MAPPING SHALLOW WATER SEAGRASS WITH

LANDSAT TM SATELLITE DATA IN TORRES STRAIT

Mervyn Thomas
Brian Long
Thomas Taranto








June 1997



REPORT MR-GIS 97/6
T O R R E S S T R A I T S E A G R A S S M A P P I N G


2
Executive Summary
The objective of this study was to map the shallow water seagrass beds of northwestern
Torres Strait, using Landsat TM satellite data. The study area was 4,545 km
2
. It was
sampled by divers in November / December 1993 at 251 sites. Percentage cover of
seagrass, water depth and substrate type were recorded at each site. A spatial statistical
model was developed, relating seagrass cover with the pixel values of blue, green and red
light recorded by the satellite. The usefulness of this model for prediction of seagrass
density from satellite imagery was assessed. Landsat TM satellite data did not provide an
acceptable basis for spatial prediction of seagrass density outside the area sampled.
Nevertheless, Landsat TM data may be useful in improving the interpolative mapping of
seagrass density within the sampled area. In this study it improved the predicted residual
sums of squares statistic by 2.3%.
Introduction
Seagrass is critical habitat for dugongs, turtles, and some commercially important prawns
and fish. Torres Strait has one of the largest areas of seagrass in Australia; seagrass beds
in Torres Strait are larger than the Gulf of Carpentaria by a factor of 10 and are
equivalent to the total estimated area of seagrass along the Queensland coast (Long and
Poiner, 1997). Torres Strait supports one of the largest populations of dugongs in the
world which is a reflection of the importance of seagrass there.
The attenuation of light through the water column is a major limiting factor for the use
of Landsat TM technology to map subtidal habitats. Red light penetrates to 5 m, green
to 15 m and blue to 30 m in waters with moderate suspended sediments (typical of
coastal waters in the Great Barrier Reef lagoon. Much of central Torres Strait, however,
is shallow - with large tracts of seabed < 15 m deep. Thus Landsat satellite data may
prove useful for mapping the shallow water sub tidal habitats in much of the Torres
Strait region. The purpose of this study was to test the utility of Landsat TM satellite data
to map seagrass beds in northwestern Torres Strait where water depths are < 15 m for
most of the study area.
Materials and Methods
Description of the study area
Torres Strait lies between the NW coast of Cape York Peninsula and the S coast of
Papua New Guinea, and connects the Coral and Arafura Sea (Fig. 1). Wolanski et al.
(1988), Harris (1988) and Bode and Mason (1994) have described the physical
oceanography and sedimentary geology of the Torres Strait. The Straits are shallow (< 15
m) with strong tidal currents due to large pressure gradients between the Arafura and
Coral Sea (Bode and Mason, 1994). Water speeds exceeding 2.5 m.s
-1
occur in the narrow
channels between some islands and reefs (Admiralty, 1973).


T O R R E S S T R A I T S E A G R A S S M A P P I N G


3
PNG
100 km 50 0
Cape York
Moa Is.
Badu Is.
Orman Reefs
Dauan Is.
Boigu Is.
Buru Is.
Aldai Reef
Mabuiag Is.
AUSTRALIA
Torres Strait
PNG
Mai River
142 143 E
10 S
N

Figure 1. Map of Torres Strait, showing the boundaries of the study area sampled for seagrass in
November 1993.
The strong tidal currents have created sand waves in many areas of Torres Strait (Harris,
1988) including north western Torres Strait. There are two distinct seasons in Torres
Strait: a dry season and a wet season. The dry season runs for seven months from May to
November with an average rainfall of 21.4 mm month
-1
. The wet monsoon season lasts
for five months from December to April with an average monthly rainfall of 311 mm at
Thursday Island (Admiralty, 1973). The prevailing winds for the two seasons are also
distinct. During the dry season, south-east trade winds blow from E and SE 90% of the
time. Wet monsoon winds are more variable; blowing from the NE, N and NW for 30%
of the time. The average wind speed is lower in the wet monsoon, 5 knots.h
-1
, than dry
season, 7.9 knots.h
-1
, and the number of calm days is also lower in the dry season, < 1
day.month
-1
than wet monsoon, 2.1 days.month
-1
. There are more gales during the
monsoon than dry season (6 and < 1 days.month
-1
respectively). There is little net flow
of water through Torres Strait although there are seasonal differences in the direction of
net flow. The dry season has a net westerly flow with the south-east trade winds There is
a net eastwardly flow over the wet monsoon season, when westerlies and north westerlies
prevail (Wolanski et al., 1988). The winds and currents stir up the bottom sediments in
shallow water areas of central Torres Strait which results in a turbidity maximum zone in
central Torres Strait (Harris, 1988).
The southern limits of the study area were Badu and Moa Island, situated mid-way across
the Straits. Boigu and Dauan Island near the S coast of Papua New Guinea formed the
northern boundary. The eastern limit of the study area was formed by a line NE from
T O R R E S S T R A I T S E A G R A S S M A P P I N G


