Supplementary Material
Table 1: For the combined data, and then for each reef, linear, asymptote, sigmoid,
exponential and 2nd order polynomial models were tested for best-fit to modelled variables
when numerically considered appropriate. The model in bold is the selected model based on
AIC criteria. A linear model was selected when the AIC value was less than two units greater
than the model with the lowest AIC value. ‘*’ indicates that the model incorporated first
order autoregressive correlation structure because it significantly improved the fit of the
model.
Coral Recovery vs Reassembly
Data
All Reefs
model
AIC
Linear*
271.5
Sigmoid*
281.7
Exponential*
276.3
2nd order polynomial*
271.6
Recovery through time
Reassembly
Data
All Reefs
Thetford
Reef 19138
model
Coral recovery
AIC
model
AIC
Linear*
266.9
Linear*
148.8
Asymptote*
281.0
Asymptote*
155.8
Sigmoid*
280.3
Sigmoid*
151.7
Exponential*
274.0
Exponential*
160.1
2nd order polynomial*
270.1
2nd order polynomial*
155.0
linear
42.7
linear
14.2
asymptote
42.2
asymptote
10.3
sigmoid
41.0
sigmoid
21.1
exponential
45.9
exponential
29.2
2nd order polynomial
41.7
2nd order polynomial
10.7
linear
59.4
linear
30.3
Horseshoe
Green Island
Fitzroy Island
Low Isles
asymptote
61.3
asymptote
32.2
sigmoid
61.0
sigmoid
33.8
exponential
60.0
exponential
34.6
2nd order polynomial
61.3
2nd order polynomial
32.2
linear
36.1
linear
4.3
asymptote
34.6
asymptote
4.8
sigmoid
33.8
Sigmoid*
-11.2
exponential
37.2
exponential
15.2
2nd order polynomial
4.7
linear
41.6
linear
26.0
sigmoid
49.5
sigmoid
26.0
exponential
40.9
exponential
26.6
2nd order polynomial
40.7
2nd order polynomial
27.2
linear
43.5
linear
31.9
Sigmoid*
58.6
asymptote
31.2
exponential
41.3
sigmoid
26.3
2nd order polynomial*
34.4
exponential
36.0
2nd order polynomial
30.4
linear
31.2
linear
24.7
Sigmoid*
43.5
sigmoid
37.2
Asymptote*
45.9
asymptote
37.2
exponential
30.9
exponential
19.2
2nd order polynomial
30.1
2nd order polynomial
18.4
Table 2: The results of a SIMPER (Similarity Percentages - species contributions) analysis
for comparisons of coral assemblage composition between the pre-disturbance year and the
last surveyed recovery year for each reef community. The cut off for low contributions was
90%.
Thetford Reef (1999) and Thetford Reef (2010)
Bray-Curtis Dissimilarity = 17.70
Taxonomic group
Thetford Reef
1999 (% cover)
Thetford Reef
2010 (% cover)
Dissimilarity Contribution
(%)
(%)
Tabulate Acropora
26.78
35.39
4.31
24.33
Pocillopora
6.01
10.07
2.03
11.46
Isopora
3.11
0.37
1.37
7.76
Branching Acropora
3.96
1.77
1.10
6.19
Soft Coral
34.43
36.55
1.06
5.97
Digitate Acropora
4.14
2.14
1.00
5.65
Platygyra
2.67
0.73
0.97
5.47
Echinopora
2.13
0.73
0.70
3.94
Stylophora
2.65
1.28
0.69
3.88
Seriatopora
1.63
0.49
0.57
3.22
Encrusting Porites
1.51
2.62
0.56
3.16
Encrusting Montipora
2.35
1.40
0.47
2.67
Lobophyllia
0.87
0.12
0.38
2.13
Favia
1.35
0.67
0.34
1.93
Favites
0.95
0.31
0.32
1.82
Massive Porites
2.05
1.65
0.20
1.14
Reef 19138 (1996) and Reef 19138 (2007)
Bray-Curtis Dissimilarity = 17.81
Reef 19138 1996
(% cover)
Reef 19138
2007 (% cover)
Tabulate Acropora
32.64
43.34
5.35
30.02
Branching Acropora
14.01
9.38
2.31
12.98
Encrusting Porites
0.70
3.20
1.25
7.01
Encrusting Montipora
9.84
7.75
1.05
5.87
Seriatopora
2.17
0.14
1.02
5.71
Soft Coral
6.14
4.35
0.89
5.02
Hydnophora
2.76
1.44
