Dataset Overview | National Centers for Environmental Information (NCEI)

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 2023 (NCEI Accession 0204647)

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The Puerto Rico Coral Reef Monitoring Program data files include 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 1999-2023. At present, 42 permanent stations are surveyed biannually (21 per year). For the benthic characterization, a set of five 10-meter-long permanent transects are surveyed at each station. Sessile-benthic reef communities are characterized by the continuous intercept chain-link method, following the Caribbean Coastal Marine Productivity (CARICOMP) (1994) protocol. Demersal diurnal non-cryptic reef fish populations and motile megabenthic invertebrates are surveyed by sets of five 10 x 3 meters wide (30 m2) belt-transects centered along the reference line of transects used for sessile-benthic characterizations at each reef station. From 2004-2013, a diver completed a Active Search Census (ASEC) survey for 30 minutes annotating sizes and abundances of fish and macro invertebrate’s species of interest. From 2015-2023, 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 (20 x 3 meters band transect) in order to identify commercially and ecologically important fish and megabenthic invertebrates species (parrotfishes, doctorfishes, snappers, groupers, hogfishes, barracuda, mackerels, sharks, lobsters and queen conch). For each fish individual within the 30-minute ASEC survey and 60m2 band transects, a visual total length (TL) estimate in centimeters is recorded. The cephalothorax length (measurement from the tip of the rostrum to end of the thorax), also known as carapace length (CL) in centimeters is used to report the size of lobsters (Panulirus spp., Scyllarides spp.) within belt-transects. Queen conch (Lobatus gigas) length is reported as the total (diagonal) shell length in centimeters. With the length-weight relationship information available in FishBase.org, biomass estimates are calculated for commercially and ecologically important fish 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.

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 2023 (NCEI Accession 0204647). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0204647. Accessed [date].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0204647

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Download Data	HTTPS (download) Navigate directly to the URL for data access and direct download. FTP (download) These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
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Ordering Instructions	Contact NCEI for other distribution options and instructions.
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 2023-11-30
Spatial Bounding Box Coordinates	West: -67.95077 East: -65.1971 South: 17.8843 North: 18.4896
Spatial Coverage Map

General Documentation

NCEI Dataset Landing Page
Navigate directly to the URL for a descriptive web page with download links.
Descriptive Information
Navigate directly to the URL for a descriptive web page with download links.

Associated Resources

Annual Reports of the Coral Reef Monitoring Program
- Annual Reports of the Coral Reef Monitoring Program
  DNER web page that houses all of the Coral Reef Monitoring Program's annual reports
Mortality, recovery, and community shifts of scleractinian corals in Puerto Rico one decade after the 2005 regional bleaching event
- Mortality, recovery, and community shifts of scleractinian corals in Puerto Rico one decade after the 2005 regional bleaching event (download)
  Journal Article
Reef habitats and associated sessile-benthic and fish assemblages across a euphotic–mesophotic depth gradient in Isla Desecheo, Puerto Rico
- Reef habitats and associated sessile-benthic and fish assemblages across a euphotic–mesophotic depth gradient in Isla Desecheo, Puerto Rico (download)
  Online journal article

