Lauren T. Toth 20250604 tabular and raster digital data Lauren T. Toth Selena A. Johnson Erin Lyons Connor Jenkins Anastasios Stathakopoulos Sierra Bloomer Jennifer Mallon Ian Combs 20250604 tabular and raster digital data U.S. Geological Survey data release doi.org/10.5066/P13HMEON St. Petersburg, FL U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center https://doi.org/10.5066/P13HMEON During the summers of 2022 and 2023, U.S. Geological Survey (USGS) researchers conducted underwater surveys aimed at quantifying the impact that past coral restoration by Mote Marine Laboratory had on the reef-accretion process. The surveys were conducted along paired transects representing restored and non-restored areas of eight offshore reefs and three patch-reef sites in the Lower Florida Keys. At each location on each reef, USGS researchers conducted photographic surveys (these images are published in an accompanying release by Johnson and others, 2025) to generate structure-from-motion (SfM) products (point clouds, orthomosaics, and digital surface models [DSMs]), which were used to quantify percent cover of corals and other benthos and topographic complexity. USGS researchers also conducted census surveys of bioeroding parrotfishes, urchins, and sponges at each site. The percent cover and census-survey data were used in an associated study (Toth and others, 2025) to quantify differences in carbonate budgets (gross carbonate production, bioerosion, and reef-accretion potential) between restored and non-restored areas of each reef. The SfM were also used to quantify the impact of restoration on topographic complexity at the offshore sites by measuring the impact of digitally removing outplanted coral colonies. Following USGS data management protocols, these data were assigned the following field activity numbers (FANs), 2022-324-FA, 2022-353-DD, and 2023-311-FA. Additional survey and data details are available on the Coastal and Marine Geoscience Data System (CMGDS) at https://cmgds.marine.usgs.gov/. 20220711 20230718 ground condition Complete None planned Lower Florida Keys -81.8783 -81.3626 24.6216 24.4517 USGS Metadata Identifier USGS:0cb09b6b-7c38-4c6f-a1dc-afc4033ab4be ISO 19115 Topic Category biota elevation oceans USGS Thesaurus reef ecosystems coelenterates ecology ecological processes ecosystem functions remediation ecosystem monitoring ecosystem management erosion topography Geographic Names Information System Florida Keys State of Florida No access constraints. Please see 'Distribution Information' for details. These data are marked with a Creative Common CC0 1.0 Universal License. These data are in the public domain and do not have any use constraints. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Lauren T Toth U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center Research Physical Scientist mailing and physical

