The following captions describe the contents of the “Online resources” referred to in Chapter 2 of this thesis. These resources are compressed into the zip file "Chapter2". Software tools, procedures, and data outputs from the analyses are described in detail in Chapter 2. This chapter was published in Coral Reefs (DOI: https://doi.org/10.1007/s00338-021-02118-6).

Online resource 1. Supplementary figures S1–S9, Supplementary tables S1–S4, and Supplementary texts 1 and 2. This resource tabulates and describes small datasets and provides conceptual illustrations and detailed descriptions of the analytical procedures.

Online resource 2. Volume- and biomass conversions. ‘Samples’ lists raw results of the tissue analyses. Organisms are summarized in ‘summary’ and different benthic groups are summarized in ‘communities’. Volume- and biomass standardizations for fleshy algae and subgroups thereof are based on their average canopy heights.

Online resource 3. Hidden cave surfaces and volumes. All surveyed quadrats are listed in rows, and columns show individual (hardly accessible and, thus, hand-measured) cavities in each quadrat. ‘hidden cavity surface areas’ displays total surface areas and ‘hidden cavity volumes’ displays cavity volumes, as approximated from simple geometrical shapes.

Online resource 4. Coral cryptic surface ratios. Proportion of cryptic surface in percent of live coral surface for individuals of sheeting and stalking corals.

Online resource 5. Percent cover. ‘horizontal percent cover’ sheet lists raw results from horizontal (i.e. top-down) coral point counts. Sites are summarized in ‘horizontal site summaries’ and communities are summarized in ‘horizontal communities’. The tab ‘horizontal cover incl layers’ displays cover data that was used to calculate 3D metrics of reef communities (see Methods – ‘Relative cover on exposed and cryptic reef surfaces’). Percent cover and respective site summaries for percent cover on vertical and cryptic surfaces are provided in the following tabs.

Online resource 6. Absolute 3D surface cover. Surface areas of individual benthic biota for the total reef (reef summaries), as well as exposed areas (exposed summaries) and cryptic areas (cryptic summaries) individually. Communities are summarized in ‘communities’.

Online resource 7. Biovolumes and canopy heights. Canopy height measurements for individual surface types (horizontal, vertical, and cryptic) are listed in ‘canopy heights’, and summarized by site and surface type in ‘canopy summaries’. ‘emergent organisms’ lists in situ measured biovolumes of massive sponges and gorgonians. Total volumes are summarized by site in ‘reef volumes’ (total reef), ‘exposed volumes’ (exposed reef), and ‘cryptic volumes’ (cryptic reef). Benthic groups are summarized in ‘communities’.

Online resource 8. Standing stock of ash-free dry weights. Total weights are summarized by site in ‘reef summaries’ (total reef), ‘exposed summaries’ (exposed reef), and ‘cryptic summaries’ (cryptic reef). Benthic groups are summarized in ‘communities’.

Online resource 9. Standing stock of organic carbon. Total weights are summarized by site in ‘reef summaries’ (total reef), ‘exposed summaries’ (exposed reef), and ‘cryptic summaries’ (cryptic reef). Benthic groups are summarized in ‘communities’.	

Online resource 10. Standing stock of organic nitrogen. Total weights are summarized by site in ‘reef summaries’ (total reef), ‘exposed summaries’ (exposed reef), and ‘cryptic summaries’ (cryptic reef). Benthic groups are summarized in ‘communities’.

Online resource 11. Site coordinates and substrate surface areas. ‘substrates’ sheet lists relief and surface areas of horizontal, vertical, and cryptic reef surfaces, as well as all surfaces combined (i.e. total surface area). Sites are summarized and coordinates are provided in ‘site summaries’.

Coral reef 3D reconstructions. 3D models of 191 m2 of coral reef benthos are provided in an interactive format on Sketchfab (www.sketchfab.com) under the account ‘coralreefs.kornder’. Models are named by site and quadrat (e.g. Carmabi 1 – 16 chronologically relate to the 16 rows with site = Carmabi across all Online resources).


