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Puerto Rico Long-Term Coral Reef Monitoring Program database compilation: substrate cover percent, octocoral colony counts, macro invertebrate densities, fish densities, and fish biomass from 1999 to 2025 (NCEI Accession 0204647)

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The Puerto Rico Coral Reef Monitoring Program data files include all raw data (by transect) for 86 stations where substrate cover by sessile-benthic categories and fish and motile megabenthic invertebrate taxonomic composition and densities have been characterized from 1999-2025. At present, 42 of these stations are permanent and are surveyed biannually. For the benthic characterization, at each reef station, a set of five 10 meters long permanent transects are surveyed. Sessile-benthic reef communities are characterized by the continuous intercept chain-link method, following the CARICOMP (1994) protocol. Demersal diurnal non-cryptic reef fish populations and motile megabenthic invertebrates are surveyed by sets of five 10 meters long by 3 meters wide (30 m2) belt-transects centered along the reference line of transects used for sessile-benthic characterizations at each reef station. Upon completion of the 10 meters belt-transect survey the diver swims along the same depth and physiographic reef zone for an extra 10 meters to identify fishes and megabenthic invertebrates of commercial value (snappers, groupers, hogfishes, barracuda, mackerels, sharks, lobsters and queen conch) and/or fish species that are considered important reef herbivores (parrotfishes, doctorfishes). For each fish individual within belt-transects, a visual total length (TL) estimate in centimeters was recorded. The cephalothorax length (measurement from the tip of the rostrum to end of the thorax), also known as carapace length (CL) in centimeters was used to report the size of lobsters (Panulirus spp., Scyllarides sp) within belt-transects. Queen conch (Strombus gigas) length was reported as the total (diagonal) shell length in centimeters. With the length-weight relationship information available in FishBase.org, biomass estimates have been calculated for commercially and ecologically important species. The PRCRMP data files also include a site classification spreadsheet with descriptors for each monitoring station, some of which can be used as spatial and temporal factors for statistical analyses. These descriptors include information about depth, habitat type, distance from shore, marine protected areas attributes, coordinates, and other metadata.
  • Cite as: Puerto Rico Department of Natural and Environmental Resources (2019). Puerto Rico Long-Term Coral Reef Monitoring Program database compilation: substrate cover percent, octocoral colony counts, macro invertebrate densities, fish densities, and fish biomass from 1999 to 2025 (NCEI Accession 0204647). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0204647. Accessed [date].
gov.noaa.nodc:0204647
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Distributor NOAA National Centers for Environmental Information
+1-301-713-3277
ncei.info@noaa.gov
Dataset Point of Contact NOAA National Centers for Environmental Information
ncei.info@noaa.gov
Time Period 1999-01-01 to 2025-09-30
Spatial Bounding Box Coordinates
West: -67.95077
East: -65.1971
South: 17.8843
North: 18.7169
Spatial Coverage Map
General Documentation
Associated Resources
  • Annual Reports of the Coral Reef Monitoring Program
  • García-Sais, J. R., Williams, S. M., & Amirrezvani, A. (2017). Mortality, recovery, and community shifts of scleractinian corals in Puerto Rico one decade after the 2005 regional bleaching event. PeerJ, 5, e3611. https://doi.org/10.7717/peerj.3611
  • Garcia-Sais, J. R. (2010). Reef habitats and associated sessile-benthic and fish assemblages across a euphotic–mesophotic depth gradient in Isla Desecheo, Puerto Rico. Coral Reefs, 29(2), 277–288. https://doi.org/10.1007/s00338-009-0582-9
Publication Dates
  • publication: 2019-10-17
  • revision: 2025-12-01
  • creation: 2019-10-08
Data Presentation Form Digital table - digital representation of facts or figures systematically displayed, especially in columns
Dataset Progress Status Complete - production of the data has been completed
Historical archive - data has been stored in an offline storage facility
Data Update Frequency As needed - NCEI Accession 0204647 was revised and a new version of the archival package was published. Updates to existing archival packages may provide additional files or replace obsolete files. The latest version contains the most complete and up-to-date representation of this archival information package. All of the files received prior to this update are available in the preceding version of this accession. Please see journal.txt in the /about directory for additional details on changes made.
Supplemental Information
In this accession, NCEI has archived multiple versions of these data. The latest (and best) version of these data has the largest version number.
