’Océan

Indien Ouest. Atlas of Western Indian Ocean Coral Reefs, Centre IRD de Nouméa,

Nouméa, Nouvelle-Calédonie, CD-ROM.

Elvidge CD, Dietz JB, Berkelmans R, Andréfouët S, Skirving WJ, Strong AE, Tuttle BT

(2004) Satellite observation of Keppel Islands (Great Barrier Reef) 2002 coral reef

bleaching using IKONOS data. Coral Reefs 23:123-132

Hernandez-Cruz L, Purkis S, Riegl B (2006) Documenting decadal spatial changes in seagrass

and Acropora palmata cover by aerial photography analysis in Vieques, Puerto Rico:

1937-2000 Bulletin of Marine Science 79:401-414

Hochberg EJ, Andréfouët S, Tyler MR (2003) Sea surface correction of high spatial resolution

Ikonos images to improve bottom mapping in near-shore environments. IEEE Trans

Geociences and Remote Sensing 41:1724-1729

Palandro D, Andréfouët S, Dustan P, Muller-Karger FE (2003) Change detection in coral reef

communities using the Ikonos sensor and historic aerial photographs. Int J Remote

Sensing 24:873-878

Palandro D, Andréfouët S, Hu C, Hallock P, Muller-Karger F, Dustan P, Brock J, Callahan M,

Kranenburg C, Beaver C (2008) Quantification of two decades of coral reef habitat

decline in the Florida Keys National Marine Sanctuary using Landsat data (1984-2002).

Remote Sensing of Environment 112:3388-3399

Palandro D, Andréfouët S, Muller-Karger F, Dustan P, Hu C, Hallock P (2003) Detection of

changes in coral communities using Landsat 5/TM and Landsat 7/ETM+ data. Canadian

J Remote Sensing 29:201-209

Purkis SJ, Riegl B (2005) Spatial and temporal dynamics of arabian gulf coral assemblages

quantified from remote-sensing and in situ monitoring data. Marine Ecology Progress

Series 287:99-113

Scopélitis J, Andréfouët S, Phinn S, Chabanet P, Naim O, Tourrand C, Done T (2009)

Changes of coral communities over 35 years: Integrating in situ and remote-sensing data

on Saint-Leu Reef (la Reunion, Indian Ocean). Estuarine Coastal and Shelf Science

84:342-352

Scopélitis J, Andréfouët S, Phinn S, Arroyo L, Dalleau M, Cros A, Chabanet P (2010) The

next step in shallow coral reef monitoring: combining remote sensing and in situ

approaches. Marine Pollution Bulletin 60:1956-1968

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Scopélitis J, Andréfouët S, Phinn S, Done T, Chabanet P (2011) Coral colonisation of a

shallow reef flat in response to rising sea-level: quantification from 35 years of remote

sensing data at Heron Island, Australia. Coral Reefs 30:951–965

Stoddart DR (1978) Descriptive reef terminology. In: Johannes RE, Stoddart DR (eds) Coral

reefs: research and methods. UNESCO, Paris, p 5-15.

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ALDABRA, SEYCHELLES

Material and Methods

Study site

Aldabra Atoll is an uplifted atoll, part of the Aldabra Group in the southwest of Seychelles

(Figs. 1 and 2). Aldabra has been well studied historically and in modern times, in particular

through the activity of the Seychelles Island Foundation (http://www.sif.sc), “a public trust

established to safeguard the treasures of Aldabra and promote its use purely for research and

education”. Given its high environmental value, Aldabra is a UNESCO World Heritage Area

since 1982, and an official Ramsar site since 2010. There are virtually no human activities

conducted on the atoll, except the on-going monitoring and research activities taking place

from a station located on the western side of the atoll.

Figure 1: Location of Aldabra in the Western Indian Ocean and in Seychelles. Aldabra is the largest atoll of the

Aldabra group (from Andréfouët et al. 2009)

http://www.sif.sc/

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Figure 2: Geomorphological map of Aldabra Atoll made from a Landsat image (30 meter resolution) using the

Millennium Coral Reef Mapping Project classification scheme (from Andréfouët et al. 2009).

Imagery

An archived Worldview 2 image (Fig. 3) acquired the 22nd

March 2011 was used to create the

habitat map. The targeted area is a 64 km2 polygon covering the north-western corner of the

atoll, which is the most complex area of the atoll, geomorphologically speaking.

Image parameters were:

DigitalGlobe Catalog ID 1030010009187100

Standard Orthoready Multispectral 4 bands

Spectral bands: Blue 450-510nm, Green 510-580 nm, Red 630-690 nm, NIR1 770-895 nm

Nearest Neighbour Resampling

Projection UTM WGS84, zone 38S

Spatial resolution: 2 meters

16 bits

Geotiff format

The image was of excellent quality, with no surface and atmospheric effects due to wind and

sunglint. In particular the reef front down to around 20 meters was clearly visible. Small

clouds and shadow are present in the west side. A quicklook is presented Figure 4.

As an historical reference, we had access (courtesy Dr Sarah Hamylton, U. Wollongong) to a

pansharpened RGB Quickbird image, acquired the 25th

April 2004 (ID=

1010010002E29E00), resampled at 1 meter resolution. This image was resampled at 2 meters

to match the Worldview specifications. A quicklook is presented Figure 4. The image was of

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good environmental quality, with moderate sea surface effects. Unfortunately, the pan-

sharpened products can not be corrected for sea surface effects due to the lack of near-infra

red band. Also, pan-sharpening is a process that degrades the radiometric signal with depth.

Figure 3: Quicklook of the 22

nd March 2011 WorldView2 image showing the processed area (11.5 km x 7.7 km)


th April 2004 pan-sharpened Quickbird image

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Processing

The habitat map was created using the following “user’s” flow-chart (Fig. 5), as

recommended in Andréfouët (2008). Items in grey boxes show steps independent of the

thematic scope. Arrows point to most frequent need of iterations to enhance accuracy, and

frequency of these iterative actions is ranked(1, 2, 3).

Specifically for the Aldabra image, steps 6, 7, 8, 9 and 11 were performed.

Figure 5: Typical steps recommended in Andréfouët (2008) when creating habitat maps with a user focus for

applied management and research.

Results

Habitat classification scheme and habitat map

The northwest corner of Aldabra Atoll offers a very rich geomorphological configuration due

to the presence of a deep pass and associated lagoon channels, and due to two rim sections

exposed differently to dominant wind and waves, resulting in contrasted rim structures. The

islands are wide, with mangroves, creating specific habitats with terrestrial influence in their

vicinity. In addition, the central area presents a shallow sedimentary terrace and a deeper

lagoon with numerous patch reefs and different types of reef flats depending on their position

relative to the pass.

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Given the present structure and image quality, the following classes were interpreted from the

WorldView2 2011 image. Numbers in parenthesis refer to the code used in the GIS products.

To follow Stoddart’s (1968) guidelines for implementing terminology, some of the terms used

here may be evolving in the future when distributing the products to users, by reference to

classical reef terminology and to be consistent with previous descriptions (see Bibliography

on Aldabra Atoll), in order to avoid unnecessary confusions.

