Combined supporting information file.

Table A. Details of the 23 study sites in the Bonaparte Archipelago. Table B. Location, co-ordinates, method and approximate area surveyed of our study sites and additional sites used for comparative purposes. Table C. Co-ordinates for physical variables. Table D. Annotated species list. Listed are the specimen accession numbers and site occupancy at local, group and regional scales including known depth zone i.e. <5m (intertidal) or >5m (subtidal) based upon the specimen-based records in the Queensland Museum coral database. Table E. Summary of significance results from one-way analysis of variance comparing the mean SST and Kd(490) time-series data between locations. Figure A. Permutated species accumulation curves. The local species diversity was adequately surveyed after approximately 20 sites were surveyed in the Bonaparte Archipelago. Figure B. Semi-quantitative spatial comparison of coral species diversity. This figure illustrates that the three Bonaparte Island groups (Maret I., Berthier I., and Montalivet I., in blue) have a similar level of diversity to that estimated for other more typical and less physically extreme reef locations such as Dent I. and Border I. on the Great Barrier Reef and Christmas I., an offshore oceanic location in the NE Indian Ocean. The level of diversity per 100m2 is higher than Ashmore Reef (Offshore Kimberley); Lizard I. (Northern GBR); Kosrae and Maju ro Atoll (Central Pacific) and the Red Sea. Data summarized from [37], [72–77]. Figure C. Species level diversity within genera at the 23 intertidal survey sites. Note: 27 genera were represented by a single species (Table D in S1 File). Figure D. Daily tidal cycle at North Maret Island on selected spring and neap tides over our survey period in October 2007. During spring low tides (i.e. tides ≤ 2m), corals growing on the intertidal reef platform at North Maret I. are exposed to the air for up to 3.5 hours at a time whereas at neap tide, corals remain submerged by at least 1m of water. See Fig. 5 for a time-series analysis showing the proportion of tides occurring at 1m intervals from 0–1m up to 7–8m. Figure E. Time series (2002–2014) showing SST data based on 8-day averages for 5 locations. This figure shows at North Maret I. SST surpassed the +1°C bleaching threshold in Feb-March 2013. Figure F. Spatial comparison of Kd(490), 2002–2014. Kd(490) represents the diffuse attenuation coefficient of down-welling irradiance at 490 nm and is used as a measure of turbidity. Figure G. Kd(490) time series for North Maret I. from 2002–2014. The blue line represents the average winter turbidity level and the red represents the average summer turbidity.
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