4
Moa Island through the Orman reefs and N to Dauan Island The 142
nd
meridian of
longitude formed the western boundary (Fig. 1).
Field sampling: Inter-reefal areas
The seagrass at 251 subtidal sites in the study area were sampled in November /
December 1993 (Fig. 2). The study area was first divided into primary sampling units
which were each 4.5 km east-west and 4.2 km north-south. The primary sampling unit
area, 18.9 km
2
, was chosen on the basis of three factors:
estimated time taken to sample a site (15 min),
time to travel between sites,
total time (three weeks) available for field sampling.
All primary sampling units were sampled, giving complete sampling coverage of the
study area. It was impractical to sample the whole primary sampling unit (18.9 km
2
), and
100 m
2
sites were sampled in each unit. The position of each site within each primary
sampling unit was chosen randomly. Global Positioning System (GPS) satellite navigation
was used to locate the sites in the field. At all sites divers searched an area of
approximately 100 m
2
and estimated the percentage cover of seagrass and algae as well as
recording descriptions of the substratum. Seagrass samples were also collected, sorted
and enumerated to species level, but for this study we only used the presence/absence
data. Water visibility (m) and water depth (m) were also recorded at each site and a
sediment sample was taken for grain-size analysis.
Figure 2. Map of Torres Strait study area showing sites sampled for seagrass.
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0 25 50 75 Kilometers
N
#
Recent samplesites
Torres 100k Basemap
foreshore
island
mainland
reef
T O R R E S S T R A I T S E A G R A S S M A P P I N G


5
Data analysis
The data analysis occurred in two stages. In the first stage, and exploratory analysis was
used, to identify the appropriate functional form of predictive relationships, and to
characterise large scale spatial trends and small scale spatial dependencies. The second
stage involved estimating the parameters of a predictive relationship, using generalised
least squares, based on a spatially structured error covariance matrix. The predictive
relationship was then assessed using cross validation.
The exploratory analysis was based on a generalised additive model (GAM) (Hastie and
Tibshirani, 1990). Square root of percentage cover of seagrass was analysed using a
normal error structure with a constant variance. Smoothing spline models were fitted to
each wavelength, to and to sample depth. Large-scale spatial trends were modelled using
a loess smoother in two dimensions (Easting and Northing). Partial residual plots were
used to display the fitted relationships for each predictor.
Small-scale spatial dependence was investigated using the residuals of the GAM model. A
robust semi-variogram (Cressie and Hawkins, 1980) was calculated and plotted. The
semi-variogram displays half the variance of the difference between two residuals, as a
function of the respective inter-site distances. There is evidence of small-scale spatial
dependence if the semi-variogram increases as distance between the sites increases.
An exponential theoretical semi-variogram model was fitted by eye. The model was of
the form:
ij = e
-dij

where
ij is the correlation between sites i and j, and
dij is the distance between the sites.
Informal fitting was appropriate, since the successive distance variance pairs of the
semi-variogram are not statistically independent. In this circumstance estimation by least
squares has little advantage over a less formal approach.
In the second stage of the analysis, parameters were estimated using generalised least
squares, and a spatially structured covariance matrix incorporating the fitted semi-
variogram. F tests were used to test the importance of large-scale spatial trends, depth
information and image variables.
Model assumptions were investigated using graphical displays of residuals.
The importance of the Landsat TM image variables was investigated using cross
validation. Cross-validated predicted residual sums of squares (PRESS statistics) were
obtained for models with and without the image variables. That is, each observation was
dropped in turn, and generalised least squares estimates of the parameters were obtained.
These parameters, together with the covariance of the errors for the dropped point and
all other points were used to predict the sea grass cover for the dropped observation. The
prediction may be regarded as a form of universal Kriging (Ripley, 1981). After
T O R R E S S T R A I T S E A G R A S S M A P P I N G


6
predictions were produced, the dropped observation was re-instated and the next
observation dropped. The process was repeated until all observations had been dropped
in turn, and predicted residual sums of squares (PRESS) were accumulated.
All calculations were performed with Splus
Results
Seagrass
Seagrass was found throughout the study area but highest covers were generally found in
the southern half of the study area (Fig. 3).
Figure 3. Bubble plot of percentage seagrass cover in the Torres Strait study area.
Water depth
The depth of water in the study area was shallow (< 17 m) and deepest areas were in the
north east (Fig. 4). Only 17.5 km
2
was deeper than 15 m, the penetration limit of green
light in this water type. More than half the area (54%) was shallower than 7 m (Table 1).
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Torres 100k Basemap
foreshore
island
mainland
reef
%Seagrass cover
#
<1%
#
1- 15
# 15- 35
# 35-60
# 60- 95
0 25 50 75 Kilometers
N
T O R R E S S T R A I T S E A G R A S S M A P P I N G