0.66
3.71
Stylophora
2.97
1.70
0.63
3.54
Fungia
1.04
0.00
0.52
2.91
Merulina
0.88
0.07
0.41
2.28
Echinopora
2.60
3.33
0.37
2.05
Mycedium
0.17
0.88
0.36
2.00
Turbinaria
0.79
0.14
0.33
1.84
Favia
1.13
1.77
0.32
1.79
Massive Porites
3.89
3.26
0.31
1.75
Leptoria
0.09
0.54
0.23
1.28
Galaxea
0.87
0.48
0.20
1.10
Taxonomic group
Dissimilarity Contribution
(%)
(%)
Horseshoe Reef (1997) and Horseshoe Reef (2011)
Bray-Curtis Dissimilarity = 31.6
Taxonomic group
Tabulate Acropora
Horseshoe Reef
1997 (% cover)
Horseshoe Reef
2011 (% cover)
31.94
48.54
Dissimilarity Contribution
(%)
(%)
8.30
26.25
Foliose Montipora
10.47
1.21
4.63
14.65
Encrusting Porites
3.85
11.82
3.98
12.60
Soft Coral
10.32
5.08
2.62
8.29
Encrusting Montipora
11.94
6.80
2.57
8.13
Isopora
3.81
0.19
1.81
5.72
Seriatopora
2.12
4.26
1.07
3.38
Massive Porites
0.33
2.41
1.04
3.30
Stylophora
3.10
1.33
0.88
2.79
Pocillopora
4.01
2.92
0.54
1.72
Echinopora
2.40
1.40
0.50
1.59
Cyphastrea
0.13
1.08
0.48
1.51
Digitate Acropora
4.14
3.24
0.45
1.42
Green Island Reef (1996) and Green Island Reef (2009)
Bray-Curtis Dissimilarity = 19.86
Taxonomic group
Green Island Reef Green Island Reef Dissimilarity Contribution
1996 (% cover)
2009 (% cover)
(%)
(%)
Massive Porites
11.77
18.61
3.42
17.22
Soft Coral
30.42
23.85
3.28
16.52
Branching Acropora
18.95
14.42
2.27
11.41
Encrusting Montipora
3.45
6.55
1.55
7.82
Tabulate Acropora
19.77
17.43
1.17
5.90
Lobophyllia
1.02
3.15
1.06
5.34
Pocillopora
0.16
1.70
0.77
3.87
Digitate Acropora
1.74
0.26
0.74
3.71
Encrusting Porites
0.17
1.57
0.70
3.52
Favites
1.91
0.79
0.56
2.84
Stylophora
0.17
0.92
0.37
1.87
Merulina
0.70
0.13
0.28
1.43
Galaxea
1.05
1.57
0.26
1.32
Echinopora
0.88
0.39
0.24
1.22
Favia
1.40
0.92
0.24
1.20
Fungia
0.69
0.26
0.22
1.09
Leptastrea
0.52
0.92
0.20
1.01
Diploastrea
0.00
0.39
0.20
0.99
Foliose Montipora
0.51
0.13
0.19
0.95
Branching Porites
0.90
0.52
0.19
0.94
Fitzroy Island Reef (1997) and Fitzroy Island Reef (2011)
Bray-Curtis Dissimilarity = 25.50
Taxonomic group
Fitzroy Island Reef
1997 (% cover)
Fitzroy Island Reef Dissimilarity Contribution
2011 (% cover)
(%)
(%)
Branching Acropora
15.19
2.53
6.33
24.83
Encrusting Porites
2.64
12.56
4.96
19.46
Soft Coral
36.78
44.42
3.82
14.98
Seriatopora
4.00
0.86
1.57
6.14
Massive Porites
3.75
1.33
1.21
4.75
Galaxea
0.26
2.53
1.13
4.44
Encrusting Montipora
3.02
4.46
0.72
2.82
Branching Porites
5.51
4.25
0.63
2.47
Pachyseris
2.89
4.12
0.61
2.41
Lobophyllia
2.38
1.33
0.52
2.05
Echinopora
2.00
1.00
0.50
1.96
Merulina
3.12
2.19
0.46
1.81
Fungia
1.73
0.93
0.40
1.56
Foliose Montipora
8.18
8.91
0.37
1.43
Low Isles Reef (1996) and Low Isles Reef (2009)
Bray-Curtis Dissimilarity = 35.83
Taxonomic group
Low Isles Reef
1996 (% cover)
Low Isles Reef
2009 (% cover)
Dissimilarity
(%)
Contribution
(%)
Soft Coral
24.47
42.07
8.80
24.55
Encrusting Porites
4.90
14.91
5.00
13.96
Foliose Montipora
10.40
1.70
4.35
12.14
Branching Acropora
6.94
1.92
2.51
7.01
Echinopora
5.46
1.70
1.88
5.26
Merulina
3.39
0.52
1.44
4.01
Fungia
3.80
1.03
1.38
3.86
Encrusting Montipora
4.09
1.77
1.16
3.23
Seriatopora
3.78
1.55
1.11
3.11
Branching Porites
6.65
8.41
0.88
2.46
Galaxea
3.95
5.68
0.87
2.41
Tabulate Acropora
4.81
3.17
0.82
2.28
Pectinia
1.26
0.07
0.59
1.65
Pavona
1.11
0.30
0.41
1.14
Platygyra
0.07
0.89
0.41
1.14
Lobophyllia
2.01
2.73
0.36
1.00
Goniastrea
0.87
0.15
0.36
1.00