National Coral Reef Monitoring Program: Coral demographic data (adult and juvenile corals, species, colony length, condition, etc.) collected during Stratified Random Surveys (S...

The data described here result from benthic coral demographic surveys within belt transects of specified length and width for two life stages (juveniles and adults) across the US Pacific since 2013. This data is collected as part of the NOAA Pacific Islands Fisheries Science Center (PIFSC) and Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) led National Coral Reef Monitoring Program (NCRMP) missions around the Mariana Archipelago, American Samoa, Pacific Remote Island Areas, and the Hawaiian Archipelago since 2013.

The in-situ diver coral demographic surveys are part of the Rapid Ecological Assessment (REA) surveys for corals and fish conducted during ESD-led NCRMP missions. From 2013 to 2017, a two-stage stratified random sampling (StRS) design was used to survey the coral reef ecosystems across sub-island sectors and three depth strata (shallow: 0-6m, mid: 6-18m and deep: >18m). Starting in 2018 a one-stage StRS design was employed. These sites represent a broad range of depths (1-25 m), habitat types (aggregate reef, patch reef, pavement, rock and boulder and rubble), coral cover, and diving conditions. Allocation of sampling effort was proportional to strata area and variance in coral density. The StRS design effectively reduces estimate variance through stratification using environmental covariates and by sampling more sites rather than sampling more transects at a site. Therefore, site-level estimates and site to site comparisons should be used with caution.

Starting in 2023 coral demographic data was also derived by the GIS analysis of benthic Structure from Motion (SfM) imagery. The source imagery was collected during in-water surveys conducted by divers, and is documented separately here: https://www.fisheries.noaa.gov/inport/item/63095.During each SfM survey, an 18m transect line was deployed along the isobath and photographed using underwater cameras while swimming in a back and forth swim pattern for later processing. At depths of 0-18m, SfM surveys were conducted over a 3 x 20m area and at depths >18m, a 3 x 13m area was surveyed, both with the transect running down the middle of the survey area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for juvenile and adult coral colony demographic metrics.

The data provide information on adult coral colony counts, morphology, size, partial mortality (old and recent dead), presence and causation of disease and other compromised health conditions, including bleaching. Juvenile colony surveys include morphology and size. Taxonomic identification of adult colonies is to the lowest taxonomic level possible and genus level for juveniles. Some segment observations were repeated for internal quality control starting in 2019, and indicated with a repeat segment flag and transectnum = -999; use column OG_OR_RPT_SEG to filter for only original segments. Refer to data dictionaries for details on column conditions.

The raw data also include individual observations of crustose coralline algae diseases and Alcyonarian disease type and lesion size as well as the presence of other Anthozoans, such as other cnidarians including Alcyonareans, Zoantharians, Corallimorpharians, and Antipatharians (does not apply to PMNM surveys conducted in 2014 and 2015 or surveys conducted after 2017).

The National Coral Reef Monitoring Program (NCRMP) details a long-term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various Coral Reef Conservation Coral Reef Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis.

This metadata record consolidates four metadata records for coral demography from different Pacific Islands Regions which are be referenced under 'Related Items'

Taxa codes/names and their genera can be updated over time. See reference table for taxonomic name changes.

Winston M, Couch C, Ferguson M, Huntington B, Swanson D, Vargas-Angel B. 2019. Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys, 2018 Update. NOAA Tech. Memo. NOAA-TM-NMFS-PIFSC-92, 66 p. doi:10.25923/w1k2-0y84

Suka R, Asbury M, Couch C, Gray A, Winston M, Oliver T. 2019. Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-93, 54 p. doi:10.25923/h2q8-jv47

Couch CS, Oliver, TA, Suka R, Lamirand M, Asbury M, Amir C, Vargas-Angel B, Winston M, Huntington B, Lichowski F, Halperin A, Gray A, Garriques J, & Samson J. 2021. Comparing coral colony surveys from in-water observations and structure-from-motion imagery shows low methodological bias. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.647943

Charendoff J.A., Couch C, Oliver T, Lamirand M, Amir C, Basden I, Torres-Pulliza D, Asbury M, Winston M, Huntington B, Lichowski F, Osborn N, Ehrenberg J, Garriques J, Samson J. 2023. Comparing coral demographic surveys from in situ observations and structure-from-motion photogrammetry on high diversity reefs shows low methodological bias but highlights persistent areas of concern. U.S. Dept. of Commerce, NOAA Technical Memorandum NMFS-PIFSC-153,52 52 p. doi:10.25923/8r7f-t404

Torres-Pulliza D, Charendoff J, Couch CS, Suka R, Gray A, Lichowski F, Amir C, Lamirand M, Asbury M, Winston M, Basden I, Oliver T 2024. Processing Coral Reef Imagery Using Structure-from-Motion Photogrammetry: Standard Operating Procedures (2023 Update) U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-159, 91 p. https://doi.org/10.25923/cydj-z260

The NOAA National Coral Reef Monitoring Program (NCRMP) details a long term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various NOAA Coral Reef Conservation Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis.

NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at 10 priority coral reefs across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the CRCP and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), and many other partners. The PIFSC Ecosystem Sciences Division (ESD) at NOAA Fisheries is leading biological monitoring in the U.S. Pacific Islands Region.

The biological component of NCRMP in the Pacific provides a triennial ecological characterization at a broad spatial scale of general reef condition for reef fishes, corals and benthic habitat (i.e., fish species composition/density/size, benthic cover, and coral density/size/condition). Innovative analysis techniques are then used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region's resources and how they are changing over time.

As more data are generated, we will continue to update this record.

Dataset includes metadata for each survey site (site information, survey date and location); site characteristics (depth, reef type, habitat); data collection method (Diver or SfM); individual adult and juvenile coral observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. The raw data also include individual observations of crustose coralline algae diseases and Alcyonarian disease recorded disease type and lesion size (does not apply to surveys conducted after 2017). Finally, the third type of raw data include presence of other Anthozoans, such as other cnidarians including Alcyonareans, Zoantharians, Corallimorpharians, and Antipatharians (does not apply to PMNM surveys conducted in 2014 and 2015 or surveys conducted after 2017).

Juvenile Coral Annotations Data Dictionary

https://www.fisheries.noaa.gov/inport/item/63244

Adult Coral Annotations Data Dictionary

https://www.fisheries.noaa.gov/inport/item/63239

Reference table for genus and species codes data dictionary

https://www.fisheries.noaa.gov/inport/item/72887

While every effort has been made to ensure that these data are accurate and reliable within the limits of the current state of the art, NOAA cannot assume liability for any damages caused by errors or omissions in the data, nor as a result of the failure of the data to function on a particular system. NOAA makes no warranty, expressed or implied, nor does the fact of distribution constitute such a warranty.

U.S. Pacific Island Areas

Not applicable

Not applicable

NOAA Ecosystem Science Division (ESD) Data Sharing Recommendations, version 9.0 updated August 12, 2015:

ESD welcomes the opportunity to collaborate on research issues contributing to the scientific basis for better management of marine ecosystems. ESD has a very diverse set of field activities that generates large volumes of data using an array of data collection protocols.

The following recommendations are for your consideration as you use this data:

1) Data analyses should take all field exigencies into account. The most effective way to do this would be active collaboration with ESD principal investigators.

2) In all presentations, product releases, or publications using data generated by ESD, proper acknowledgement of both ESD and the individuals responsible for data collection is expected. Citing the DOI (if available) is preferred, a non-DOI example is listed below.

3) If you collect or generate data for the same study areas, ESD requests that you share relevant information on complimentary data collections.

4) Those receiving data are strongly urged to inform the ESD Data Management Team of any errors and discrepancies that are discovered during the course of using these data. They are further urged to bring to the attention of the Team all problems and difficulties encountered in using these data. This information is necessary in order to improve the collections and to facilitate more efficient and economical data processing and retrieval. The users are asked to supply copies of any missing data that may be located, and to provide information as to significant subsets and special aggregations of data that are developed in using the material provided.

Example citation:

"This publication makes use of data products provided by the Ecosystem Science Division (ESD), Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), with funding support from the NOAA Ocean Acidification Program (OAP). The analysis and interpretations presented here are solely that of the current authors.

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

None

Please cite NOAA Fisheries, Ecosystem Science Division (ESD) when using the data.

Example:

Pacific Islands Fisheries Science Center, 2023: National Coral Reef Monitoring Program: Stratified Random Surveys (StRS) of Coral Demography (Adult and Juvenile Corals) across the US Pacific since 2013, https://www.fisheries.noaa.gov/inport/item/71550.

None

None

PIFSC Oracle database view: V_NCRMP_CORAL_OBS_E and V_NCRMP_CORAL_OBS_F

For SfM-derived coral demography starting in 2023, a Canon SL2 or SL3 DSLR digital camera in an Ikelite underwater housing was used to take photographs of each site. Coded markers 0.25 m long were used underwater to provide a scale and depth for each mosaic. Orthomosaic images were created using Agisoft Metashape (version 1.8.0 or later). The custom software Viscore was used for accessing raw imagery. Sampling boundaries and coral demographic measurements were created in ArcGIS Pro (version 2.8.0 or later). All statistics were performed in R (Version 4.1.2 or later).

