Data Management Plan

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 islands and atolls of the Pacific Remote Island Areas from 2014 to 2018. 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 species level and genus level for juveniles.

A two-stage stratified random sampling (StRS) design was employed to survey the coral reef ecosystems of the Pacific Remote Island Areas from 2014 to 2017, and starting in 2018 a one-stage StRS design was employed. The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats in the 0–30 m depth range. The stratification scheme included island, reef zone, and depth (i.e., shallow: >0–6 m; mid-depth: >6–18 m; and deep: >18–30 m), as well as reef zone (i.e., forereef, backreef, lagoon, and protected slope; the latter three only at Johnston and Kingman). Sampling effort allocation was determined based on strata area and sites randomly located within strata. The StRS design effectively reduces estimate variance through stratification using environmental covariates and by sampling more sites rather than more transects per site. Therefore, site-level estimates and site-to-site comparisons should proceed with caution.

The data were 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 islands and atolls of the Pacific Remote Island Areas from 2014 to 2018.

Phoenix (Baker and Howland) and Line Islands (Jarvis, Kingman, and Palmyra), and Johnston Atoll. These six of the seven PRIA are routinely surveyed as part of the American Samoa RAMP (ASRAMP) missions (Johnston, Baker and Howland during the first leg of ASRAMP, and Jarvis, Kingman, and Palmyra during the last leg of ASRAMP).

Wake Island, one of the seven PRIA, is routinely surveyed as part of the Mariana Archipelago RAMP (MARAMP) missions.

Jarvis Island

Lineage Statement:
The stratified random sampling (StRS) design and belt transect methodology for adult and juvenile corals, employed by the PIFSC Ecosystem Sciences Division (ESD) since 2013. A two-stage StRS design was employed from 2014 to 2017 and starting in 2018 a one-stage design was employed.

Process Steps:

• A stratified random sampling (StRS) design was employed to survey the coral reef ecosystems in the region (two-stage StRS from 2014 to 2017 and switched to a one-stage StRS design in 2018. The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats. The stratification scheme included island, reef zone, and depth. Depth categories of shallow (>0-6 m), mid (>6-18 m) and deep (>8-30 m) were also incorporated into the stratification scheme. Allocation of sampling effort was proportional to strata area. Sites were randomly selected within each stratum. A geographic information system (GIS) and digital spatial databases of benthic habitats (NOAA National Centers for Coastal Ocean Science NCCOS), reef zones (IKONOS satellite imagery, NDGC 1998) bathymetry (NDGC 1998, ESD benthic mapping data), and marine reserve boundaries (NOAA) were used to facilitate spatial delineation of the sampling survey domain, strata, and sample units. Map resolution was such that the survey domain could be overlain by a grid using a GIS with individual cells of size 50 m by 50 m in area. The two-stage sampling scheme following Cochran (1977) was employed to control for spatial variation in population parameters at scales smaller than the grid cell minimum mapping unit (2,500 sq. meters). Grid cells containing hard-bottom reef habitats were designated as primary sample units (referred to as sites), while the second-stage sample unit was defined as a diver visual belt transect of fixed area (10 sq. meters or less). The primary sample units were the same for both sampling schemes (one-stage and two-stage). (Citation: Swanson D, Bailey H, Schumacher B, Ferguson M, Vargas-Angel B. 2018. Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-71, 63 p. doi:10.25923/39jh-8993.)
• At each site, benthic Rapid Ecological Assessment (REA) surveys were conducted within two 10 sq. meter belt transects from 2014 to 2017 and within one 10 sq. meter transect starting in 2018. Transects were 18 meters in length. Adult coral colonies (>=5 cm) were surveyed within four (1.0 x 2.5 m) segments at 5 meter increments along the 18 meter transect in the following manner: 0-2.5 m (segment 1); 5.0-7.5 m (segment 3); 10-12.5 m (segment 5); and 15 - 17.5 m (segment 7). All colonies whose center fell within 0.5 m on either side of each transect line were identified to lowest taxonomic level possible (species or genus), measured for size (maximum diameter to nearest cm), and morphology was noted. In addition, partial mortality and condition of each colony was assessed. Partial mortality was estimated as percent of the colony in terms of old dead and recent dead. The cause of recent mortality was identified if possible. The condition of each colony including disease (not attributed to recent tissue loss) and bleaching was noted along with the extent (percent of colony affected) and level of severity (range from moderate to acute). The lowest taxonomic level of coral identification was genus except for a select number of species 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 conducting the surveys. The list of coral species is included for each survey year. Within the same four segments per transect as the adult coral surveys, crustose coralline algae (CCA) diseases and Alcyonarian disease are surveyed. In each segment, each occurrence of a specific disease is identified and the lesion is measured (maximum diameter). In addition to the adult coral surveys, CCA diseases, and Alcyonarian disease, the presence of other Anthozoans (other cnidarians including Alcyonareans, Zoantharians, coralliomorphs and Antipatharians) are also noted. These data exist as individual records coded for each group. This portion of the survey was not conducted in 2018. Juvenile coral colonies (<5 cm) were surveyed within three (1.0 x 1.0 m) segments along the same two transects from 2014 to 2017 or along the single transect in 2018: 0-1.0 m (segment 1); 5.0-6.0 m (segment 3); and 10.0-11.0 m (segment 5). Juvenile colonies were distinguished in the field by a distinct tissue and skeletal boundary (not a fragment of a larger colony). Each juvenile colony was identified to lowest taxonomic level (genus or species) and measured for size by recording both the maximum and perpendicular diameter to the nearest 2 mm. (Citation: Swanson D, Bailey H, Schumacher B, Ferguson M, Vargas-Angel B. 2018. Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-71, 63 p. doi:10.25923/39jh-8993.)
• Raw data include individual colony records with the corresponding physical data which reflect the description of the site. An individual colony record for adult corals includes colony species/genus identification, morphology, maximum diameter (cm), percent old dead, percent recent dead, cause of recent dead general category, cause of recent dead specific category, condition, extent and severity. Juvenile coral colony records include colony species/genus identification, morphology, maximum diameter (cm) and perpendicular diameter (cm). For species level identification of adult and juvenile corals, check the species list for each year to ensure species identification across all divers conducting the surveys. Individual records for crustose coralline algae diseases use the taxon code CALG and the Alcyonarian disease uses the taxon code for the octocoral genus. The colony length measurement is the maximum diameter of the lesion for both disease types. The raw presence/absence data for other Anthozoans include the general identification code and 0 or -1 to represent absence or presence respectively. The physical data for all records includes the following: region, island, site, date (day, month, year), latitude (dd), longitude (dd), transect, segment, segment length, segment width, minimum depth (ft), and maximum depth. (Citation: Swanson D, Bailey H, Schumacher B, Ferguson M, Vargas-Angel B. 2018. Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-71, 63 p. doi:10.25923/39jh-8993.)

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.

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

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.