Purpose These datasets are collected to: (a) Know the conditions of the species in coral reefs with ecological and economic importance. (b) Identify the trends of reef communities in response to environmental and human pressures. (c) Determine the most effective management strategies for the conservation and management of Puerto Rico coral reefs.
Use Limitations
  • accessLevel: Public
  • Distribution liability: NOAA and NCEI make no warranty, expressed or implied, regarding these data, nor does the fact of distribution constitute such a warranty. NOAA and NCEI cannot assume liability for any damages caused by any errors or omissions in these data. If appropriate, NCEI can only certify that the data it distributes are an authentic copy of the records that were accepted for inclusion in the NCEI archives.
Dataset Citation
  • Cite as: Puerto Rico Department of Natural and Environmental Resources (2019). Puerto Rico Long-Term Coral Reef Monitoring Program database compilation: substrate cover percent, octocoral colony counts, macro invertebrate densities, fish densities, and fish biomass from 1999 to 2025 (NCEI Accession 0204647). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0204647. Accessed [date].
Cited Authors
Principal Investigators
  • Jorge García-Saís
    Reef Research, Inc.
Collaborators
Contributors
Resource Providers
Points of Contact
Publishers
Acknowledgments
  • Funding Agency: NOAA Coral Reef Conservation Program
  • Funding Agency: Puerto Rico Department of Natural and Environmental Resources (DNER)
Theme keywords NODC DATA TYPES THESAURUS NODC OBSERVATION TYPES THESAURUS WMO_CategoryCode
  • oceanography
CoRIS Discovery Thesaurus
  • Numeric Data Sets > Benthic
  • Numeric Data Sets > Biology
  • Numeric Data Sets > Fish Census
CoRIS Theme Thesaurus
  • EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat
  • EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat
  • EARTH SCIENCE > Biosphere > Zoology > Corals
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Anthozoans/Octocorals
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Diseases > Bleaching
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis > Transect monitoring
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > In Situ Biological
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Macroinvertebrate Census > Belt Transect
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Reef Fish Census
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Reef Fish Census > Belt Transect
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals)
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Benthic biology
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Coral Cover
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Habitats
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Hard Coral Cover
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Hard Coral Cover Dead percentage
  • EARTH SCIENCE > Oceans > Marine Biology > Coral
  • EARTH SCIENCE > Oceans > Marine Biology > Coral Communities
  • EARTH SCIENCE > Oceans > Marine Biology > Macroinvertebrates
  • EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates
  • EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Biomass
  • EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Census
  • EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Census > Macroinvertebrates
  • EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Macroinvertebrates
Global Change Master Directory (GCMD) Science Keywords Provider Keywords
  • Active Search Census (roving dive)
  • Band transect
  • Chain transect
  • Line transect
Data Center keywords NODC COLLECTING INSTITUTION NAMES THESAURUS NODC SUBMITTING INSTITUTION NAMES THESAURUS
Instrument keywords NODC INSTRUMENT TYPES THESAURUS Global Change Master Directory (GCMD) Instrument Keywords
Place keywords NODC SEA AREA NAMES THESAURUS CoRIS Place Thesaurus
  • COUNTRY/TERRITORY > United States of America > Puerto Rico > Puerto Rico (18N066W0000)
  • OCEAN BASIN > Atlantic Ocean > Caribbean Sea /North Atlantic Ocean > Puerto Rico > Puerto Rico (18N066W0000)
Global Change Master Directory (GCMD) Location Keywords
Project keywords NODC PROJECT NAMES THESAURUS Provider Project Names
  • DNER - NOAA CRCP Cooperative Agreement
  • Puerto Rico Long-Term Coral Reef Monitoring Program
Keywords NCEI ACCESSION NUMBER
Keywords Send2NCEI Submission Package ID
  • 2T93CH
Use Constraints
  • Cite as: Puerto Rico Department of Natural and Environmental Resources (2019). Puerto Rico Long-Term Coral Reef Monitoring Program database compilation: substrate cover percent, octocoral colony counts, macro invertebrate densities, fish densities, and fish biomass from 1999 to 2025 (NCEI Accession 0204647). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0204647. Accessed [date].
Access Constraints
  • Use liability: NOAA and NCEI cannot provide any warranty as to the accuracy, reliability, or completeness of furnished data. Users assume responsibility to determine the usability of these data. The user is responsible for the results of any application of this data for other than its intended purpose.
Fees
  • In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
Lineage information for: dataset
Processing Steps
  • 2019-10-17T17:41:16Z - NCEI Accession 0204647 v1.1 was published.
