Appendix 1. By period comparison of coral cover for each of the IO major reef regions. The non-parametric Kruskal-Wallis (K-W) test was used to compare difference in mean values and the Kolmogorov-Simirnov (K-S) test to compare differences in the cumulative distribution functions. See Table 1 for region and country names. Regional codes are included in parentheses; see Table 1 and Fig. 1.

Region / K-W/ K-S statistic / Per 1 vs Per 2 / Per 1 vs Per 3 / Per 1 vs Per 4 / Per 2 vs Per 3 / Per 2 vs Per 4 / Per 3 vs Per 4
CIOI (4) / 2 / Z / 8.06 / 1.48 / 55.85 / 4.06 / 45.5 / 3.52 / 192.41 / 7.01 / 150.3 / 6.26 / 13.94 / 1.9
p / 0.005 / 0.024 / <0.0001 / <0.0001 / <0.0001 / <0.0001 / <0.0001 / <0.0001 / <0.0001 / <0.0001 / 0.0002 / 0.001
EAFR (5) / 2 / Z / 20.01 / 2.05 / 4.01 / 1.75 / 9.29 / 1.64
p / <0.0001 / <0.0001 / 0.045 / 0.004 / 0.002 / 0.009
EIO (6) /  / 0.62 / 0.84 / 6.67 / 1.42 / 2.92 / 1.65
p / 0.43 / 0.49 / 0.01 / 0.04 / 0.09 / 0.009
GULF (7) / 
p
IND-SRI (8) /  / 19.82 / 2.37 / 0.03 / 0.76 / 24.49 / 2.59
p / <0.0001 / <0.0001 / 0.87 / 0.61 / <0.0001 / <0.0001
MOZ-SAF (9) /  / 0.12 / 0.69
p / 0.73 / 0.72
RS-GA (10) /  / 0.77 / 0.57 / 0.003 / 0.89 / 2.3 / 1.21
p / 0.38 / 0.9 / 0.96 / 0.4 / 0.13 / 0.11
SWIOI (11) /  / 2.36 / 1.27 / 7.53 / 1.61 / 3.54 / 1.51
p / 0.13 / 0.08 / 0.006 / 0.01 / 0.06 / 0.02
Overall IO /  / 2.37 / 1.1 / 50.87 / 3.29 / 8.97 / 1.51 / 162.14 / 5.76 / 57.17 / 3.77 / 63.1 / 3.76
p / 0.12 / 0.18 / <0.0001 / <0.0001 / 0.003 / 0.02 / <0.0001 / <0.0001 / <0.0001 / <0.0001 / <0.0001 / <0.0001

Appendix 2. By region comparison of coral cover for the 10 IO regions for each period. The non-parametric Kolmogorov-Simirnov test was used and significant p values indicated in bold font. See Table 1 for region and country names. Regions with sample size < 20 in a certain period were excluded from the analysis.

