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 2020 (NCEI Accession 0204647)


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            title:  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 2020 (NCEI Accession 0204647)
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                date:  2019-10-17
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                date:  2020-04-16
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                  Anchor:  https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/1730 NOAA National Centers for Environmental Information
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                  Anchor:  https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/person/details/5304 Miguel Gerardo Figuerola Hernandez
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                  Anchor:  https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/2019 Puerto Rico Department of Natural and Environmental Resources (DRNA)
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                        linkage: http://drna.pr.gov/
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                individualName:  Miguel Figuerola-Hernández
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                individualName:  Juan Cruz Motta
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                  Anchor:  https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/224 University of Puerto Rico; Department of Marine Sciences - Mayaguez
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                individualName:  Jorge García-Saís
                organisationName:  Reef Research, Inc.
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                  Anchor:  https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/224 University of Puerto Rico; Department of Marine Sciences - Mayaguez
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                individualName:  Stacey Williams
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                individualName:  Mariana León
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                  Anchor:  https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/224 University of Puerto Rico; Department of Marine Sciences - Mayaguez
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        abstract:  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 1999-2020. 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 2015-2020, 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.
        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.
        credit:  Related Funding Agency: NOAA Coral Reef Conservation Program (NOAA CRCP)
        credit:  Related Funding Agency: Puerto Rico Department of Natural and Environmental Resources (DNER)
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                description:  NCEI Accession 0204647 v1.1 was published.
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                description:  NCEI Accession 0204647 was revised and v2.2 was published.
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                                    linkage: https://www.ncei.noaa.gov/archive/accession/0204647/2.2
                                    protocol:  HTTPS
                                    name:  NCEI Accession 0204647 v2.2
                                    description:  published 2019-11-14T20:24:24Z
                                    function:  (CI_OnLineFunctionCode) download
                            role: (inapplicable)
            processStep:  (LE_ProcessStep)
                description:  NCEI Accession 0204647 was revised and v3.3 was published.
                rationale:  Updates were received for this data set. 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.
                dateTime:
                  DateTime:  2020-04-16T13:31:23Z
                output:  (LE_Source)
                    sourceCitation:  (CI_Citation)
                        title:  NCEI Accession 0204647 v3.3
                        date:  (CI_Date)
                            date: (inapplicable)
                            dateType:  (CI_DateTypeCode) publication
                        citedResponsibleParty:  (CI_ResponsibleParty)
                            individualName: (inapplicable)
                            contactInfo:  (CI_Contact)
                                onlineResource:  (CI_OnlineResource)
                                    linkage: https://www.ncei.noaa.gov/archive/accession/0204647/3.3
                                    protocol:  HTTPS
                                    name:  NCEI Accession 0204647 v3.3
                                    description:  published 2020-04-16T13:31:23Z
                                    function:  (CI_OnLineFunctionCode) download
                            role: (inapplicable)
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    dataQualityInfo:  (DQ_DataQuality)
        scope:  (DQ_Scope)
            level:  (MD_ScopeCode) dataset
        lineage:  (LI_Lineage)
            processStep:  (LE_ProcessStep)
                description:  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..
            processStep:  (LE_ProcessStep)
                description:  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..
            processStep:  (LE_ProcessStep)
                description:  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..
            processStep:  (LE_ProcessStep)
                description:  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..
            processStep:  (LE_ProcessStep)
                description:  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..
            processStep:  (LE_ProcessStep)
                description:  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..
            processStep:  (LE_ProcessStep)
                description:  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..
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    metadataMaintenance:  (MD_MaintenanceInformation)
        maintenanceAndUpdateFrequency:  (MD_MaintenanceFrequencyCode) asNeeded
        maintenanceNote:  Metadata are developed, maintained and distributed by NCEI. Updates are performed as needed to maintain currentness.
        maintenanceNote:  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.
        contact:  (CI_ResponsibleParty)
            organisationName:  NOAA National Centers for Environmental Information
            role:  (CI_RoleCode) custodian
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    acquisitionInformation:  (MI_AcquisitionInformation)
        instrument:  (MI_Instrument)
            identifier:  (MD_Identifier)
                code:  chain
            type:  chain
            description:  A 10-meter chain to be used in a linear transect method of measurement A 1-meter chain may be laid across a coral reef surface so that it follows the topography of the coral reef surface with descriptions of the coral made where each link touches the coral.
        instrument:  (MI_Instrument)
            identifier:  (MD_Identifier)
                code:  swimmer/diver
            type:  swimmer/diver
            description:  not an instrument - use as observation type
        instrument:  (MI_Instrument)
            identifier:  (MD_Identifier)
                code:  visual observation
            type:  visual observation
            description:  not an instrument - maybe an observation type