Level 1:

Island (1)

Forereef (2)

Outer Reef flat (3)

Terrace (4)

Inner Lagoon Reef flat (5)

Pass (6)

Lagoon (7)

Level 2 (details each Level 1 category). A third level (level 3) can be added, when type of

benthic cover can be inferred even without ground-truthing

Island

o Freshwater ponds (1.1)

o Beach, sand and coastal non vegetated areas (1.2)

o Beach rock(1.3)

o Vegetated area (including mangroves) (1.4)

Forereef

o Deep sand plain (2.1)

o Deep low relief hardground and rubbles (2.2)

o Lower slope escarpment (2.3)

o Lower slope (2.4)

o Spur and groove zone (2.5)

o Upper slope sand pools (2.6)

o Lower slope sand pool (2.7)

o Upper platform (2.8)

Upper platform without seagrass (2.8.1)

Upper platform with seagrass (2.8.2)

o Crest (2.9)

Crest with seagrass (2.9.1)

Crest without seagrass (2.9.2)

Outer Reef flat

o Reef flat (3.1)

Rubble deposit (3.1.1)

Sand ridge (3.1.2)

Cemented rubble deposit, pavement (3.1.3)

Pavement (3.1.4)

Pavement with algae or seagrass (3.1.5)

Sand (3.1.6)

Sand with seagrass (3.1.7)

Heterogeneous (scattered corals) (3.1.8)

Heterogeneous 2 (uplifted?) (3.1.9)

o Spillways (include coral zones) (3.2)

o Shallow pass (3.3)

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o Channel (3.4)

Terrace

o Sedimentary terrace under terrestrial and mangrove influence (4.1)

o Sand ridge (4.2)

o Sedimentary terrace (may include scattered coral colonies, algae, etc.) (4.3)

Sedimentary terrace with seagrass (4.3.1)

Sand terrace (4.3.2)

Sedimentary terrace (may include scattered coral colonies, algae,

seagrass, etc.) (4.3.3)

o Sedimentary terrace under spillway influence (hard-bottom present) (4.4)

o Low relief patch reef (4.5)

o Island terrace with numerous coral colonies (4.6)

o Terrace with numerous coral colonies (4.7)

Inner Lagoon Reef flat

o Pass reef flat (high current) (5.1)

o Basin (5.2)

o Reef flat (5.3)

Sand-rubble (5.3.1)

Heterogeneous (with corals) (5.3.2)

o Reticulated reef flat (5.4)

Pass

o Pass (6.1)

o Pass slope (6.2)

o Subtidal patch (6.3)

o Channel (6.4)

o Channel patch reef (subtidal and intertidal) (6.5)

Lagoon

o Deep lagoon (7.1)

o Shallow lagoon with constructions (7.2)

o Escarpment (7.3)

o Subtidal patch reef (include halo of rubbles) (7.4)

o Patch reef terrace (7.5)

o Patch reef edge and slopes (include halo of rubbles) (7.6)

The map product includes in its full complexity 53 classes representing the geomorphological

diversity of the studied portion of Aldabra, and for some classes, additional information on

benthic cover, mostly when seagrass beds are present.

We point to the usual problem of the exact definition of boundaries for several, gradually

changing, classes across the reefs flats and terraces. There are uncertainties, and sometimes

subjectivity, on where to put for mapping purposes a crisp boundary in an area which is

gradually changing, thus with fuzzy indeterminate boundaries.

Below (Figs 6-7), views of the final classification habitat map are shown. The colours

assigned to each class is the average of the Red-Green-Bands digital counts for the extent of

the class, yielding a color scheme that mimicks the true color RGB image. Figures 6 and 7

illustrate the level of details (spatial and thematic) achieved for the geomorphological product.

For actual labels and surface areas for each of the classes, see the corresponding GIS files.

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Figure 6: Geomorphological classification (top) and true color (bottom) views of Aldabra north-west corner. The

classification includes 53 classes.

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Figure 7: Geomorphological classifications (rigth) and true color (left) views of Aldabra north-west corner. Panel

A illustrates the western reef flats and forereefs. Panel B illustrates the lagoon patch reefs, pass channels and reef

flats.

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Change detection

It is pointed out that purely analytical, physics-based, methods performed on pan-sharpened

images are difficult, and gives noisy products. The thresholds in radiometric differences

needed to conclude on the existence of a significant change, above the noise level, are high.

Therefore, often, these changes associated to high spectral differences can be visually

detected. No reliable change detection could be performed on the forereefs given the sea

surface effects on the 2004 Quickbird image.

Visual examination of the image pair in the shallow areas shows very little significant

changes between 2004 and 2011 (Fig. 8). Changes are noted on the western outer reef flat

(Fig. 8, panel A), for the extent and boundaries of seagrass beds (class 3.1.7) but without

obvious loss. In addition, the sedimentary terraces (4.3) show higher algal coverage in April

2004 than in March 2011 (Fig. 8, panel B), but this is certainly related to normal algal

biomass fluctuation. All reef flat areas do not suggest any changes, except minor sediment

movements (Fig. 8, panel C).

We conclude that no significant changes in structures and cover have occurred in Aldabra

between 2004 and 2011, for the studied area. However, it is pointed out that benthic changes

may be possible even if non detectable here. This includes coral mortality or coral growth

along reef flats. The lack of patterns worthy of investigations do not call for further

registration and analytical methods (e.g., after image radiometric normalization using physics

based approach, or through inter-calibration using pseudo-invariant features).

Discussion and perspectives The mapping of Aldabra is a favourable case-study given the image quality and the wide

shallow areas in very clear waters, suitable for remote sensing assessment. However, it is a

complex area and the mapping of gradually changing reef flat and terraces is difficult. The

geomorphologic complexity in 53 classes is high considering an atoll case study. However,

this is a fairly standard richness for an island reef complex., or for large continental

complexes.

Clearly, with adequate ground-truthing the different geomorphological zones mapped here

could be mapped in greater detail (beyond Level 2 and Level 3) to provide habitat

characterization using at least geomorphology, benthic cover and architecture. Limited recent

ground-truthing exists, and is currently submitted to publications (Hamylton et al. submitted).

Further, it should be possible to extend the mapping to the entire atoll.

The geomorphological mapping of the portion of Aldabra processed here took approximately

5 days of work full time. Further work on documenting the classes with the existing

references is needed, in order to finalize the description of the classes.

It is proposed to provide this product to the Seychelles Island Foundation to stimulate use of

the products and receive feedbacks.

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Figure 8: Three examples of paired images (each covering 1 km x 1.5 km) between 2004 and 2011. Minor

changes are visible (yellow arrows) on the A and B pairs. They reveal changes in flora coverage through

movement of seagrass beds (A), and development of algae (B, possibly cyanobacteria). The panel C do not

suggest any significant changes.

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Bibliography on Aldabra Atoll

Braithwaite CJR, Taylor JD, Kennedy WJ (1973) The evolution of an atoll: The depositional

and erosional history of Aldabra, Philos Trans R Soc Lond B 266: 307-340

Farrow GE, Brander KM (1971) Tidal studies on Aldabra. Philos Trans R Soc Lond B 260

93-121

Fryer JCF (1910) The structure and formation of Aldabra and neighbouring islands -- with

notes on their fauna and flora. Trans Linn Soc 14:397-442

Hamylton S, Hagan AB, Spencer T. Submitted. Spatial modelling of benthic cover using

remote sensing data in the Aldabra lagoon, Western Indian Ocean.

Hamylton S, Hagan AB, Spencer T. In press. Observations of dugongs at Aldabra Atoll,

Western Indian Ocean: lagoon habitat mapping and cluster analysis of sighting records.

International Journal of Geographical Information Science

Macnae W (1971) Mangroves on Aldabra, Phil Trans R Soc Lond B 260: 237–247

Potts M, Whitton BA (1980) Vegetation of the intertidal zone of the lagoon of Aldabra, with

particular reference to the prokaryotic communities. Proc R Soc London B208:13-55

Price JH (1971) The shallow sublittoral marine ecology of Aldabra. Phil Trans R Soc Lond B

260:123-171

Stoddart DS, Taylor JD and Fosberg, FR (1971) Geomorphology of Aldabra Atoll. Philos

Trans R Soc Lond B 260:31–65

Taylor JD (1971) Intertidal zonation at Aldabra Atoll. Phil Trans R Soc Lond B 260:173-213

Taylor JD (1978) Faunal response to the instability of reef habitats: Pleistocene molluscan

assemblages of Aldabra Atoll. Phil Trans R Soc Lond B 21:1-30

Trudgill S (1972) Process studies of limestone erosion in littoral and terrestrial environments

with special reference to Aldabra Atoll, Indian Ocean. Unpublished PhD thesis,

University of Bristol, UK. 398p.

Acknowledgments We acknowledge Dr Sarah Hamylton, University of Wollongong, Australia, for providing the

2004 Quickbird image for this pilot study, and for sharing references.

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TOLIARA, MADAGASCAR


Study site

The Grand Recif de Toliara (or GRT) is a 17 km long barrier reef, off the coast of the city of

Toliara (Figs. 1 and 2). The GRT is a remarkable site. It used to be one of the most studied

reef site worldwide, with numerous extensive descriptive, quantitative and functional

researches. The GRT has been well studied historically in the 1960s and early 1970s and then

again in modern times (especially past 2004) aftr an interruption around the mid-1970S.