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St. Petersburg FL 33701 United States 727-502-8029 ltoth@usgs.gov The collection of these data was funded by the U.S. Geological Survey Coastal/Marine Hazards and Resources Program and a Mote Marine Laboratory 'Protect Our Reefs' Grant. Environment as of Metadata Creation: Microsoft Windows 11 Enterprise Version 23H2; Microsoft Excel Version 2402; ReefBudget Caribbean Version 2.0; CoralNet Version 2.0; Agisoft Metasahpe Pro Version 2.0 or later Lauren T. Toth Selena A. Johnson Erin O. Lyons Jason Spadaro Anastasios Stathakopoulos Sierra K. Bloomer Jennifer Mallon Connor M. Jenkins Sara D. Williams Ian Combs Zachary Craig Erinn Muller 2025 publication Scientific Reports Unknown Online Springer Nature https://doi.org/10.1038/s41598-025-04818-3 Selena A. Johnson Lauren T. Toth Connor M. Jenkins Erin O. Lyons 20250604 raster digital data U.S. Geological Survey data release doi:10.5066/P1WHKTRD St. Petersburg, FL U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center https://doi.org/10.5066/P1WHKTRD Christopher T. Perry Ines D. Lange 2019 publication Online University of Exeter https://geography.exeter.ac.uk/reefbudget/ Travis A. Courtney Ines D. Lange S. Sannassy Pilly Joseph E. Townsend S. Chan Christopher T. Perry D. J. Kriegman Andreas J. Andersson 20240807 2.0 software Online Zenodo https://doi.org/10.5281/zenodo.13257132 Lauren T. Toth Anastasios Stathakopoulos Ilsa B. Kuffner 20180426 tabular and raster digital data U.S. Geological Survey data release doi:10.5066/F7NV9HJX Petersburg, FL U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center https://doi.org/10.5066/F7NV9HJX D. W. Kinsey 1985 publication Proceedings of the Fifth International Coral Reef Congress, Tahiti Volume 4 Tahiti, French Polynesia International Association for Biological Oceanography Pages 505-526 Daniel T.I. Bayley Andrew O.M. Mogg 20200829 publication Methods in Ecology and Evolution Volume 11, Issue 11 Online Wiley Pages 1410-1420 https://doi.org/10.1111/2041-210X.13476 Alexander R. Ilich Benjamin Misiuk Vincent Lecours Steven A. Murawski 20230526 publication Transactions in GIS Volume 27, Issue 4 Online Wiley Pages 1164-1204 https://doi.org/10.1111/tgis.13067 No formal attribute accuracy tests were conducted. No formal logical accuracy tests were conducted. The data set is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details. No formal positional accuracy tests were conducted. The horizontal coordinates were collected in the World Geodetic System of 1984 (WGS 84) coordinate system. Study locations: Surveys were conducted at eight offshore reefs and three patch-reef sites in the Lower Florida Keys where Mote Marine Laboratory researchers have been actively restoring coral populations in recent years. The reefs at Looe Key, Summerland Ledges, American Shoal, and Mote Site C were surveyed in the summer of 2022 (July 11-18) and the sites at Sand Key, Rock Key, Eastern Dry Rocks, Marker 32, Dog's Leg, Cat's Paw, and Cook Island were surveyed in the summer of 2023 (July 11-18). Restored and non-restored areas of the reef were surveyed at each site. For restored transects, SCUBA (self-contained underwater breathing apparatus) divers identified areas of the reef with a high density of outplanted corals and placed transects within those areas. Non-restored transects were placed on nearby areas of the reef (adjacent spurs or ledges for offshore reef sites) where no outplants were present. 20230717 Coral_reef_site_data.csv Coral_reef_site_data.xlsx Lauren T. Toth U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center Research Physical Scientist mailing and physical

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St. Petersburg FL 33701 United States 727-502-8029 ltoth@usgs.gov Photographic surveys for Structure-from-Motion (SfM): At each site, except for Summerland Ledges, 10–12 (approximately 10 x 2 meters [m] in size) photographic transects were surveyed by SCUBA divers using a downward facing Canon Powershot S120 camera in an underwater housing set to collect RAW image format in continuous shoot mode. Summerland Ledges is an experimental restoration site consisting of two 10 x 10 m restored area and one 10 x 10 m control plot. The two restored plots at Summerland Ledges were surveyed 2m from the reef base using a dual Nikon D7000 DSLR camera system and the control plot was surveyed using a Canon EOS R at the surface. The number of transects varied per site depending on the availability of restored or control reef. All images were collected 1-2m from the reef base using a double-lawnmower swim pattern ensuring 70-80% forward and lateral overlap between images. Prior to image acquisition, the diver used a metric field tape to delineate the sampling area then placed 3-4 coded 25-centimeter (cm) scalebar targets evenly throughout the transect areas to provide accurate scale for models. For more information about the photographic surveys and access to the associated imagery, refer to Johnson and others (2025). 20230717 Selena A. Johnson U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center Research Physical Scientist mailing and physical

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St. Petersburg FL 33701 United States 727-502-8053 selenajohnson@usgs.gov Structure-from-motion data processing: SfM data products (point clouds, digital surface models, and orthomosaics) were generated using Agisoft Metasahpe Pro v2.0 or later generally following the protocols of Bayley and Mogg (2020). For a thorough description of the workflow and settings, refer to Toth and others (2025) supplemental information section. Briefly, the images from each transect were checked for proper orientation then uploaded into Metashape. Three-dimensional (3D) Models were then generated using the following basic steps: 1) align images into a sparse point cloud, 2) scale model and run initial bundle adjustment for lens calibration, 3) reduce number of low quality points in the model to improve accuracy, 4) orient and position the model in local coordinates, 5) generate dense 3D point cloud, 6) segment point cloud into classes: noise, reef base, canopy, and outplants, 7) filter point cloud based on segmentation classes to generate digital surface models (DSMs), 8) render orthomosaics and 9) export all SfM data products. The open-source R Multiscale DTM package (Ilich and others, 2023) was used to calculate structural complexity metrics from 1-centimeter (cm) resolution exports of the DSMs. The package calculates 15 metrics encompassing terrain attributes from five common terrain groups: slope, aspect, curvature, relative position, and roughness. For this study, four included Multiscale DTM roughness metrics were extracted with a 5x5 neighborhood window size: adjusted standard deviation, roughness index, and vector ruggedness. These metrics were found to be highly correlated so the analysis focused on vector ruggedness (VRM). The impact of restoration on average reef elevation (relative to the lowest point of each transect model) and overall surface area-to-planar-area ratio (rugosity) of the transects was also evaluated. SfM data are published in individual zipped folders, per study site (the eight offshore reefs and three patch-reef sites) and organized into sub-folders per data product: DEMs (Tagged Image File format, .tif), orthomosaics (.tif), and point clouds (LASer file, .las). 2024 Coral_reef_topographic_complexity_data.csv Coral_reef_topographic_complexity_data.xlsx AmericanShoal_SfMproducts.zip CatsPaw_SfMproducts.zip CookIsland_SfMproducts.zip DogsLeg_SfMproducts.zip EasternDryRocks_SfMproducts.zip LooeKey_SfMproducts.zip Marker32_SfMproducts.zip RockKey_SfMproducts.zip SandKey_SfMproducts.zip SiteC_SfMproducts.zip Summerland_SfMproducts.zip Selena A. Johnson U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center Research Physical Scientist mailing and physical