7
Table 1. Breakdown of areas by 1 m depth intervals for the Torres Strait study area.
Depth interval Area (km
2
) Depth interval Area (km
2
)
0-1 25.06
1-2 160.27 9-10 375.28
2-3 233.57 10-11 257.89
3-4 258.06 11-12 156.31
4-5 406.42 12-13 60.61
5-6 747.72 13-14 27.92
6-7 662.97 14-15 21.26
7-8 651.03 15-16 16.82
8-9 482.49 16-17 0.78


0 10 20 30 40 50 Kilometers
Depth
1-5
6-7
8-9
10-11
12-17
N

Figure 4. Depth contours (m) for the Torres Strait study area.
T O R R E S S T R A I T S E A G R A S S M A P P I N G


8
Exploratory analysis of Seagrass Cover
The functional form of the relationship fitted for each predictor was displayed using
partial residual plots. Figure 5 shows the smoothing splines and partial residuals for
intensity in the Red, Green and infrared bands and for depth. The solid lines represent
the fitted smoothing spline, and the broken lines represent the standard error. Given the
size of the standard error, the Red band intensities seem to be adequately modelled by
linear trends, but there does seem to be some evidence of curvature for the Green and
infrared bands, and for depth. Curvature in the Green band relationship seems to be
restricted to the highest few values, suggesting that percentage coverage of Seagrass
drops off more rapidly with intensity of the green band at high vales of the green band
than at low values. All of the plots show a high degree of variation in seagrass coverage.
Red Band
S
m
o
o
t
h

T
r
a
n
s
f
o
r
m
a
t
i
o
n
20 25 30 35
-
0
.
4
0
.
0
0
.
4
0
.
8

Green Band
S
m
o
o
t
h

T
r
a
n
s
f
o
r
m
a
t
i
o
n
25 30 35 40 45
-
1
.
5
-
0
.
5
0
.
5

Infra Red Band

S
m
o
o
t
h

T
r
a
n
s
f
o
r
m
a
t
i
o
n
5 10 15
-
0
.
4
0
.
0
0
.
4

Depth
S
m
o
o
t
h

T
r
a
n
s
f
o
r
m
a
t
i
o
n
6 7 8 9 10
-
0
.
4
0
.
0
0
.
4
0
.
8

Figure 5. Smoothing Splines Fitted to Predictor Variables
Figure 6 shows the spatial trend fitted by loess estimation. There is a high density region
centred on Longitude 142.3, Latitude 9.8, and a low density region in the north east
corner of the study area.
T O R R E S S T R A I T S E A G R A S S M A P P I N G


9
Longitude
L
a
t
i
t
u
d
e
142.0 142.1 142.2 142.3 142.4 142.5
-
1
0
.
0
-
9
.
8
-
9
.
6
-
9
.
4
-0.2 0.2

Figure 6: The Spatial Trend Surface fitted to partial residuals by Loess estimation


No formal tests of linear or non linear dependence of seagrass cover on predictor
variables were performed in this analysis. The purpose of the exploratory investigation is
merely to identify appropriate models and error structures.

A histogram of residuals was plotted, and residuals were plotted against fitted values
(Fig. 7). Several problems were evident. First, a number of linear bands of residuals can
be seen in the plot of residuals versus fitted values. These bands were caused by the
many observations with zero cover. Secondly, there seemed to be some suggestion that
the variance of the residuals increased with the predicted value - despite the square root
transformation used. This phenomenon was not, however, improved by using a
stronger transformation (such as the logarithm), and was also a result of the presence
of many observations with no seagrass. There was also some suggestion that the residual
distribution was skewed with a longer tail to the right.
T O R R E S S T R A I T S E A G R A S S M A P P I N G


10

Predicted
R
e
s
i
d
u
a
l
s
0.0 0.2 0.4 0.6 0.8
-
0
.
4
0
.
0
0
.
4

Predicted
A
b
s
o
l
u
t
e

R
e
s
i
d
u
a
l
s
0.0 0.2 0.4 0.6 0.8
0
.
0
0
.
2
0
.
4
0
.
6
-0.4 -0.2 0.0 0.2 0.4 0.6
0
.
0
1
.
0
2
.
0
3
.
0
Residuals