Actors include in particular governmental agencies (Intitut Halieutique et des Sciences

Marines), international research institutions (IRD, ECOMAR/Université de la Réunion, JCU),

donors (Western Indian Ocean Marine Science Association) and conservation NGOs

(Wildlife Conservation Society, Blue Ventures Conservation, etc.). As a result of the large

historical sampling efforts, the GRT is still identified as the most biodiverse reef in the

Western Indian Ocean. The GRT is subjected to high human pressure through fishing

activities performed year long using very low-tech and destructive techniques. A massive

degradation of the reef conditions has been reported in the early 1980s.

Figure 1: Location of the Grand Recif de Toliara in the Western Indian Ocean and in Madagascar. The processed

area is the black square on the southern tip of the GRT. The geomorphological information for the region was

interpreted from a Landsat image (30 meter resolution) using the Millennium Coral Reef Mapping Project

classification scheme (from Andréfouët et al. 2009).

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Imagery

An archived Worldview 2 image (Fig. 3) acquired the 5th

May 2011 was used to create the

habitat map. The targeted area is a 28.8 km2 polygon covering the southern tip of the GRT.


DigitalGlobe Catalog ID 103001000A5F3000






16 bits

Geotiff format

The image was of excellent quality, with no surface and atmospheric effects due to wind and

sunglint. In particular the reef front and the lagoon inner slope down to around 20 meters were

clearly visible. A quicklook is presented Figure 3.

As an historical reference, we had access to a number of image sources:

A Quickbird Standard Multispectral image acquired the 18th

March 2006

(ID=203001001534DE00), at 2.4 meter resolution. This 2011 WorldView image was

resampled at 2.4 meters to match the Quickbird specifications. A quicklook is

presented Figure 4. The image was of fair environmental quality, with significant

waves breaking along the crest and obstructing the forereefs.

Historical vertical aerial black and white photographs were also available. No

metadata exist. First, a low altitude 1962 series at 1/10000 from Institut Géographique

National provided good quality data, after scanning at 300 dpi. Second, a 1973 high

altitude series was inspected, but it provided limited quality data, partly due to image

saturation. The exact days of acquisition remain uncertain for both series.

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th May 2011 WorldView2 image showing the processed area ( 5km x 7km)

Figure 4: Quicklook of the 18th

March 2006 Quickbird image, extraction matching the WorldView2 image

coverage (Fig.3)

Processing

The habitat map was created using the following “user’s” flow-chart (Fig. 5), as

recommended in Andréfouët (2008). Items in grey boxes show steps independent of the

thematic scope. Arrows point to most frequent need of iterations to enhance accuracy, and

frequency of these iterative actions is ranked(1, 2, 3).

Specifically for the GRT image, steps 6, 7, 8, 9 and 11 were performed.

22



The change detection analysis was performed here considering the 2011 WorldView2 image,

as well as the 2006 Quickbird image, and the 1973 and 1962 black and white aerial

photographs. We focussed on areas where good coverage was available for all the images,

across a 50 year long time series (results in Fig. 7). The two multispectral images were

radiometrically normalized using the digital counts of the WoldView2 image as reference. All

images were interpreted to map reef flat features showing degradation. The most visible loss

occurred in the “reef flat with transverse coral stripes” area, on the outer reef flats. This work

also benefited from limited ground-truth data collected in 2007 and available for the southern

part of the GRT. Ground-truth data includes quantitative measures of benthic coverage on

various habitat locations selected using the 2006 Quickbird image.

Results


The southern tip of the GRT offers a moderately rich geomorphological configuration, typical

of a wide barrier reef. Main geomorphological zones include the forereef, boulder tract and

the reef flat which shift lagoonward into a seagrass-dominated sedimentary terrace. The inner

lagoon slope presents several patch reefs and low relief hard-ground.

23

Given the present structure and image quality, the following classes were interpreted from the


To follow Stoddart’s (1968) guidelines for implementing terminology, some of the terms used

here may be evolving in the future when distributing the products to users, by reference to

classical reef terminology and to be consistent with previous descriptions (see Bibliography

on GRT), in order to avoid unnecessary confusions.

Level 1:

Forereef (2)

Outer Reef flat (3)

Terrace (4)


Pass (6)

Lagoon (7)



Forereef

o Lower slope (2.4)



o Pass (2.11)

Outer Reef flat

o Reef flat (3.1)


Pavement (3.1.4)



Transverse stripes (3.1.10)

o Sand pools and basin (3.5)

o Boulder tract (3.6)

Terrace

o Sand ridge (4.2)


Sedimentary terrace with dense seagrass (4.3.1)


Sedimentary terrace (may include scattered coral colonies, algae, etc.)

(4.3.3)

Sand terrace and shallow basin with isolated coral heads (4.3.4)

Sedimentary terrace with medium density seagrass (4.3.5)


o Pavement patch (4.8)


o Reef flat (5.3)


Pass

o Pass slope (6.2)

Lagoon

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7.6.1 Patch reef edge with seagrass

o Inner slope (7.8)

Sedimentary inner slope (7.8.1)

Seagrass inner slope (7.8.2)

o Coral heads on inner slope (7.9)

The map product includes in its full complexity 26 classes representing the geomorphological

diversity of the studied portion of the GRT, and for some classes, additional information on

benthic cover.





Below (Figs 6), views of the final classification habitat map are shown. The colours assigned

to each class is the average of the Red-Green-Bands digital counts for the extent of the class,

yielding a color scheme that mimics the true color RGB image. Figure 6 illustrate the level of

details (spatial and thematic) achieved for the geomorphological product. For actual labels

and surface areas for each of the classes, see the corresponding GIS files.

25

Figure 6: Geomorphological classification (top) and true color (bottom) views of the processed area (5km x

7km). The classification includes 26 classes.

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Change detection

No reliable change detection could be performed on the forereefs given the sea surface effects

on the 2006 Quickbird image.

Between 2006 and 2011, several changes are visible in the back reef and inner slope of the

south of the GRT. These are related first to sediment dynamics. The 2006 image has a layer of

sediment partially covering the pseudo-invariant features from these areas. Sediment have

also covered in 2006 several seagrass beds and hardgrounds which are more clearly visible

again in 2011, while in the same time the sand bar parallel to the lagoon slope was narrower

in 2006 than 2011 (and 1962 and 1973). In addition, changes due to cyanobacteria

development on sandy bottom are visible. Finally, erosion of dead coral framework is

apparent on the reef flat with transverse stripes area, next to the reef crest.

Sediment dynamics and back reef changes between 2006 and 2011 can be explained by the

passage of the category 3 cyclone Boloetse, passing next to Toliara 4th

February 2006, just

few weeks before the Quickbird image acquisition. After Boloetse, no cyclones are reported.

Boloetse came from the west as a category 4, thus with likely high wave energy which could

have stirred sediments in the inner slope and lagoons, resulting in visible deposits on the 2006

image. In 2011, five years of regular tide and wave driven flushing of the reef flat would have

removed these sediments, and allow the re-widening of the long sand bar parallel to the

lagoon slope.

Boloetse could be responsible also for the loss of the transverse strips. Similar loss was noted

by Scopélitis et al. (2010) after the passage of cyclone Erika in New Caledonia in 2003.

However, the reduction of these stripes needs to be understood in a larger temporal context,

since the image time series reveal continuous loss since 1962. The 2007 survey suggests with

3 stations that these stripes were between 2006 and 2011 dead coral framework (coral

cover<5%), cemented by coralline algae, and with sometimes significant coverage (15-50%)

by green and brown macroalgae (Halimeda, Ulva, and Sargassum). Similar loss of stripes are

also visible between 1962 and 1973, and afterwards, but at a time where the coral were

thriving and made continuous live carpets (Pichon 1978).

The time series of images clearly reveal modifications of geomorphological zones and the loss

of coral communities throughout the GRT reef flats between 1962 and 2006/2011. Most

spectacular are the reef flats with transverse stripes (Fig. 7), which are easily visible in shape

and color. Between1962 and 2011, 77% of the initial coral stripes surface was lost (0.45 km2)

for the area shown Figure 7.