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St. Petersburg FL 33701 United States 727-502-8053 selenajohnson@usgs.gov Quantifying percent cover of reef benthos: Percent cover of calcifying reef taxa (corals and crustose coralline algae) and other benthos were quantified by conducting point-count analysis of a 10 x 1 meter (m) belt transect within the two-dimensional (2D) orthomosaics described above using the online software, CoralNet (https://coralnet.ucsd.edu/). Briefly, 10, non-overlapping 1 x 1 m images were extracted from each orthomosaic and the benthos beneath each of 150 points were identified. All coral taxa were identified to species, except for Orbicella, Pseudodiploria, and Millepora spp. which were later pooled by genera. Other benthos, including crustose coralline algae, macroalgae, sponges, gorgonians, zoanthids, consolidated bare substrate (which was generally covered in turf algae), and unconsolidated substrate (sand and rubble) were identified categorically. 2023 Coral_reef_percent_cover_data.csv Coral_reef_percent_cover_data.xlsx Lauren T. Toth U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center Research Physical Scientist mailing and physical

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St. Petersburg FL 33701 United States 727-502-8029 ltoth@usgs.gov Bioerosion census surveys: USGS researchers conducted census surveys of bioeroding parrotfish, sponges, and urchins following the ReefBudget v2 protocol (Perry and Lange, 2019) in the same reef areas where the structure-from-motion surveys were conducted. Divers recorded the number and size of bioeroding sponges (Cliona aprica, C. caribbaea, C. tenuis, C. varians, C. delitrix, and Siphonodictyon coralliphagum) and bioeroding urchins (Diadema antillarum, Echinometra lucunter, Ec. viridis, and Eucidaris tribuloides) along the same 10-m transects surveyed for structure-from-motion. Sponge surveys were conducted within a 1-m belts around the transects and urchin surveys were conducted within 2-m belts. Researchers also recorded the species, size, and life phase of bioeroding parrotfish (Sparisoma viride, Sp. aurofrenatum, Sp. rubripinne, Sp. chrysopterum, Scarus vetula, Sc. taeniopterus, Sc. iseri, Sc. guacamaia, Sc. coeruleus, and Sc. coelestinus) within 8–10 larger (25 x 4 m) belt-transects to estimate site-level parrotfish bioerosion. Note that because of the larger size of the parrotfish transects and their highly mobile nature, parrotfish surveys could not be conducted separately in restored and non-restored areas of the reefs. 2023 Coral_reef_sponge_census_data.csv Coral_reef_sponge_census_data.xlsx Coral_reef_urchin_census_data.csv Coral_reef_urchin_census_data.xlsx Coral_reef_parrotfish_census_data.csv Coral_reef_parrotfish_census_data.xlsx Lauren T. Toth U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center Research Physical Scientist mailing and physical