Publication Dates	publication: 2019-10-17 revision: 2024-01-08
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
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 2023 (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	Puerto Rico Department of Natural and Environmental Resources
Principal Investigators	Jorge García-Saís Reef Research, Inc.
Collaborators	Miguel G. Figuerola-Hernández Puerto Rico Department of Natural and Environmental Resources (DRNA) Juan Cruz Motta University of Puerto Rico; Department of Marine Sciences - Mayaguez Fernando Melendez University of Puerto Rico; Department of Marine Sciences - Mayaguez Stacey Williams Coastal Survey Sollutions LLC Jorge Sabater Coastal Survey Solutions LLC Milton Carlo Coastal Survey Solutions LLC Tania Metz Puerto Rico Department of Natural and Environmental Resources (DRNA) Mariana León Puerto Rico Department of Natural and Environmental Resources (DRNA) René Esteves Coastal Survey Solutions LLC Roberto Castro
Contributors	University of Puerto Rico; Department of Marine Sciences - Mayaguez
Resource Providers	Miguel G. Figuerola-Hernández Puerto Rico Department of Natural and Environmental Resources (DRNA) Puerto Rico Department of Natural and Environmental Resources (DRNA)
Points of Contact	Ernesto Díaz Puerto Rico Department of Natural and Environmental Resources (DRNA)
Publishers	NOAA National Centers for Environmental Information
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 BENTHIC SPECIES BENTHIC SPECIES - TAXA COUNTS biological data BIOMASS CORAL CORAL - CENSUS CORAL - SPECIES IDENTIFICATION DEPTH - SENSOR FISH BIOMASS FISH CENSUS FISH SPECIES HABITAT - BENTHIC MACROINVERTEBRATE CENSUS REEF AND/OR BOTTOM REGIME - PERCENT COVER species abundance SPECIES IDENTIFICATION - COUNT SPECIES IDENTIFICATION - ORGANISM LENGTH NODC OBSERVATION TYPES THESAURUS biological in situ survey survey - biological survey - coral reef survey - swimmer/diver visual observation 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 EARTH SCIENCE > BIOLOGICAL CLASSIFICATION EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/VERTEBRATES > FISH EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC EARTH SCIENCE > BIOSPHERE > VEGETATION > BIOMASS EARTH SCIENCE > SOLID EARTH > GEOMORPHIC LANDFORMS/PROCESSES > COASTAL LANDFORMS > CORAL REEFS Provider Keywords Active Search Census (roving dive) Band transect Chain transect Line transect
Data Center keywords	NODC COLLECTING INSTITUTION NAMES THESAURUS University of Puerto Rico; Department of Marine Sciences - Mayaguez NODC SUBMITTING INSTITUTION NAMES THESAURUS Puerto Rico Department of Natural and Environmental Resources
Instrument keywords	NODC INSTRUMENT TYPES THESAURUS chain swimmer/diver visual observation Global Change Master Directory (GCMD) Instrument Keywords VISUAL OBSERVATIONS > VISUAL OBSERVATIONS
Place keywords	NODC SEA AREA NAMES THESAURUS Caribbean Sea North Atlantic Ocean 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 OCEAN > ATLANTIC OCEAN > NORTH ATLANTIC OCEAN OCEAN > ATLANTIC OCEAN > NORTH ATLANTIC OCEAN > CARIBBEAN SEA
Project keywords	NODC PROJECT NAMES THESAURUS Coral Reef Conservation Program (CRCP) CORAL REEF STUDIES Provider Project Names DNER - NOAA CRCP Cooperative Agreement Puerto Rico Long-Term Coral Reef Monitoring Program
Keywords	NCEI ACCESSION NUMBER 0204647
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 2023 (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.
Output Datasets	NCEI Accession 0204647 v1.1 NCEI Accession 0204647 v1.1 (download) published 2019-10-17T17:41:16Z NCEI Accession 0204647 v2.2 NCEI Accession 0204647 v2.2 (download) published 2019-11-14T20:24:24Z NCEI Accession 0204647 v3.3 NCEI Accession 0204647 v3.3 (download) published 2020-04-16T13:31:23Z NCEI Accession 0204647 v4.4 NCEI Accession 0204647 v4.4 (download) published 2022-02-16T21:25:16Z NCEI Accession 0204647 v5.5 NCEI Accession 0204647 v5.5 (download) published 2024-01-08T16:22:14Z

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.

Output Datasets

NCEI Accession 0204647 v1.1
- NCEI Accession 0204647 v1.1 (download)
  published 2019-10-17T17:41:16Z

NCEI Accession 0204647 v2.2
- NCEI Accession 0204647 v2.2 (download)
  published 2019-11-14T20:24:24Z

NCEI Accession 0204647 v3.3
- NCEI Accession 0204647 v3.3 (download)
  published 2020-04-16T13:31:23Z

NCEI Accession 0204647 v4.4
- NCEI Accession 0204647 v4.4 (download)
  published 2022-02-16T21:25:16Z

NCEI Accession 0204647 v5.5
- NCEI Accession 0204647 v5.5 (download)
  published 2024-01-08T16:22:14Z

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..

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: 2024-09-17T19:17:02Z
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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 2023 (NCEI Accession 0204647)

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