<p>Supplementary Material</p><p>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 </p><p>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.</p><p>Coral Recovery vs Reassembly Data model AIC All Reefs Linear* 271.5 Sigmoid* 281.7 Exponential* 276.3 2nd order 271.6 polynomial*</p><p>Recovery through time Reassembly Coral recovery Data model AIC model AIC All Reefs 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 Thetford 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 Reef 19138 linear 59.4 linear 30.3 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 Horseshoe 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 Green Island 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 Fitzroy Island 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 Low Isles 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</p><p>Table 2: The results of a SIMPER (Similarity Percentages - species contributions) analysis </p><p> for comparisons of coral assemblage composition between the pre-disturbance year and the </p><p> last surveyed recovery year for each reef community. The cut off for low contributions was </p><p>90%.</p><p>Thetford Reef (1999) and Thetford Reef (2010)</p><p>Bray-Curtis Dissimilarity = 17.70</p><p>Taxonomic group Thetford Reef Thetford Reef Dissimilarit Contribution 1999 (% cover) 2010 (% cover) y (%) (%)</p><p>Tabulate Acropora 26.78 35.39 4.31 24.33</p><p>Pocillopora 6.01 10.07 2.03 11.46</p><p>Isopora 3.11 0.37 1.37 7.76</p><p>Branching Acropora 3.96 1.77 1.10 6.19</p><p>Soft Coral 34.43 36.55 1.06 5.97 Digitate Acropora 4.14 2.14 1.00 5.65</p><p>Platygyra 2.67 0.73 0.97 5.47</p><p>Echinopora 2.13 0.73 0.70 3.94</p><p>Stylophora 2.65 1.28 0.69 3.88</p><p>Seriatopora 1.63 0.49 0.57 3.22</p><p>Encrusting Porites 1.51 2.62 0.56 3.16</p><p>Encrusting Montipora 2.35 1.40 0.47 2.67</p><p>Lobophyllia 0.87 0.12 0.38 2.13</p><p>Favia 1.35 0.67 0.34 1.93</p><p>Favites 0.95 0.31 0.32 1.82</p><p>Massive Porites 2.05 1.65 0.20 1.14</p><p>Reef 19138 (1996) and Reef 19138 (2007)</p><p>Bray-Curtis Dissimilarity = 17.81</p><p>Taxonomic group Reef 19138 1996 Reef 19138 Dissimilarity Contribution (% cover) 2007 (% cover) (%) (%)</p><p>Tabulate Acropora 32.64 43.34 5.35 30.02</p><p>Branching Acropora 14.01 9.38 2.31 12.98</p><p>Encrusting Porites 0.70 3.20 1.25 7.01</p><p>Encrusting Montipora 9.84 7.75 1.05 5.87</p><p>Seriatopora 2.17 0.14 1.02 5.71</p><p>Soft Coral 6.14 4.35 0.89 5.02</p><p>Hydnophora 2.76 1.44 0.66 3.71</p><p>Stylophora 2.97 1.70 0.63 3.54</p><p>Fungia 1.04 0.00 0.52 2.91</p><p>Merulina 0.88 0.07 0.41 2.28</p><p>Echinopora 2.60 3.33 0.37 2.05</p><p>Mycedium 0.17 0.88 0.36 2.00 Turbinaria 0.79 0.14 0.33 1.84</p><p>Favia 1.13 1.77 0.32 1.79</p><p>Massive Porites 3.89 3.26 0.31 1.75</p><p>Leptoria 0.09 0.54 0.23 1.28</p><p>Galaxea 0.87 0.48 0.20 1.10</p><p>Horseshoe Reef (1997) and Horseshoe Reef (2011)</p><p>Bray-Curtis Dissimilarity = 31.6</p><p>Taxonomic group Horseshoe Reef Horseshoe Reef Dissimilarity Contribution 1997 (% cover) 2011 (% cover) (%) (%)</p><p>Tabulate Acropora 31.94 48.54 8.30 26.25</p><p>Foliose Montipora 10.47 1.21 4.63 