What is the Biological Condition Gradient (BCG)?

The BCG is a numerical model that was initially developed as an approach to assess the biological condition (or “health”) of a freshwater body relative to expectations of “having a composition and diversity comparable to that of the natural habitat” (see Bradley et al. 2020 and Santavy et al. 2012).

Currently, the BCG can be fed information about different components of coral reef sites (e.g. reef fish assemblages or benthic species) and uses that information to deliver a value between 1 and 6 that represents the relative health of those ecosystems (figure 1). The BCG is therefore a useful tool to describe how biological conditions change incrementally along a gradient of increasing anthropogenic stress.

Figure 1 Diagram for interpreting the BCG model (EPA 2016)

Since fish and benthic assemblages may respond differently to stressors, combining fish and benthic BCG models would allow for a more robust understanding of these systems (Bradley et al. 2020).

If the fish and benthic BCGs are additionally coupled with water quality data, the BGC provides a statistically stronger framework to understand the state of coral reef sites. This information can then used to inform management decisions like identifying which water bodies containing coral reefs should be prioritized, protected and/or restored (Bradley et al. 2020).

CCRI’s role regarding the BCG

In accordance with the guidance of the U.S. Environmental Protection Agency (EPA 2002, 2013) and in support of the U.S. Clean Water Act and biocriteria, the Caribbean Coral Reef Institute (CCRI) and the Puerto Rico Department of Natural and Environmental Resources (PR-DNER) developed a two-year monitoring program for: 1) seawater chemistry, 2) benthic communities, and 3) fish assemblages.

Project Goals

  1. Calculate the BCG level of seawater chemistry, reef fish assemblages, and benthic assemblages at 42 sites (figure 2) studied by the Puerto Rico Coral Reef Monitoring Program
  2. statistically assess stressor-response relationships and,
  3. use this data to support management in coral reef sites.

This project is currently administered and conducted by CCRI from the University of Puerto Rico at Mayaguez (UPRM). The funding provided has allowed us to build the first seawater quality monitoring laboratory from a public institution in Puerto Rico and is located at UPRM’s Isla Magueyes Marine Laboratory in La Parguera, Lajas P.R. The Water Quality Laboratory became fully functional on May 2023.

Study Sites

Figure 2 Map of the 42 PRCRMP sites where monitoring of water quality parameters, fish and coral assemblages will occur quarterly from May 2023 – May 2025. Numbers next to the site code in the legend correspond to approximate depth in meters. For more details, access our Quality Assurance Project Plan (QAPP)

The BCG application

CCRI is collaborating to create a “BCG shiny app”, which would allow us to upload data on corals, reef fish, and water quality parameters to calculate the BCG and create a map that showcases the BCG results for each location.
The application is publicly available (click here) but is currently working ONLY with coral assemblage data collected using Line-Point-Intercept (LPI) and benthic demographic (DEMO) methods.

Figure 3 Screenshot of the web based shiny application to calculate the BCG.

How to use the app

  • You can download practice datasets by clicking here.
  1. Go to:
  2. Download the template_v2.xlsx from the How to use this appsection on the “Preface and guide of use“:
  3. Read and follow the instructions on the first sheet titled “INSTRUCTIONS” to complete the sheets titled: “LPI”, “MOBILE_FAUNA”, and “DEMO”.
    • In order for the BCG to work properly, DO NOT edit the name or change the position of the sheets or columns in any of the template documents.
  4. Go to: “Upload your data” in the Main Menu, click Browse…“, and select the template_v2.xlsx you prepared in step 3.
    • Once you select the file, upload should start automatically and the application will show a preview of the uploaded data.
  5. Select the model you wish calculated (BCG requires both LPI and DEMO data while the BSAT model only requires LPI data).
  6. On the bottom of this page, select Temporal (e.g., YEAR) and Spatial (e.g., SITE) factors to consider for analysis.
  7. Continue to Quality Control in the Main Menu and click Go!
    • This process may take a few minutes depending on the size of your dataset and internet connection speed.
  8. Click on Download data to recover a list of Species names that:
    • Were identified by but need to be added to the Master List
    • Were identified by but might have been misspelled
    • Were not identified and need to be included in the Master List as a biological variable or otherwise.
      • If new species need to be added to the Master List, contact us at
  1. Continue on to BCG results
    • This process may also take a couple of minutes depending on the size of your dataset.
    • Once the process is finished, you can:
      • Download metrics
      • Download results
      • Download map
  2. Review your data
    • In figure 4 only site SECO30 (in green) had a BCG level 3.
      • All other sites measured between levels 4 – 6 showing the vast degradation of coral health in Puerto Rico compared to “pristine” sites.
Figure 4. BCG results for Line-Point-Intercept (LPI) data at 21 PRCRMP sites surveyed by DRNA between 2022 – 2023.

Meet our team!

UPRM – CCRI – Department of Marine Sciences

U.S. Environmental Protection Agency (EPA)

  • Izabela Wojtenko
  • Carol Lynes – USEPA Quality Assurance Officer

Subcontracted personnel