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St. Petersburg FL 33701 United States 727-502-8029 ltoth@usgs.gov Calculating coral reef carbonate budgets: To calculate gross carbonate production (in kilograms per meter squared per year [kg m-2 y-1]), the percent cover of each reef calcifier (from the point count analysis) was multiplied by area-normalized taxon-specific calcification rates (Courtney and others, 2024) and summed for each transect. Microbioerosion along each transect was estimated by multiplying the total area of consolidated, non-calcifying reef substrate (from the point-count analysis) by the western Atlantic mean microbioerosion rate of 0.24 kg m-2 y-1 (Perry and Lange, 2019). Bioerosion by parrotfish, sponges, and urchins were estimated by multiplying by the species-, size-, and, for parrotfish, life-phase-specific bioerosion rates suggested in ReefBudget v2 (Perry and Lange, 2019). Those data were summed with microbioerosion to estimate total bioerosion. Total bioerosion was subtracted from gross carbonate production to estimate net carbonate production. Reef-accretion potential was estimated according to the following equation (Kinsey, 1985): Reef-accretion potential=(Net carbonate production)/(p(1-porosity)), where p is the density of calcium carbonate (2.9 grams per cubic centimeter; Kinsey, 1985) and porosity was estimated from cores of geologic reef framework in the Florida Keys built by branching or massive corals (for offshore and patch-reef sites, respectively; Toth and others, 2018). 2024 Coral_reef_carbonate_budget_data.csv Coral_reef_carbonate_budget_data.xlsx Lauren T. Toth U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center Research Physical Scientist mailing and physical

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St. Petersburg FL 33701 United States 727-502-8029 ltoth@usgs.gov 0.0001 0.0001 Decimal degrees World Geodetic System 1984 (WGS 84) WGS_1984 6378137.0 298.257223563 Coral reef restoration surveys: Comma-separated values (.csv) and Microsoft Excel (.xlsx) files describing reef site information, benthic composition, bioeroder abundance, carbonate budgets, and topographic complexity of coral reefs in the Lower Florida Keys. Reef surveys were conducted in areas of each reef with and without corals outplanted by Mote Marine Laboratory’s coral restoration program. Detailed attribute descriptions for these files are included data dictionary (Data_Dictionary_Coral_reef_restoration_surveys.docx). These metadata are not complete without this file. The entity and attribute information were generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information. Structure-from-motion data products: USGS researchers conducted photographic surveys to generate SfM products (point clouds, orthomosaics, and digital elevation models), which were used to quantify percent cover of corals and other benthos and topographic complexity. The SfM data are published in individual zipped folders, per study site (the eight offshore reefs and three patch-reef sites) and organized into sub-folders per data product: DEMs (.tif), orthomosaics (.tif), and point clouds (.las). These files can be opened in any software capable of opening Geographic Information System (GIS) files. The entity and attribute information were generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information. U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center USGS SPCMSC Data Management mailing and physical

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Saint Petersburg FL 33701 United States 727-502-8000 gs-g-spcmsc_data_inquiries@usgs.gov Coral_reef_site_data.csv, Coral_reef_site_data.xlsx, Coral_reef_sponge_census_data.csv, Coral_reef_sponge_census_data.xlsx, Coral_reef_urchin_census_data.csv, Coral_reef_urchin_census_data.xlsx, Coral_reef_parrotfish_census_data.csv, Coral_reef_parrotfish_census_data.xlsx, Coral_reef_percent_cover_data.csv, Coral_reef_percent_cover_data.xlsx, Coral_reef_carbonate_budget_data.csv, Coral_reef_carbonate_budget_data.xlsx, Coral_reef_topographic_complexity_data.csv, Coral_reef_topographic_complexity_data.xlsx, Data_Dictionary_Coral_reef_restoration_surveys.docx, *.tif, and *.las Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. tabular digital data, LASer file, TIFF, Microsoft Word document https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Coral_reef_site_data.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Coral_reef_percent_cover_data.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Coral_reef_parrotfish_census_data.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Coral_reef_sponge_census_data.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Coral_reef_urchin_census_data.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Coral_reef_carbonate_budget_data.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Coral_reef_topographic_complexity_data.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/AmericanShoal_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/CatsPaw_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/CookIsland_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/DogsLeg_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/EasternDryRocks_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/LooeKey_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Marker32_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/RockKey_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/SandKey_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/SiteC_SfMproducts.zip https://coastal.er.usgs.gov/data-release/doi-P13HMEON/data/Summerland_SfMproducts.zip None 20250604 U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center USGS SPCMSC Data Management mailing and physical

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Saint Petersburg FL 33701 United States 727-502-8000 gs-g-spcmsc_data_inquiries@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata FGDC-STD-001.1-1999