Regions / Period 1 / Period 2 / Period 3 / Period 4
2 / p / Z / p / 2 / p / Z / p / 2 / p / Z / p / 2 / p / Z / p
AUSW v CIOI / 30.77 / <0.0001 / 2.58 / <0.0001
AUSW v EAFR / 72.36 / <0.0001 / 1.12 / 0.16
AUSW v EIO / 185.48 / <0.0001 / 1.57 / 0.02
AUSW v GULF / 187.34 / <0.0001 / 0.91 / 0.38
AUSW v IND-SRI / 199.01 / <0.0001 / 1.39 / 0.04
AUSW v MOZ-SAF / 207.41 / <0.0001 / 1.49 / 0.03
AUSW v RS-GAD / 227.2 / <0.0001 / 1.77 / 0.004
AUSW vSWIOI / 248.25 / <0.0001 / 1.49 / 0.02
CIOI v EAFR / 3.1 / 0.08 / 1.21 / 0.11 / 44.41 / <0.0001 / 3.19 / <0.0001 / 54.42 / <0.0001 / 3.84 / <0.0001
CIOI v EIO / 13.76 / 0.001 / 1.74 / 0.005 / 98.7 / <0.0001 / 4.31 / <0.0001 / 185.87 / <0.0001 / 6.29 / <0.0001
CIOI v GULF / 14.94 / 0.002 / 1.4 / 0.04 / 95.08 / <0.0001 / 2.25 / <0.0001 / 187.91 / <0.0001 / 1.88 / 0.002
CIOI v IND-SRI / 15.52 / 0.004 / 0.79 / 0.56 / 93.78 / <0.0001 / 1.12 / 0.17 / 200.41 / <0.0001 / 3.97 / <0.0001
CIOI v MOZ-SAF / 116.01 / <0.0001 / 3.24 / <0.0001 / 209.41 / <0.0001 / 3.39 / <0.0001
CIOI v RS-GAD / 19.98 / 0.001 / 1.84 / 0.002 / 22.61 / 0.001 / 1.06 / 0.22 / 137.36 / <0.0001 / 3.6 / <0.0001 / 230.13 / <0.0001 / 5.37 / <0.0001
CIOI v SWIOI / 27.02 / <0.0001 / 1.49 / 0.02 / 234.52 / <0.0001 / 6.6 / <0.0001 / 251.62 / <0.0001 / 5.9 / <0.0001
EAFR v EIO / 18.4 / <0.0001 / 2.05 / <0.0001 / 25.64 / <0.0001 / 3.06 / <0.0001
EAFR v GULF / 13.53 / 0.001 / 1.71 / 0.006 / 19.89 / <0.0001 / 1.1 / 0.18 / 26.41 / <0.0001 / 0.8 / 0.55
EAFR v IND-SRI / 13.87 / 0.003 / 1.06 / 0.22 / 29.06 / <0.0001 / 1.72 / 0.005 / 26.99 / <0.0001 / 1.86 / 0.002
EAFR v MOZ-SAF / 34.75 / <0.0001 / 1.21 / 0.11 / 35.96 / <0.0001 / 0.89 / 0.4
EAFR v RS-GAD / 20.54 / 0.001 / 0.8 / 0.55 / 37.49 / <0.0001 / 1.19 / 0.12 / 48.62 / <0.0001 / 1.66 / 0.008
EAFR v SWIOI / 25.66 / <0.0001 / 1.39 / 0.04 / 87.93 / <0.0001 / 3.35 / <0.0001 / 53.16 / <0.0001 / 2.81 / <0.0001
EIO v GULF / 11.07 / 0.001 / 1.91 / 0.001 / 1.54 / 0.22 / 0.89 / 0.41
EIO v IND-SRI / 21.92 / <0.0001 / 2.42 / <0.0001 / 3.55 / 0.17 / 1.12 / 0.17
EIO v MOZ-SAF / 26.12 / <0.0001 / 0.9 / 0.4 / 18.55 / <0.0001 / 2.19 / <0.0001
EIO v RS-GAD / 28.83 / <0.0001 / 1.41 / 0.04 / 38.24 / <0.0001 / 2.83 / <0.0001
EIO v SWIOI / 5.12 / 0.16 / 0.56 / 0.92 / 62.83 / <0.0001 / 1.7 / 0.006 / 41.07 / <0.0001 / 1.7 / 0.006
GULF v IND-SRI / 2 / 0.16 / 0.75 / 0.63 / 2.13 / 0.15 / 1.06 / 0.21 / 0.23 / 0.63 / 0.76 / 0.6
GULF v MOZ-SAF / 14.06 / 0.001 / 1.32 / 0.06 / 4.49 / 0.11 / 0.67 / 0.76
GULF v RS-GAD / 16.36 / 0.001 / 1.66 / 0.008 / 18.52 / <0.0001 / 1.45 / 0.03 / 5.28 / 0.15 / 0.54 / 0.93
GULF v SWIOI / 20.67 / <0.0001 / 1.17 / 0.13 / 60.11 / <0.0001 / 2.81 / <0.0001 / 17.24 / 0.002 / 0.85 / 0.46
IND-SRI v MOZ-SAF / 13.24 / <0.0001 / 2.04 / <0.0001 / 4.45 / 0.04 / 1.18 / 0.13
IND-SRI v RS-GAD / 4.53 / 0.1 / 1 / 0.27 / 16.58 / <0.0001 / 2.08 / <0.0001 / 5.26 / 0.07 / 1.24 / 0.09
IND-SRI v SWIOI / 11.4 / 0.01 / 0.79 / 0.57 / 46.19 / <0.0001 / 2.79 / <0.0001 / 17.22 / 0.001 / 0.57 / 0.9
MOZ-SAF v RS-GAD / 1.1 / 0.29 / 0.7 / 0.7 / 0.57 / 0.45 / 0.79 / 0.56
MOZ-SAF v SWIOI / 21.29 / <0.0001 / 1.49 / 0.24 / 16.18 / <0.0001 / 1.72 / 0.005
RS-GAD v SWIOI / 8.64 / 0.003 / 1.9 / 0.002 / 20.36 / <0.0001 / 2.23 / <0.0001 / 12.21 / <0.0001 / 2.03 / 0.001