The folder "Relative_cover_images" contains the pictures that were analyzed in Coral Point Count with Excel extension (CPCe). The manual is available here:

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwibz7en3IP-AhWvhv0HHVPBA5oQFnoECBAQAQ&url=https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FMujiyanto_Mujiyanto%2Fpublication%2F306475164_Manual_CPCe_versi_41_Manual_guide_for_identificatioan_coral_point_with_CPCe_mujiyanto%2Flinks%2F57be60fe08aeda1ec38628d4%2FManual-CPCe-versi-41-Manual-guide-for-identificatioan-coral-point-with-CPCe-mujiyanto.pdf&usg=AOvVaw2TaYH2xT1XcLTrd0lkHTGP

and further helpful notes can be downloaded here:
https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwiM1IDh8oP-AhXFu6QKHYgYCNsQFnoECA4QAQ&url=https%3A%2F%2Fhcas.nova.edu%2Ftools-and-resources%2Fcpce%2Fcpce_41_help.pdf&usg=AOvVaw3eImXi6Sy7co6SZxjKbM_f

The subfolders are structured per site, with additional subfolders for the transects (i.e., T1 and T2) per site, and the analyzed surface type (i.e., Horizontal, Vertical, or Cryptic). CPCe returns the analysis report for each image as a "cpc" file that can be opened in CPCe as long as this cpc file and its related image is stored in CPCe's directory. It also returns summaries of the analysis per transect and meta-data in xlsx and csv format. All of these files are stored as per the naming convention above in their respective subfolders, with the additional abbreviation and numbering of surface type (H = horizontal -> one image per cube, V = vertical -> 3 images per cube, C = cryptic -> 3 images per cube). For instance, the image titled "SBT1C1V1" in the subfolder "Snake_bay"->"T1"->"Vertical" is the third image of a vertical surface in the first cube of transect 1 at Snake Bay, corresponding to the numbers in the third row where the column "Site" says "Snake Bay" in the supplementary datasets published online (see MS1 in the Data Journal). The respective cpc file has the same name and the summaries in xlsx and csv returned by CPCe for this transect are titled "SBT1V". An exception from this are the CPCe output files from horizontal cover analyses at some sites (i.e., East, Eastpoint, Jeremi, Porto Marie, Santa Martha, and Sea Aquarium), which are missing from the dataset. Repeating the analysis using 80 stratified random points per image (see Chapter 2 Methods for details) should yield CPCe outputs similar to those underlying the analysis in Chapter 2. In addition, each last subfolder contains an xlsx file titled "Areas" that lists the absolute surface areas of each image in that folder.


Large sets of raw images for the photogrammetric reconstruction of the reef benthos presented in Chapter 2 are compressed here as individual zip files. The analysis and results are published online at https://doi.org/10.1007/s00338-021-02118-6.

zip files are named by "Site_name" (e.g., "Eastpoint" or "Snake_bay"). Each site contained 2 transects with 8 photoquadrats per transects. The photoquadrats are referred to as "cubes" since all benthos below is analyzed. Images underlying individual reconstructions of each cube are sorted in folders named after abbreviations of site and numbering of transects and cubes. For instance, the subfolder "EPT1C1" in the zip file "Eastpoint" contains the images for the 3D model of Cube 1 of Transect 1 at Eastpoint, titled "Eastpoint_1" on sketchfab.com (profile: coralreefs.kornder). Each site contains a total of 16 cubes (2 transects á 8 cubes) and those 16 cubes are consecutively numbered on sketchfab. For instance, the subfolder "SBT2C8" in the zip file "Snake_bay" contains the images for the 3D model of Cube 8 of Transect 2 at Snake bay, titled "Snake_bay_16" on sketchfab. To keep the zip files small, some sites were packed into two zip files, one for each of the two transects. In addition, the zip files "Conversion_overhangs" and "Error_estimate" contain the images underlying additional 3D reconstructions to estimate the discrepancy between 3D modeled and hand-measured surface areas of hardly inaccesible cavities and the general modeling error of the digital reconstructions, respectively (see Methods in Chapter 2 for details).