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 (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. (DOC)

表A. 波拿巴群岛（Bonaparte Archipelago）23个研究样地的详细信息。
表B. 本研究样地及用于对比分析的额外样地的位置、坐标、调查方法与近似调查面积。
表C. 物理变量的坐标信息。
表D. 带注释的物种名录。名录收录了标本馆藏号，以及物种在局域、类群和区域尺度上的样地占用情况，同时包含基于昆士兰博物馆珊瑚数据库标本记录的已知深度带（如5米潮下带）。
表E. 单因素方差分析（one-way analysis of variance）的显著性结果汇总，用于比较不同样地间海表温度（SST, Sea Surface Temperature）与Kd(490)时间序列数据的均值差异。
图A. 置换物种累积曲线（permutated species accumulation curves）。在波拿巴群岛中，当调查约20个样地后，局域物种多样性即可得到充分采样覆盖。
图B. 珊瑚物种多样性的半定量空间对比。该图显示，三个波拿巴岛群（蓝色标注的马雷岛群、贝蒂埃岛群与蒙塔利韦岛群）的多样性水平，与大堡礁的登特岛、博德岛，以及印度洋东北部远洋离岸海域的圣诞岛这类更典型、物理环境极端性更低的珊瑚礁生境的估算多样性水平相近。其每100平方米的物种多样性水平高于阿什莫尔礁（金伯利近海）、蜥蜴岛（大堡礁北部）、科斯雷与马朱罗环礁（中太平洋）以及红海。数据汇总自文献[37]、[72–77]。
图C. 23个潮间带调查样地内属级阶元下的物种水平多样性。注：有27个属仅包含单一物种（详见补充材料S1文件中的表D）。
图D. 2007年10月调查期间，马雷岛北岛的每日潮汐周期（涵盖选取的大潮与小潮时段）。在大潮低潮（即潮位≤2米）时，马雷岛北岛潮间带礁坪上的珊瑚会一次暴露于空气中长达3.5小时；而在小潮期间，珊瑚始终处于至少1米深的海水之下。详见图5，该图展示了2002–2014年潮汐占比的时间序列分析，涵盖0–1米至7–8米共1米间隔的潮位区间。
图E. 2002–2014年的时间序列数据，展示基于8日平均的5个样地的海表温度（SST）。该图显示，马雷岛北岛的海表温度在2013年2–3月超过了+1℃的珊瑚白化阈值。
图F. 2002–2014年Kd(490)的空间对比。Kd(490)指490 nm波长下行辐照度的漫衰减系数，可作为浊度的衡量指标。
图G. 2002–2014年马雷岛北岛的Kd(490)时间序列。蓝色线代表冬季平均浊度水平，红色线代表夏季平均浊度水平。（DOC）