  • 2019-11-14T20:24:24Z - NCEI Accession 0204647 was revised and v2.2 was published.
    Rationale: Updates were received for this dataset. These updates were copied into the data/0-data/ directory of this accession. These updates may provide additional files or replace obsolete files. This version contains the most complete and up-to-date representation of this archival information package. All of the files received prior to this update are available in the preceding version of this accession.
  • 2020-04-16T13:31:23Z - NCEI Accession 0204647 was revised and v3.3 was published.
    Rationale: Updates were received for this dataset. These updates were copied into the data/0-data/ directory of this accession. These updates may provide additional files or replace obsolete files. This version contains the most complete and up-to-date representation of this archival information package. All of the files received prior to this update are available in the preceding version of this accession.
  • 2022-02-16T21:25:16Z - NCEI Accession 0204647 was revised and v4.4 was published.
    Rationale: Updates were received for this dataset. These updates were copied into the data/0-data/ directory of this accession. These updates may provide additional files or replace obsolete files. This version contains the most complete and up-to-date representation of this archival information package. All of the files received prior to this update are available in the preceding version of this accession.
  • 2024-01-08T16:22:14Z - NCEI Accession 0204647 was revised and v5.5 was published.
    Rationale: Updates were received for this dataset. These updates were copied into the data/0-data/ directory of this accession. These updates may provide additional files or replace obsolete files. This version contains the most complete and up-to-date representation of this archival information package. All of the files received prior to this update are available in the preceding version of this accession.
  • 2025-12-01T19:59:43Z - NCEI Accession 0204647 was revised and v6.6 was published.
    Rationale: Updates were received for this dataset. These updates were copied into the data/0-data/ directory of this accession. These updates may provide additional files or replace obsolete files. This version contains the most complete and up-to-date representation of this archival information package. All of the files received prior to this update are available in the preceding version of this accession.
Output Datasets
Lineage information for: dataset
Processing Steps
  • Parameter or Variable: REEF AND/OR BOTTOM REGIME - PERCENT COVER (measured); Units: cover percent; Observation Category: in situ; Sampling Instrument: Chain transect; Sampling and Analyzing Method: Sessile-benthic reef communities are characterized by the continuous intercept chain-link method (as modified from Porter, 1972), following the CARICOMP (1994) protocol. This method provides information on the percent linear cover by sessile-benthic biota and other substrate categories along transects. It allows construction of reef community profiles by assignment of metric units to each substrate transition, which serves as a high precision baseline for monitoring. The chain has links of 1.42 cm long, marked every 10 links for the facilitation of counting underwater. The exact position of the chain was guided by a series of steel nails set into available hard (abiotic) substrates along transects. Individual measurements of substrate categories, as recorded from the number of chain links are sorted, added and divided by the total distance (in chain links) on each transect to calculate the cumulative percent linear cover by each substrate species and category.
  • Parameter or Variable: species abundance (measured); Units: Number of colonies; Observation Category: in situ; Sampling Instrument: Line transect; Sampling and Analyzing Method: Octocorals, except for encrusting forms (e.g. Erythropodium caribaeorum, Briareum asbestinum) are counted as the number of colonies intercepted per transect, whenever any of their branches crossed the transect reference line. Hard live coral colonies under the transect line are counted and examined visually for the prevalence of apparent infectious diseases. Colonies of similar coral species growing close together and sharing attachment surfaces are counted as individual colonies if separated by a distance of 15 cm or more.
  • Parameter or Variable: species abundance (measured); Units: individuals per 30 squared meter; Observation Category: in situ; Sampling Instrument: Band transect; Sampling and Analyzing Method: Demersal diurnal non-cryptic reef fish populations and motile megabenthic invertebrates are surveyed by sets of five 10 m long by 3 m wide (30 squared meters) belt-transects centered along the reference line of transects used for sessile-benthic characterizations at each reef station. Transect width was marked with flagging tape stretched and tied to weights on each transect side. Each transect is surveyed for 12 - 15 minutes depending on the complexity of the fish community on each transect. The initial one or two minutes are dedicated to the detection of elusive and/or transitory species that swim away of the “belt-transect” area as soon as they detect a diver (e.g. snappers, jacks, mackerels, groupers, hogfish, large parrotfishes, etc.). During the next three to four minutes, the diver swam over both sides of the transect area counting fishes that form schooling aggregations over the reef (e.g. Chromis spp., Clepticus spp., etc.) and other transitory species as they enter the survey area, including the wrasses (e.g. Thalassoma, Halichoeres spp.) which tend to be attracted to divers and thereby, may increase in density during the survey. A second run over both sides of transects was performed during the next four to six minutes in order to count demersal and territorial fishes (e.g. Stegastes spp., Gramma loreto, squirrelfishes, etc.) that remain within the transect area. The last two or three minutes are dedicated to counting the small gobies, echinoderms, mollusks, and crustaceans associated with coral heads and crevices on both sides of transects.
