*2.3. Coral Reef Cover Analysis*

The percentage cover of the substrates at the different study sites was compiled and processed using the Reef Check Substrate data entry sheet in the Microsoft Excel application [39]. To investigate differences in the benthic community between the study sites, Principal Component Analysis and Bray–Curtis Cluster Analysis were carried out using PAST version 3.22 (Øyvind Hammer, Oslo, Norway) [40]. The mean percentage covers of substrate categories were analysed using IBM SPSS Statistics (Version 27.0, IBM, Armonk, NY, USA). Mann–Whitney *U*-tests were used to test for differences in the substrate between the Palk Bay and Palk Strait reefs. Differences in proportions of main benthic categories (HC, SC, RC, NIA, RB) amongst sites were tested using a Kruskal–Wallis test. To assess the status of the reefs, a coral mortality index (CMI) was calculated by dividing the percentage values of dead coral cover by the combined value of live and dead coral cover. If the CMI was greater than 0.33, the reef was considered likely to have been impacted by natural or anthropogenic stressors [41]. Sites were also classified based on the amount of live coral cover as excellent (75–100% live coral), good (50–74.9% live coral), fair (25–49.9% live coral), or poor (0–24.9% live coral) [41].