A separate study (Andréfouët et al. in prep.) strongly suggests that the cause of the changes is

due to destructive fishing practices, with a high frequentation of fishermen tramping over,

breaking and moving coral colonies in search of benthic invertebrates. The rate of destructive

fishing has increased since the early 1970s and it was well quantified by Salimo (1997). The

rates of loss of coral colonies are compatible with the patterns seen on the images across time.

We conclude that significant changes in structures and cover continue to occur on the GRT,

especially on the outer reef flat. However, it is pointed out that other benthic changes may be

possible even if non detectable here. This includes coral mortality or coral growth along reef

flats.

27

Figure 7: The processed area for change detection between 1962 and 2011 is shown on the upper left panel. All

available imagery for change detection are shown on the upper right. For 2006 and 2011, the availability of

multispectral imagery allows showing both color and black and white views. 2006 black and white panels

correspond to the green band which is used to mimic the black and white aerial photographs from 1962 and

1973. Letter “A” refers to the historical presence of reef flat with transverse coral stripes (dark). Arrows indicate

the location of pseudo-invariant features. Below, maps of the changes in the extent of the reef flat with

transverse coral stripes. or the year 1962, the extent of the habitat is shown as a red contour overlaid on the aerial

photographs. On subsequent years, this initial contour is filled in red, and the current year contour is shown

(yellow in 1973, green in 2006 and white in 2011), overlaid on the last image available (2006 for zone 1 and 2,

2011 for zone 3). For clarity, not all contours can be shown overlaid on a single image.

28

Discussion and perspectives The mapping of the Grand Recif de Toliara is a favourable case-study given the image quality

and the wide shallow areas in very clear waters, suitable for remote sensing assessment.

However, it is a complex area and the mapping of gradually changing reef flat and terraces is

difficult. The geomorphologic complexity is normal considering a barrier reef case study.

The change detection story is remarkable because 50 years of information were available,

albeit not in a continuous manner. The environmental and socio-economic drivers of the

changes are beyond the scope of the present remote sensing assessment, but they have been

investigated and discussed in two manuscripts in preparation. Given the wealth of data

available on this reef, it needs to be considered for further work in the Mozambique Channel.

Given the availability of adequate ground-truthing for most of the different geomorphological

zones, the GRT could be mapped in greater detail (beyond Level 2 and Level 3) to provide

habitat characterization using at least geomorphology, benthic cover and architecture. For this

purpose, the acquisition of the rest of the GRT coverage with the WorldView2 image used

here is required to have an updated view of the reef, as well as a clear view of the forereefs.

The geomorphological mapping of the portion of GRT processed here took approximately 2

days of work full time. The change detection took an additional 3 days, however, this does not

include the data mining and efforts required to collect and scan the aerial photographs. This

took nearly 3 years of efforts. This also does not include the field work conducted in the

austral winter 2007.

Bibliography on the Grand Récif de Toliara

Andréfouët S, Guillaume MMM, Delval A, Rasoamanendrika FMA, Blanchot J, Bruggemann

JH (in prep). Changes on the reef flat habitats of the Grand Récif of Toliara (SW

Madagascar) spanning 50 years. Submitted.

Ateweberhan M, McClanahan TR (2010) Relationship between historical sea-surface

temperature variability and climate change-induced coral mortality in the western Indian

Ocean. Marine Pollution Bulletin 60, 964–970.

Ateweberhan M, McClanahan TR, Graham NAJ, Sheppard CRC (2011) Episodic

heterogeneous decline and recovery of coral cover in the Indian Ocean. Coral Reefs,

DOI 10.1007/s00338-011-0775-x

Bellemans M (1989) Résultats de l'enquête cadre des pêcheries traditionnelles côtières

Malgaches, 1987/1988. Bilan diagnostic des caractéristiques structurelles. Projet

PNUD/FAO/MAG/85/04. Rapp

Bruggemann J.H., Rodier M., Guillaume M.M.M., Andréfouët S., Arfi R., Cinner J., Pichon

M., Ramahatratra F., Rasoamanendrika F.M.A., Zinke J., McClanahan T.R.. Wicked

social-ecological problems forcing unprecedented change on the latitudinal margins of

coral reefs: the case of southwest Madagascar. Submitted.

Cinner JE (2007) The role of taboos in conserving coastal resources in Madagascar.

Traditional Marine Resource Management and Knowledge Information Bulletin 15:15-

23

29

Cinner JE, Wamukota A, Randriamahalzo H, Rabearisoa A (2009) Toward institutions for

community-based management of inshore marine resources in the Western Indian

Ocean. Marine Policy 33:489-496

Clausade M, Gravier N, Picard J, Pichon M, Roman M-L, Thomassin B, Vasseur P, Vivien M

& Weydert P (1971). Coral reef morphology in the vicinity of Tuléar (Madagascar):

contribution to a coral reef terminology. Téthys Supplément 2:1-74

Faure G, Guillaume M, Payri C, Thomassin B, Van Praet M & Vasseur P (1984). Sur un

phénomène remarquable de blanchiement et de mortalité massive des Madréporaires

dans le complexe récifal de l'île Mayotte (S.W. océan Indien). C.R. Acad. Sc., 299 sér.

III (15) :637-642

Gabrié C, Vasseur P, Randriamiarana H, Maharavo J, Mara E (2000) The coral reefs of

Madagascar. In : McClanahan TR, Sheppard CRC, Obura DO. Coral reefs of the Indian

Ocean. Their ecology and conservation. Oxford University Press. pp 411-443

Gaudy R (1973) Les copépodes pélagiques de la région de Tuléar (Madagascar). 1. –

L’environnement physique. Téthys 5:117-132

Harmelin-Vivien ML (1979) Ichthyofaune des récifs coralliens de Tuléar (Madagascar :

Ecologie et relations trophiques. Thesis manuscript, Université d’Aix-Marseille II, 165

pp + appendix

Harris A, Manahira G, Sheppard A, Gough C, Sheppard C (2010). Demise of Madagascar’s

once Great Barrier Reef – change in coral reef condition over 40 years. Atoll Res Bull

574: 1-16

Koechlin B (1984) Une communauté de semi-nomades marins de Madagascar: processus

historique et changements irréversibles de l’écosystème Vezo. In : Gunda B (ed.) The

fishing culture of the world. Maison d’édition de l’Académie des Sciences de Hongrie:

745-776

Kuleshov Y, Qi L, Fawcett R, Jones D (2008) On tropical cyclone activity in the Southern

Hemisphere: trends and the ENSO connection. Geophysical Research Letters 35:

(L14S08) doi:10.1029/2007GL032983.

Lagouin Y (1959) La pêche côtière malgache dans la région de Tuléar. Bull Madagascar

153:95-106

Laroche J, Ramananarivo N (1995) A preliminary survey of the artisanal fishery on coral

reefs of the Tuléar Region (southwest Madagascar) Coral Reefs 14: 193-200

Laroche J, Razanoelisoa J, Fauroux E, Rabenavanana MW (1997) The reef fisheries

surrounding the south-west coastal cities of Madagascar. Fisheries Management and

Ecology 4:285-299

Maina J, de Moel H, Vermaat JE, Grove C, Bruggemann JH, Guillaume MMM, Madin J,

Mertz-Kraus R, Zinke J Linking coral river runoff proxies with climate variability,

hydrology and land-use in Madagascar catchments. (submitted to Global Change

Biology)

McClanahan TR, Ateweberhan M, Omukoto J, Pearson L (2009) Recent seawater temperature

histories, status, and predictions for Madagascar's coral reefs. Marine Ecology Progress

Series 380:117-128

McClanahan TR, Graham NAJ, MacNeil MA, Muthiga NA, Cinner JE, Bruggemann JH,

Wilson SK (2011) Critical thresholds and tangible targets for ecosystem-based

30

management of coral reef fisheries. Proceedings of the National Academy of Sciences

doi/10.1073/pnas.1106861108

Pichon M (1978) Recherches sur les peuplements à dominance d’anthozoaires dans les récifs

coralliens de Tuléar (Madagascar). Atoll Res Bull 222 : 1-447

Randriambololona CJM (2009) Résultats de l’enquête cadre dans la zone du projet d’Appui

aux Communautés des Pêcheurs de Toliara (PACP). Rapport Final. Ministère de

l’agriculture, de l’élevage et de la pêche.