14.65</p><p>Encrusting Porites 3.85 11.82 3.98 12.60</p><p>Soft Coral 10.32 5.08 2.62 8.29</p><p>Encrusting Montipora 11.94 6.80 2.57 8.13</p><p>Isopora 3.81 0.19 1.81 5.72</p><p>Seriatopora 2.12 4.26 1.07 3.38</p><p>Massive Porites 0.33 2.41 1.04 3.30</p><p>Stylophora 3.10 1.33 0.88 2.79</p><p>Pocillopora 4.01 2.92 0.54 1.72</p><p>Echinopora 2.40 1.40 0.50 1.59</p><p>Cyphastrea 0.13 1.08 0.48 1.51</p><p>Digitate Acropora 4.14 3.24 0.45 1.42</p><p>Green Island Reef (1996) and Green Island Reef (2009)</p><p>Bray-Curtis Dissimilarity = 19.86</p><p>Taxonomic group Green Island Reef Green Island Reef Dissimilarity Contribution 1996 (% cover) 2009 (% cover) (%) (%)</p><p>Massive Porites 11.77 18.61 3.42 17.22</p><p>Soft Coral 30.42 23.85 3.28 16.52</p><p>Branching Acropora 18.95 14.42 2.27 11.41</p><p>Encrusting Montipora 3.45 6.55 1.55 7.82</p><p>Tabulate Acropora 19.77 17.43 1.17 5.90</p><p>Lobophyllia 1.02 3.15 1.06 5.34</p><p>Pocillopora 0.16 1.70 0.77 3.87</p><p>Digitate Acropora 1.74 0.26 0.74 3.71</p><p>Encrusting Porites 0.17 1.57 0.70 3.52</p><p>Favites 1.91 0.79 0.56 2.84</p><p>Stylophora 0.17 0.92 0.37 1.87</p><p>Merulina 0.70 0.13 0.28 1.43</p><p>Galaxea 1.05 1.57 0.26 1.32</p><p>Echinopora 0.88 0.39 0.24 1.22</p><p>Favia 1.40 0.92 0.24 1.20</p><p>Fungia 0.69 0.26 0.22 1.09</p><p>Leptastrea 0.52 0.92 0.20 1.01</p><p>Diploastrea 0.00 0.39 0.20 0.99</p><p>Foliose Montipora 0.51 0.13 0.19 0.95</p><p>Branching Porites 0.90 0.52 0.19 0.94</p><p>Fitzroy Island Reef (1997) and Fitzroy Island Reef (2011)</p><p>Bray-Curtis Dissimilarity = 25.50</p><p>Taxonomic group Fitzroy Island Reef Fitzroy Island Reef Dissimilarity Contribution 1997 (% cover) 2011 (% cover) (%) (%)</p><p>Branching Acropora 15.19 2.53 6.33 24.83</p><p>Encrusting Porites 2.64 12.56 4.96 19.46</p><p>Soft Coral 36.78 44.42 3.82 14.98 Seriatopora 4.00 0.86 1.57 6.14</p><p>Massive Porites 3.75 1.33 1.21 4.75</p><p>Galaxea 0.26 2.53 1.13 4.44</p><p>Encrusting Montipora 3.02 4.46 0.72 2.82</p><p>Branching Porites 5.51 4.25 0.63 2.47</p><p>Pachyseris 2.89 4.12 0.61 2.41</p><p>Lobophyllia 2.38 1.33 0.52 2.05</p><p>Echinopora 2.00 1.00 0.50 1.96</p><p>Merulina 3.12 2.19 0.46 1.81</p><p>Fungia 1.73 0.93 0.40 1.56</p><p>Foliose Montipora 8.18 8.91 0.37 1.43</p><p>Low Isles Reef (1996) and Low Isles Reef (2009)</p><p>Bray-Curtis Dissimilarity = 35.83</p><p>Taxonomic group Low Isles Reef Low Isles Reef Dissimilarity Contribution 1996 (% cover) 2009 (% cover) (%) (%)</p><p>Soft Coral 24.47 42.07 8.80 24.55</p><p>Encrusting Porites 4.90 14.91 5.00 13.96</p><p>Foliose Montipora 10.40 1.70 4.35 12.14</p><p>Branching Acropora 6.94 1.92 2.51 7.01</p><p>Echinopora 5.46 1.70 1.88 5.26</p><p>Merulina 3.39 0.52 1.44 4.01</p><p>Fungia 3.80 1.03 1.38 3.86</p><p>Encrusting Montipora 4.09 1.77 1.16 3.23</p><p>Seriatopora 3.78 1.55 1.11 3.11</p><p>Branching Porites 6.65 8.41 0.88 2.46</p><p>Galaxea 3.95 5.68 0.87 2.41</p><p>Tabulate Acropora 4.81 3.17 0.82 2.28 Pectinia 1.26 0.07 0.59 1.65</p><p>Pavona 1.11 0.30 0.41 1.14</p><p>Platygyra 0.07 0.89 0.41 1.14</p><p>Lobophyllia 2.01 2.73 0.36 1.00</p><p>Goniastrea 0.87 0.15 0.36 1.00</p>