  • Parameter or Variable: species abundance (measured); Units: individuals per size class per 30 minute ASEC Survey; Observation Category: in situ; Sampling Instrument: Active Search Census (roving dive); Sampling and Analyzing Method: From 2004-2013, size-frequency observations were surveyed using an Active Search Census (ASEC) technique. This is a non-random, fixed-time method designed to optimize information of the numbers of highly mobile predatory and herbivorous fish individuals present at each of the main reef habitats, providing simultaneous information on size-frequency distributions. At each reef station, the total number of individuals of each species observed within a fixed time frame of 30 minutes was registered. Individuals were actively searched for in the water column and within crevices, ledges and potentially important hiding places. For each individual sighted, a length estimate was recorded. One ASEC survey was performed at each reef station.
  • Parameter or Variable: species abundance (measured); Units: individuals per size class per 60 squared meters; Observation Category: in situ; Sampling Instrument: Band transects; Sampling and Analyzing Method: Since 2015, upon completion of the 10 m long by 3 m wide belt-transect survey the diver swims along the same depth and physio-graphic reef zone for an extra 10 by 3 meters to identify fishes and megabenthic invertebrates of commercial value (snappers, groupers, hogfishes, barracuda, mackerels, sharks, lobsters and queen conch) and/or fish species that are considered important reef herbivores (parrotfishes, doctorfishes). This provides a total of 60 squared meters where a visual total length (TL) estimate (in cm) was recorded for each individual. The cephalothorax length (measurement from the tip of the rostrum to end of the thorax), also known as carapace length (CL) in cm was used to report the size of lobsters (Panulirus spp., Scyllarides spp.) within belt-transects. Queen Conch (Strombus gigas) length was reported as the total (diagonal) shell length in cm. The precision of length estimates allowed discrimination between new recruits, small juveniles, juveniles, adult and large adult size classes.
  • Parameter or Variable: BIOMASS (calculated); Units: grams per 60 squared meters; Observation Category: in situ; Sampling Instrument: Band transects; Sampling and Analyzing Method: Since 2015, the Size-frequency abundance data for the 60 squared meter band transects was compiled per species size classes made of 5cm intervals instead of the raw estimated total length (TL) reported in the annual PRCRMP reports. Once the fish and macroinvertebrates size-frequency data compilation were finished, biomass values were calculated using FishBase (ver. 02/2019) biomass calculator tools, choosing the length-weight relationship coefficients with the best geographical relation to Puerto Rico, when available. The median of each size class was used as the length value, either as fork length (FL) or total length (TL) to get biomass estimates per individual of each species size class. Then, the biomass estimates per individual of each species size class were multiplied by the number of individuals observed for that size class per. Lastly, all species size classes biomass estimates were aggregated to get the species estimated biomass per year-site-transect.
  • Parameter or Variable: BIOMASS (calculated); Units: grams per 30 minute ASEC Survey; Observation Category: in situ; Sampling Instrument: Active Search Census (roving dive); Sampling and Analyzing Method: From 2004-2013, the Size-frequency abundance data for the 30 minute Active Search Census (ASEC) survey was compiled per species size classes made of 5cm intervals instead of the raw estimated total length (TL) reported in the annual PRCRMP reports. Once the fish and macroinvertebrates size-frequency data compilation were finished, biomass values were calculated using FishBase (ver. 02/2019) biomass calculator tools, choosing the length-weight relationship coefficients with the best geographical relation to Puerto Rico, when available. The median of each size class was used as the length value, either as fork length (FL) or total length (TL) to get biomass estimates per individual of each species size class. Then, the biomass estimates per individual of each species size class were multiplied by the number of individuals observed for that size class. Lastly, all species size classes biomass estimates were aggregated to get the species estimated biomass per year-site-transect.
Acquisition Information (collection)
Instrument
  • chain
  • swimmer/diver
  • visual observation
Last Modified: 2025-12-02T16:35:26Z
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