Rodier M, Arfi R, Chevalier C, Blanchot J, Montel Y , Rougier G. Local and large scale

factors affecting hydrography and plankton variability in the Toliara coral lagoon

(Madagascar, Indian Ocean). (submitted)

Salimo (1997) Etude de la pêche – collecte à pied sur les platiers du Grand Récif de Tuléar

(Sud-Ouest de Madgascar). Report DEA d’Océanologie appliquée, IH.SM/Université de

Tuléar.

Salomon JN (1986) Le Sud-Ouest de Madagascar, étude de géographie physique. Thèse de

Doctorat d'Etat. Université d'Aix-Marseille.

Vasseur P, Gabrié C, Harmelin-Vivien M (1988) Tuléar (SW Madagascar): mission

scientifique préparatoire pour la gestion rationnelle des récifs coralliens et des

mangroves dont des mises en réserve. Rapport définitif EPHE, RL31-1988, 213pp

Vasseur P, Thomassin BA, Randriamanantsoa B, Pichon M (2000) Main changes in the last

30-40 years on coral reefs and coastal areas induced mostly by human pressure: the

Tuléar region example (SW Madagascar, Indian Ocean). 9th International Coral Reef

Symposium

Zinke J, Dullo W-C, Heiss GA, Eisenhauer A (2004) ENSO and Indian Ocean subtropical

dipole variability is recorded in a coral record off southwest Madagascar for the period

1659-1995. Earth and Planetary Science Letters 228: 177-194

Zinke J, Pfeiffer M, Timm O, Dullo W-C, Brummer GJA (2009) Western Indian Ocean

marine and terrestrial records of climate variability: a review and new concepts on land-

ocean interactions since AD 1660. International Journal of Earth Sciences 98,

doi:10.1007/s00531-008-0365-5

Acknowledgments The change detection analysis using aerial photographs is a contribution of the MASMA-GRT

programme funded by the WIOMSA. This project has also provided the 2006 Quickbird

image. As such we thank the PI Heinrich Bruggeman and Mireille Guillaume for their

support, as well as Adrien Delval and Fara Rasoamanendrika for the 2007 ground-truth data.

We thank Jean Blanchot, Alain Bidar, Olivier Gerriet and Bernard Thomassin for providing

and scanning most of the 1962 IGN aerial photographs.

31

MAYOTTE, FRANCE


Study site

Mayotte is an oceanic island, between Madagascar and the other Comoros Islands (Figs. 1 and

2). Compared to many other Indian Ocean sites, Mayotte coral reefs have been well studied,

with a wealth of information found mostly on grey literature, produced to document

monitoring activities and plans to establish new protected areas. Mayotte has been proposed

for this mapping project given the wealth of image data already available for Mayotte, and

given existing past ground-truthing data.

Figure 1: Location of Mayotte in the Western Indian Ocean (from Andréfouët et al. 2009).

32

Figure 2: Geomorphological map of Mayotte Island made from a Landsat image (30 meter resolution) using the

Millennium Coral Reef Mapping Project classification scheme (from Andréfouët et al. 2009). The 65 km2

processed area is bounded by the black polygon.

Imagery

The targeted area is a 65 km2 polygon covering a eastern section of the forereef, reef and

lagoon, including the Pamandzi Island, and the reef between the airport and the area known as

the “Passe en S”, currently a protected area, and an area with good data coverage. An

archived Worldview 2 image (Fig. 3) acquired the 18 November 2100 was purchased for this

project. This was the best image recent image available and looked workable from the

quickook, despite displaying significant surface effects due to strong wind. This could be

partially corrected but less than expected, and image quality remained too poor. We also

acquired, from the GEOSUD consortium (http://geosud.teledetection.fr/), a Rapid-Eye image,

acquired 11 September 2010 and made available late January 2012. Rapid-Eye imagery offer

multispectral (5 bands) data, at 6.5 meter spatial resolution. The image does not suffer from

surface effects but noise and lower resolution made it still a second choice compared to our

first historical IKONOS image.It was decided to keep the historical IKONOS-derived habitat

interpretation (Andréfouët and Payri, 2001) as the reference, and try to infer changes with the

new World-View and Rapid-Eye acquisitions. The IKONOS image was acquired 31st August

2000. This narrows the scope of the work to the south of the Pamandzi Island


For the World-View 2 image:

DigitalGlobe Catalog ID 10300100076A4A00



http://geosud.teledetection.fr/

33




16 bits

Geotiff format

For the Rapid-Eye image (Figure 4):

Rapid-Eye catalog ID: 4501384

Sensor: RE1

Standard Multispectral 5 bands, Level 1B

Spectral bands: Blue 440-510nm, Green 520-590 nm, Red 630-685 nm, Red-Edge 690-

730 nm, NIR1 760-850 nm

Geographic projection WGS84 (reprojected as UTM WGS 84, 38S, triangulation and

nearest neighbour using ©ENVI 4.3 software)

Spatial resolution: 6.5 meters at nadir

16 bits (12 bits true dynamics)

NITF 2.0 format

As an historical reference, we used the IKONOS multispectral standard image (Figure 5).

Geoeye ID: Rapid-Eye catalog ID: 4501384

Sensor: IKONOS-2

Standard Multispectral 4 bands


Projection as UTM WGS 84, 38S

Spatial resolution: 4meters

16 bits

Geotiff format


th November 2010 WorldView2 image showing the processed area.

34


th September 2010 Rapid-Eye image. This image covers the entire island.

Figure 5: Enhanced quicklook of the 31

st August 2000 IKONOS-2 image

Processing

The habitat map was created with the IKONOS-2 image using the following “user’s” flow-

chart (Fig. 6), as recommended in Andréfouët (2008).

35



Items in grey boxes show steps independent of the thematic scope. Arrows point to most

frequent need of iterations to enhance accuracy, and frequency of these iterative actions is

ranked (1, 2, 3). Specifically for the Mayotte image, steps 3, 6, 7, 8, 9 and 11 were performed.

The change detection analysis was performed here considering the 2010 Rapid-Eye image,

versus the IKONOS-2 image used as a reference.

Results


The studied area of Mayotte offers a moderately rich geomorphological and benthic

configuration with 18 mapped classes. Numbers in parenthesis refer to the code used in the

GIS products. To follow Stoddart’s (1968) guidelines for implementing a reef terminology,

some of the terms used here may be evolving in the future when distributing the products to

users, by reference to classical reef terminology and to be consistent with previous

descriptions (see Bibliography on Mayotte), in order to avoid unnecessary confusions.

Level 1:

Forereef (2)

Outer Reef flat (3)

Terrace (4)

Inner Reef flat (5)

Pass (6)

Lagoon (7)

36



Forereef

o Lower slope (2.4)



Outer Reef flat

o Reef flat (3.1)



Rodoliths, rubble, algae (3.1.11)

Rodoliths, rubble, coral (dead or live) (3.1.12)

Terrace









o Reef flat (5.3)

Sand-rubble (5.3.1)


Pass

o Coral slope (6.2)

o Soft bottom slope (6.6)

Lagoon

o Deep lagoon with constructions (7.7)

o Shallow lagoon (7.10)





Below (Figs 7), views of the final classification habitat map are shown. The colours assigned

to each class is the average of the Red-Green-Bands digital counts for the extent of the class,

yielding a color scheme that mimics the true color RGB image. For actual labels and surface

areas for each of the classes, see the corresponding GIS files.

37

Figure 7: Geomorphological and benthic classification (left) and true color (right) views of Mayotte processed

area (3.6 x 5.4 km). The classification includes 18 classes.

Change detection

The pair of images displays significant variation between the two images for the seagrass bed

areas on the reef flats (Fig. 8), with the complete loss of two of the mapped classes (4.3.1 and

4.3.5) and partial loss of seagrasses for a third class (4.3.3). The widespread differences

visible on the shallow areas throughout the studied area are due mostly to different algal

coverage and possibly movement of sediments along the back reef, and possible loss of coral

communities. It is not possible to conclude on occurrence of changes on the coral patches

located on the lagoon side (inner spur-and-groove system) and along the forereef.