The data set derived from the SfM imagery is only as good as the images themselves; Images with poor resolution, poor lighting, extraneous objects (fins, etc), or blur were excluded from analysis.

This data should be assessed at the genus level due to variabilities in identifying at genus or species level.

Observations were made by experienced benthic survey personnel who have been trained, undergone a series of calibration surveys and coral taxon identification testing, and have met a set of minimum standards for colony assessment and taxon identification in each region. The accuracy of species and genus level identification was high. The lowest taxonomic level of coral identification was genus except for a select number of species that were consistently identified to species by all divers conducting the surveys. The number of species may change for each survey year depending on the experience and training of the benthic divers. The list of coral species is included for each survey year. In other words, the individual records within each data set may include many more species than encompassed by the lists; however, these were not consistently identified across all surveys so these records should be assessed at the genus level.

Prior to conducting surveys, the SfM image collector was trained to swim in a back-and-forth pattern to collect imagery with 60-80% overlap. Both classroom and field training were completed before any surveys were conducted. This training ensures that all SfM image collection was conducted consistently during the mission.

Handheld GPS units were used to locate random sites and mark site locations.

The taxon code AAAA is included where the segment was surveyed and no individual colonies were found in both the juvenile and adult colony records. These are true zeros. The value -9 is a placeholder or missing value for the fields: colony length, colony width (juveniles), extent, and severity.

The average Ground Sample Distance (GSD, resolution/pixel) for the produced 3D Structure from Motion models was 0.21 cm/pix, allowing confident identification of coral species from the resulting high-resolution 2D orthomosaics.

Only sites from shallow water (0 to 30 meter depth range) hard-bottom habitats were annotated. At deep sites, bottom time is limited and therefore survey area is reduced from 3 x 20 m to 3 x 13 m. Therefore, shallower sites, 4 2.5 m2 segments were annotated and for deeper sites (>30 m) 3 2.5m2 segments were annotated along the central transect line. Within each 2.5 m2 segment, only 1m2 of the segment was sampled for juvenile demographic metrics and for all sites, regardless of depth, only the first three segments along the transect line were annotated.

Periodic examination of the data is conducted throughout each mission to check for diver bias or other discrepancies. While data are collected by divers and from SfM imagery, the same methods were applied to both survey types.

Quality control of the data occurred at a few stages from data entry to data ingestion into the Oracle database. Observations, including species identification, are periodically checked during expeditions for consistency between and among divers. Data entry is usually conducted on the same day as the surveys using a data entry interface with several data controls employed, and are quality controlled by individual divers checking entry errors at a separate time. Following a mission, the data is then run through rigorous quality control checks by the data management team before the data are migrated to the Oracle database. The data is quality controlled against the physical data sheets following data entry. There are also several queries in the MS Access / Oracle database to flag errors based on pre-defined criteria. Given the size of the data set, there remains some possibility of typographical or other errors.

Prior to generating the 3D dense point clouds and 2D orthomosaics , the JPEG imagery was evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. During annotation in ArcGIS, the original JPEG imagery was viewed alongside the orthomosaic using the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic. Annotations created in ArcGIS were quality controlled using a multi-stage process. Data were first quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing segments, data in incorrect columns, partial mortality >100%). Then data were summarized to the segment-level by annotator to identify potential issues (e.g. anomalously high or low mean values for specific metrics relative to other annotators). If issues were identified for a given annotator, that annotator reviewed and corrected each site if they did find errors.

The data is captured in several locations: physical data sheets, MS Access cruise database, and PIFSC Oracle database. The physical data sheets are housed at PIFSC. The MS Access cruise database is regularly backed up by the cruise data manager while at sea. The PIFSC Oracle database is regularly backed up by PIFSC ITS.

Coral demographic data has been collected at stratified-random sites (StRS) across US Pacific Island Regions for the National Coral Reef Monitoring Program (NCRMP) since 2013. The methodology for selecting StRS and analyzing this data can be found in the sources listed below. The methodology has continued to evolve. Starting in 2023, some data was collected with GIS analysis alongside in-water diver surveys.

The benthic SfM survey methodology, employed by the NOAA Ecosystem Sciences Division (ESD), began in 2019. Benthic imagery is collected at stratified random sites and generated into orthomosaic images using Agisoft Metashape software. Orthomosaics are imported into ArcGIS for annotation. Annotation of SfM belt orthomosaics is modelled after in situ diver adult and juvenile coral belt surveys employed by the PIFSC Ecosystem Sciences Division and includes coral species identification, maximum diameter measurement, partial mortality estimates, and disease and condition identification.