Quantiles of Standard Normal

r
e
s
-3 -2 -1 0 1 2 3
-
0
.
4
0
.
0
0
.
4

Figure 7. Distribution of Residuals from Exploratory Analysis
The estimated semi-variogram for the residuals (showing half the variance of the
difference between two residuals plotted against their distance in metres) is shown in Fig.
8. The solid line was a fitted exponential semi-variogram with a range of 2000 m and a
sill of 0.028. There seemed to be a clear spatial dependency, with the variance increasing
rapidly to a plateau, as observations move apart up to a distance of 10 km. There is clear
evidence of spatial dependence between observations up to 10 km apart. This spatial
dependence invalidated any F statistics that might have been calculated in the exploratory
analysis, and was a more serious problem for analysis than the many observations with
zero coverage. The final analysis must make explicit provision for this dependence.

T O R R E S S T R A I T S E A G R A S S M A P P I N G


11

distance
ga
m
m
a
0 10000 20000 30000 40000
0.
0
0.
01
0
0.
02
0
0.
03
0


Figure 8. Robust Semi-variogram for Residuals from Exploratory Analysis
Spatial dependency analysis

F tests to estimate the effect of image variables, depth and polynomial spatial trend were
obtained using generalised least squares, and are based on the fitted semi-variogram
(Table 2). All F statistics are significant, with the largest effect being caused by the
Landsat TM image variables.
Table 2. F-statistics to estimate the effect of image variables, depth and polynomial spatial trend. All F-
statistics are significant.

Effect Mean
Square
df F Ratio P Value
Image 0.151 3 6.02 0.001
Depth 0.088 2 3.54 0.031
Spatial
Trend
0.072 5 2.87 0.015
0.025 225 - -


The PRESS statistic for the model with all variables was 5.49 and the PRESS statistic for
the model excluding the image variables was 5.63 indicating that there is indeed some
improvement in prediction from including the image variables. Nevertheless, this
improvement is very slight. The correlation between predicted values and observed sea
grass covers in cross validation was only 0.5 indicating that the densities obtained in a
single site are very variable.
T O R R E S S T R A I T S E A G R A S S M A P P I N G


12
Discussion
The analysis reveals clear evidence of a relationship between the Landsat TM image
variables and the seagrass coverage. This is the largest single effect in the generalised least
squares analysis of variance.
The presence of large-scale spatial trends, and of small scale local spatial dependence,
implies that it is not possible to map seagrass reliably, using satellite imagery and
bathymetry alone. Even taking account of relationships between seagrass cover and both
depth and imagery, seagrass varies smoothly from region to region. This implies that
extrapolation outside the spatial envelope of the samples will not produce reliable maps
of seagrass distribution.
The large F ratio associated with the image Variables (6.02 on 3 and 225 df) indicates that
satellite imagery may, however, be used to improve interpolative maps of sea grass
density. That is the map of seagrass density obtained for the study area may be
improved by using information from the Landsat TM image.
This study provides a useful caveat against the uncritical acceptance of correlations
between seagrass coverage and Landsat TM images. Despite clear evidence for a
relationship between seagrass density and image variables, the use of Landsat TM
imagery has provided only a marginal improvement in the interpolative mapping within
the study area. The presence of large-scale spatial trends and local dependencies implies
that the analyses conducted here are of no value in extrapolative mapping outside the
study area, on the basis of Landsat imagery. These caveats are even more pressing in the
context of this study - which provides an almost optimal arena for the use of Landsat
TM satellite data to map seagrass (large shallow areas, with little variation in depth).
Acknowledgements
Many thanks to AFMA for providing funds.
References
Admiralty (1973). Australia Pilot. Vol. III. 6
th
ed. Oxford University Press, 320 pp.
Bode, L. and Mason, L.B. (1994). Numerical modelling of tidal currents in Torres Strait
and the Gulf of Papua. Report to Victorian Institute of Marine Science, 65 pp.
Cressie, N. and Hawkins, D.M. (1980) Robust estimation of the variogram, I. Journal of
the international Association for Mathematical Geology, 12, 115-125.
Harris, PT (1988). Sediments, bedforms and bedload transport pathways on the
continental shelf adjacent to Torres Strait, AustraliaPapua New Guinea. Continental
Shelf Research, 8:9791003
Hastie, T. and Tibshirani, R. (1990). Generalised Additive Models. Chapman and Hall,
London.
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13
Long, B.G. and Poiner, I.R. (1997). Seagrass communities of Torres Strait. Final report to
Torres Strait Fisheries Scientific Committee, March 1997.
Ripley, B. (1981) Spatial Statistics. Wiley, New York.
Wolanski, E., Ridd, P. and Inoue, M. (1988). Currents through Torres Strait. Journal of
Physical Oceanography, 18: 15351545