The differences between images suggest a loss of seagrass habitats, along the pass, of 0.4 km2,

including the dense Thalassodendron beds (Figure 8). Additional loss on the reef flats, with

scattered small patches of various seagrass species, including Thalassodendron, are estimated

as less than 0.1 km2 for the processed area shown Figure 7.

38

Figure 8: Paired images (each covering 2.8 km x 3.0 km) between 2000 and 2010. They reveal changes in flora

coverage, with significant loss of seagrass beds (dominated by species Thalassodendron ciliatum in 2000).

It seems that the loss of seagrass beds occurred during 2009, and in a fairly quick fashion.

Other large beds, in the north of the Pamandzi island, also located on the barrier reef, are

missing on the 2010 Rapid-Eye or World-View 2 images. The mechanisms that could have

caused these losses are unknown.

Discussion and perspectives The mapping of Mayotte is a favourable case-study given the wide shallow areas in clear

waters, suitable for remote sensing assessment. The geomorphologic and benthic complexity

in 21 classes is moderate considering an oceanic island case study, with barrier habitats.

The geomorphological mapping of the portion of Mayotte processed here took approximately

3 days of work full time. Further work on documenting the classes with the existing

references is needed, in order to finalize the description of the classes.

The seagrass loss evidenced here warrants further investigations, from remote sensing to

assess the loss for the entire island, but also in situ to try understanding what could happen.

No obvious factors (gurricanes, pollution, human constructions …) can be related to this

event. Pathogens seem more likely.

39

Acknowledgments The Rapid-Eye image was provided by the GEOSUD Equipex consortium.

Bibliography on Mayotte Island

Andréfouët S, et al. (2003) Multi-sites evaluation of IKONOS data for classification of

tropical coral reef environments. Remote Sensing of Environment 88:128-143

Arnaud JP et al. (2009) Richesses de Mayotte - Parc naturel marin de Mayotte : les

orientations. Mission d’étude pour la création d’un parc naturel marin à Mayotte,

Agence des aires marines protégées, 28 pp.

Ciccione S (2004) Mayotte, biodiversité et évaluation patrimoniale. Les tortues marines de

Mayotte. Statut écologique et conservation. Inventaire du patrimoine. Kelonia/DAF-

CDM, 19 p.

Chabanet, P. (2002). Coral reef fish communities of Mayotte (Western Indian Ocean) two

years after the impact of the 1998 bleaching event. Mar. Freshwater Res., 53, 107-113

Dinhut V, Nicet JB, Quod JP (2008) Monitoring and health state 2007 of coral reefs of

Mayotte Island. Revue D’Ecologie-La Terre et La Vie 63:103-114

Durand D, Thomassin BA (1992) Les récifs frangeants de l’île de Mayotte (« Grande Terre

»): état des platiers et du sommet des pentes externes en 1989-1990 ; bilan de santé

global, 66pp.

Gigou A, Dinhut V, Arnaud JP (2009) Richesses de Mayotte – Parc naturel marin de Mayotte:

un patrimoine naturel d’exception, Mission d’étude pour la création d’un parc naturel

marin à Mayotte, Agence des aires marines protégées, 58 pp.

Hochberg E, Atkinson M, Apprill A, Andréfouët S (2004) Spectral reflectance of coral. Coral

Reefs 23:84-95

Hochberg EJ, Atkinson MJ, Andréfouët S (2003) Spectral reflectance of coral reef bottom-

types worldwide and implications for coral reef remote sensing. Remote Sensing of

Environment 85:159-173

Loricourt A, (2005). Etude des herbiers à phanérogames marines à Mayotte, rapport de stage

de Master 2 Dynamique des Ecosystèmes Aquatiques, Univ. de Pau et des Pays de

l’Adour, 62 pp.

Pareto-Larvam, Projet de réserve naturelle du Lagon de l’Ile de Mayotte (canal du

Mozambique). Cartographie géomorphologique et écologique de 6 zones remarquables.

7 Rapports, DAF-SEM, Mayotte.

Quod, JP, Bigot L, Dutrieux E, Maggiorani JM, & Savelli A (1995). La réserve de la Passe en

S (Ile de Mayotte). Expertise biologique et cartographie des peuplements benthiques.

Report ARVAM/IARE/SCE DES PECHES, Sainte Clotilde.

Richmond, M. D. A guide to the seashores of Eastern Africa and the western Indian Ocean

islands. SIDA.

Taquet C, Taquet M, Dempster T, Soria M, Ciccione S, Roos D, Dagorn L (2006) Foraging of

the green sea turtle Chelonia mydas on seagrass beds at Mayotte Island (Indian Ocean),

determined by acoustic transmitters. Marine Ecology Progress Series 306:295-302

40

Thomassin BA et al., (1998). Les récifs coralliens frangeants de l’île de Mayotte (« Grande

Terre »): réexamen de l’état de santé et bilan de la qualité des eaux côtières pour le

compte de la DAF. GiS Lag May, 81p.

Zinke J, Reijmer JJG, & Thomassin BA (2001). Seismic architecture and sediment

distribution within the Holocene barrier reef lagoon complex of Mayotte (Comoro

Archipelago, SW Indian Ocean). Paleogeogr. Paleoclim. Paleoecol., 175, 343-368.

Zinke J, Reijmer JJG, Thomassin BA, Dullo WC, Grootes PM, Erlenkeuser H (2003)

Postglacial flooding history of Mayotte lagoon (Comoro Archipelago, southwest Indian

Ocean). Marine Geology 194:181-196

Zinke J, Reijmer JJG, Thomassin BA (2003) Systems tracts sedimentology in the lagoon of

Mayotte associated with the Holocene transgression. Sedimentary Geology 160:57-79

41

RODRIGUES, MAURITIUS


Study site

Rodrigues is an oceanic island, in the southeast of the Mautius EEZ (Figs. 1 and 2). Rodrigues

coral reefs are not vey well know, compared to other Indian Ocean sites. However, the 1st

International Marine Biodiversity Workshop held in 2001 (proceedings published in Journal

of Natural History, vol; 38:23-24, 2004) yielded a large number of communications on

Rodrigues coral reefs. Rodrigues has been proposed for this mapping project given the wealth

of mapping data already available for Mauritius Island compared to Rodrigues, and the

availability of a pair of good quality multispectral images.

Figure 1: Location of Rodrigues in the Western Indian Ocean and in Mauritius (from Andréfouët et al. 2009)

42

Figure 2: Geomorphological map of Rodrigues Island made from a Landsat image (30 meter resolution) using

the Millennium Coral Reef Mapping Project classification scheme (from Andréfouët et al. 2009). The 28 km2

processed area is bounded by the black polygon.

Imagery

An archived Worldview 2 image (Fig. 3) acquired the 1st May 2011 was used to create the

habitat map. The targeted area is a 28.3 km2 polygon covering a southeast section of the

forereef, reef and lagoon.


DigitalGlobe Catalog ID 103001000A7C4500






16 bits

Geotiff format

The image was of high quality, with some surface and atmospheric effects due to wind and

sunglint. A quicklook is presented Figure 4.

As an historical reference, we purchased Quickbird multispectral standard image, acquired the

17th

April 2005 (ID= 10100100042D2D00), at 2.4 meter resolution. A quicklook is presented

Figure 4. The image was of good environmental quality, with moderate sea surface effects.

The WorldView2 image has been resampled at 2.4 m resolution to match the Quickbird

specifications.

43


st May 2011 WorldView2 image showing the processed area (7.2 km x 6.9 km)


th April 2005 Quickbird image

44

Processing

The habitat map was created with the WorldView2 image using the following “user’s” flow-

chart (Fig. 5), as recommended in Andréfouët (2008). Items in grey boxes show steps

independent of the thematic scope. Arrows point to most frequent need of iterations to

enhance accuracy, and frequency of these iterative actions is ranked(1, 2, 3).

Specifically for the Rodrigues image, steps 3, 6, 7, 8, 9 and 11 were performed.



The change detection analysis was performed here considering the 2011 WorldView2 image

as a reference. The two multispectral images were radiometrically normalized using the

digital counts of the WoldView2 image as reference. In fact, finding pseudo-invariant features

(PIFs) in the study area prove to be difficult and a perfect empirical linear calibration was

difficult to achieve.

Results


The studied area of Rodrigues offers a moderately rich geomorphological configuration with

25 mapped classes. The processed area is not necessarily representative of all the locations

45

around Rodrigues. It is a low value considering that the reef zonations include a fringing

structure, a barrier structure and a shallow wide sedimentary terrace between. Given the

present structure and image quality, the classes listed hereafter were interpreted from the


To follow Stoddart’s (1968) guidelines for implementing a reef terminology, some of the

terms used here may be evolving in the future when distributing the products to users, by

reference to classical reef terminology and to be consistent with previous descriptions (see

Bibliography on Rodrigues), in order to avoid unnecessary confusions.

Level 1:

Island (1)

Forereef (2)

Outer Reef flat (3)

Terrace (4)


Inner Fringing Reef flat (8)



Island


o Estuaries (1.5)

Forereef



o Lower slope (2.4)



o Crest (2.9)

o Patch of deep sand plain (2.10)

Outer Reef flat

o Reef flat (3.1)





Terrace



Sedimentary terrace (may include scattered coral colonies, algae, etc.)

(4.3.3)



o Channel (4.9)



o Basin with numerous constructions(5.5)

Inner Fringing Reef flat

46

o Channel (8.1)

o Basin (8.2)

o Reef flat (8.3)

o Terrace (8.4)






Below (Figs 6-7), views of the final classification habitat map are shown. The colours

assigned to each class is the average of the Red-Green-Bands digital counts for the extent of

the class, yielding a color scheme that mimicks the true color RGB image. Figures 6

illustrates the level of details (spatial and thematic) achieved for the geomorphological

product. For actual labels and surface areas for each of the classes, see the corresponding GIS

files.

47

Figure 6: Geomorphological classification (top) and true color (bottom) views of Rodrigues processed area. The

classification includes 25 classes.

48

Change detection

The pair of images displays significant variation between the two images (Fig. 7). No reliable

change detection could be performed on the forereefs given the sea surface effects on the

2005 Quickbird image.

The widespread differences visible on the shallow areas throughout the studied area are due to

different algal coverage and possibly movement of sediments along the back reef and

sedimentary terraces. The coral, hard-bottom, communities, remained stable in extent, but

differed in color due to algal coverage (turf, cyanobacteria or fleshy algae). The variation of

floral biomass can not be simply explained by seasonal differences since the images were

taken in mid-April 2005 and early May 2011.

Figure 7: Two examples of paired images (each covering 1 km x 1.5 km) between 2005 and 2011. They reveal

changes in flora coverage, likely including cyanobacteria and fleshy algae.

49

The 17th

April 2005 image was taken few days after the passage of hurricane Adeline-Juliet,

which passed next to Rodrigues the 9th

April as a category 5 hurricane, in the southwest of the

island. Even if Adeline-Juliet did not hit directly the island, the processed area was certainly

impacted by significant waves and energy. This disturbance may have removed the

macrophyte cover resulting in a “cleaner” substrate. Indeed, the 2005 image display less floral

coverage, seagrass or algae than in 2011. Presence of very dark areas on the 2005 and 2011

image suggests seagrass beds that have shifted locations during the six year interval.

The significant differences in cover of algae were non-seasonal, but possibly induced by

hurricane impact. Understandig the natural variability calls for ground-truthing and adequate

monitoring to characterize the natural variation of algae.

Discussion and perspectives The mapping of Rodrigues is a favourable case-study given the image quality and the wide

shallow areas in very clear waters, suitable for remote sensing assessment. The

geomorphologic complexity in 25 classes is moderate considering an oceanic island case

study, with fringing and barrier habitats.

Clearly, with adequate ground-truthing the different geomorphological zones mapped here

could be mapped in greater detail (beyond Level 2 and Level 3) to provide habitat

characterization using at least geomorphology, benthic cover and architecture. Further

mapping call for a better understanding of the flora dynamlic in this reef and shallow lagoon.

The geomorphological mapping of the portion of Rodrigues processed here took

approximately 2 days of work full time. Further work on documenting the classes with the

existing references is needed, in order to finalize the description of the classes.

Bibliography on Rodrigues Island

Cazes-Duvat V (2005) The morphologic impacts of cyclone Kalunde on the beaches of

Rodrigues island (Western Indian Ocean). Zeitschrift Fur Geomorphologie 49:293-308

Chapman, B. 2000 Marine biotope classification and mapping of Rodrigues using Landsat 7

ETM+ satellite imagery. MSc thesis, University of Wales Bangor.

Chapman B, Turner JR (2004) Development of a Geographical Information System for the

marine resources of Rodrigues. Journal of Natural History 38:2937-2957

Fenner D, Clark TH, Turner JR, Chapman B (2004) A checklist of the corals of the island

state of Rodrigues, Mauritius. Journal of Natural History 38:3091-3102

Hardman E, Green JM, Desire MS, Perrine S (2010) Movement of sonically tagged bluespine

unicornfish, Naso unicornis, in relation to marine reserve boundaries in Rodrigues,

western Indian Ocean. Aquatic Conservation-Marine and Freshwater Ecosystems

20:357-361

Okal EA, Sladen A, Okal EAS (2006) Rodrigues, Mauritius, and Reunion islands field survey

after the December 2004 Indian Ocean tsunami. Earthquake Spectra 22:S241-S261

O'Leary MJ, Perry CT (2010) Holocene reef accretion on the Rodrigues carbonate platform:

An alternative to the classic "bucket-fill" model. Geology 38:855-858

50

Oliver GP, Lynch T (2004) A historical perspective of the marine biota of Rodrigues -

Introduction. Journal of Natural History 38:2927-2935

Peterson AM, Stead SM (2011) Rule breaking and livelihood options in marine protected

areas. Environmental Conservation 38:342-352

Rees SA, Opdyke BN, Wilson PA, Fifield LK (2005) Coral reef sedimentation on Rodrigues

and the Western Indian Ocean and its impact on the carbon cycle. Philos Trans R Soc

Lond Ser A-Math Phys Eng Sci 363:101-120

Riaux-Gobin C, Witkowski A, Saenz-Agudelo P, Neveux J, Oriol L, Vetion G (2011)

Nutrient status in coral reefs of the Iles Eparses (Scattered Islands): comparison to

nearby reefs subject to higher anthropogenic influences (Mozambique Channel and

Mascarenes, Indian Ocean). Oceanological and Hydrobiological Studies 40:84-90

Sauer WHH, Potts W, Raberinary D, Anderson J, Perrine MJS (2011) Assessment of current

data for the octopus resource in Rodrigues, western Indian Ocean. African Journal of

Marine Science 33:181-187

Schils T, Coppejans E, Verbruggen H, De Clerck O, Leliaert F (2004) The marine flora of

Rodrigues (epublic of Mauritius, Indian Ocean): an island with low habitat diversity or

one in the process of colonization? Journal of Natural History 38:3059-3076

Schils T, Wilson SC (2006) Temperature threshold as a biogeographic barrier in northern

Indian Ocean macroalgae. Journal of Phycology 42:749-756

Turner, J. R., Jago, C., Daby, D., Klaus, R. (2000) The Mascarene region. In Seas at the

millennium, an environmental assessment (ed. C. R. C. Sheppard), pp. 243–258.

Elsevier.

Turner J, Klaus R (2005) Coral reefs of the Mascarenes, Western Indian Ocean. Philos Trans

R Soc Lond Ser A-Math Phys Eng Sci 363:229-250

51

SYNTHESIS: CLASSIFICATION SCHEME

The compilation of the different products yielded a 3-level hierarchical typology of habitats,

which is presented below.

The numbers in parenthesis refer to the code used in the GIS products. Labels Level1 and

Level2 are part of the attributes of each polygon, as “Label1” and “Label2”.

Level 1:

Island (1)

Forereef (2)

Outer Reef flat (3)

Terrace (4)


Pass (6)

Lagoon (7)



benthic cover could be inferred.

Island (1)

o Freshwater ponds (1.1)

o Beach, sand and coastal non vegetated areas (1.2)

o Beach rock(1.3)


o Estuaries (1.5)

Forereef (2)


o Deep low relief hardground and rubbles (2.2)


o Lower slope (2.4)


o Upper slope sand pools (2.6)


o Upper platform (2.8)

Upper platform without seagrass (2.8.1)

Upper platform with seagrass (2.8.2)

o Crest (2.9)

Crest with seagrass (2.9.1)

Crest without seagrass (2.9.2)

o Patch of deep sand plain (2.10)

o Pass (2.11)

Outer Reef flat (3)

o Reef flat (3.1)


Sand ridge (3.1.2)


52

Pavement (3.1.4)


Sand (3.1.6)

Sand with seagrass (3.1.7)


Heterogeneous 2 (uplifted?) (3.1.9)


Rodoliths, rubble, algae (3.1.11)

Rodoliths, rubble, coral (dead or live) (3.1.12)

o Spillways (include coral zones) (3.2)

o Shallow pass (3.3)

o Channel (3.4)

o Sand pools and basin (3.5)

o Boulder tract (3.6)

Terrace (4)


o Sand ridge (4.2)








o Sedimentary terrace under spillway influence (hard-bottom present) (4.4)

o Low relief patch reef (4.5)

o Island terrace with numerous coral colonies (4.6)



o Channel (4.9)


o Pass reef flat (high current) (5.1)

o Basin (5.2)

o Reef flat (5.3)

Sand-rubble (5.3.1)



o Basin with numerous constructions(5.5)

Pass (6)

o Pass (6.1)

o Coral slope (6.2)

o Subtidal patch (6.3)

o Channel (6.4)

o Channel patch reef (subtidal and intertidal) (6.5)

o Soft bottom slope (6.6)

Lagoon (7)

o Deep lagoon (7.1)

o Shallow lagoon with constructions (7.2)

o Escarpment (7.3)

o Subtidal patch reef (include halo of rubbles) (7.4)

53



7.6.1 Patch reef edge with seagrass

o Deep lagoon with constructions (7.7)

o Inner slope (7.8)

Sedimentary inner slope (7.8.1)

Seagrass inner slope (7.8.2)

o Coral heads on inner slope (7.9)

o Shallow lagoon (7.10)


o Channel (8.1)

o Basin (8.2)

o Reef flat (8.3)

o Terrace (8.4)


54

GENERAL CONCLUSION AND PERSPECTIVES

Habitat mapping The various products shown for the different case studies confirm that it is doable to infer

from high resolution remote sensing images a detailed product, at geomorphological level at

least, even without specific ground-truthing. However, this lack of ground-truthing prevents

the quantification of the accuracy of each product, especially at Level 3, where errors occur. It

is not expected to have significant errors at Level 1 given the broad geomorphological zones

that this level represents. Errors nevertheless occur in the position of the boundaries of the

different classes. It is thus a marginal error compared to the surface area they represent. Level

2 classes should be also accurate for the same reasons. However, Level 3, which refers to

benthic information likely includes errors which can be significant. Literature mentions

accuracy as low as 50%, sometimes even less, for categories that account for coral, algae and

seagrass cover. Here, we restrict the level of errors by simply mentioning qualitatively the

occurrence of benthic categories in the different classes, which has the consequence to

minimize the errors compared to classes defined with quantitative cover values. However, it

would be impossible to mention quantitative cover in the definitions of the classes without

ground-truthing performed before the mapping process.

Mapping other sites is obviously possible, but to reach similar thematic richness without

errors, the mapping is fairly time-consuming and requires a dedicated technician, familiar

with coral reef structures, for few days for each product. Mapping at Level 1 is extremely fast,

but Level 2 and Level 3 are time consuming. This means that for a dedicated position, around

40 to 50 sites, similar in sizes to the 4 sites processed here, could be done in a one year time

frame at Level 2, without ground-truthing. This effort is reasonable for instance, if a project

aims to map in detail all the Marine Protected Areas of the region. Systematically mapping all

the reefs of the Western Indian Ocean is not a reasonable target without significant workforce.

Mapping at Level 3 and achieving good accuracy (>75%) will require ground-truthing for

many sites, for training and for accuracy assessment.

The value of a systematic approach is to produce a general classification scheme valid for all

the sites. With such global reference, it becomes possible to compare different sites

objectively, by measuring on the same scale habitat richness, habitat diversity and other

possible metrics useful for conservation planning, biodiversity studies and resource

assessments.

Change detection Habitat mapping provided map in a given moment in time. At habitat Level 1 or 2, it is not

expected to see any changes on a reef even after large disturbances. However, differences

could be seen at Level 3, or for certain categories of benthic cover.

Here, we observed significant changes in Toliara and Mayotte few years apart, for

respectively coral zones and seagrass zones. For Aldabra and Rodrigues, we also observed

mostly changes in algal cover over soft bottoms, but these are “routine” changes for a reef,

and part of the natural processes and variability. If a warning system, based on the regular

examination of very high resolution images is set, it would be valuable to trigger surveys for

55

the observations made for Toliara and Mayotte, but probably not for Aldabra and Rodrigues,

except if one is interested by quantifying seasonal changes of algal biomass in sediments.

The change detection performed here did not quantify the rates of changes. We only focused

on qualitative events (except for Toliara, because we had access to temporal ground-truthing

data). Next step would be to quantify the changes and to provide transition matrices for

instance. If images are used to trigger alerts in order to launch in situ surveys, the simple

assessments performed here are sufficient. It is compatible with the use of a multi-sensor

approach and the use of simple remote sensing techniques. However, we point out that in all

cases, we could not infer changes on forereefs, and on most coral zones with moderate coral

cover. The spectral information is not suitable for this and, here too, it would require detailed

ground-truthing in order to do so, combined with suitable radiometric correction techniques to

be able to match precisely the radiometric values from the before-after pair of images.

Clearly, we favoured here a qualitative approach to the problem of change detection, in

contrast with a quantitative approach that require different analytical capacities. In other

words, we assessed first qualitatively if the rates of changes would justify using quantitative

techniques (and ground-truthing).

The Rodrigues Island case study is interesting because the oldest image (from 2005) was

acquired shortly after the passage of a hurricane. It would be justified to expand the time

series with an image before that hurricane to assess hurricane-induced changes. Using the

after-hurricane image as a reference for change detection biased the assessment, if the goal

was to check possible degradations of the reefs between 2005 and 2011. Hurricanes can

generate significant changes on reefs, which can be visible on very high resolution images

(Scopélitis et al. 2009, 2010).

56

APPENDIX: METADATA (FGDC ESRI)

Each individual shapefile, one per site, is documented with the following fields:

Citation: Andréfouët S, 2012, Mozambique Channel Coral Reef Habitat Mapping.

Report to Collecte Localisation Satellites, IRD, Nouméa, January 2012. 56 pages.

Originator: IRD

Publication_Date: January 2012

Title:

Description:

Abstract: Pilot coral reef habitat-geomorphological map made from high resolution

imagery. Project A: Mozambique Channel Mapping. Part of this work was performed

under Collecte Localisation Satellite contract in the frame of the ESA-World Bank

EOWORLD initiative.

Purpose: Demonstration

Time_Period_of_Content: January 2012

Time_Period_Information: January 2012

Single_Date/Time: January 2012

Calendar_Date: January 2012

Currentness_Reference: Publication date

Status: Complete

Progress: Complete

Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate:

East_Bounding_Coordinate:

North_Bounding_Coordinate:

South_Bounding_Coordinate:

Access_Constraints: No access constraints.

Use_Constraints: No use constraints.

Native_Data_Set_Environment: Microsoft Windows XP Version 5.1 (Build 2600)

Service Pack 3; ESRI ArcCatalog 9.3.0.1770

Distribution_Information: Serge Andrefouet / Olivier Germain

Resource_Description:

Metadata_Reference_Information:

Metadata_Date: January 2012

Metadata_Contact: Serge Andrefouet

Contact_Information: Serge Andrefouet

Contact_Organization: IRD

Contact_Person:. Serge Andrefouet

Metadata_Standard_Name: FGDC Content Standards for Digital Geospatial Metadata

Metadata_Standard_Version: FGDC-STD-001-1998

Metadata_Time_Convention: local time

Metadata_Extensions: xml

Online_Linkage: <http://www.esri.com/metadata/esriprof80.html>

Profile_Name: ESRI Metadata Profile

http://www.esri.com/metadata/esriprof80.html

mozambique channel coral reef habitat map product -...

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