Endangered Species

Provisional Models for Endangered Species Pesticide Assessments

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Introduction

The tools and models on this web page were developed for use in the Steps 1 and 2 analyses of national level assessments of the risks of chlorpyrifos, diazinon and malathion to endangered and threatened species and designated critical habitat. These tools and models are provided to allow the public access to applications of the methods described in the Biological Evaluations (BEs) developed for these three chemicals. A number of these tools and models are provided here in order to provide transparency. Given that the BEs and pending Biological Opinions (BiOps) are intended to pilot interim scientific methods for future pesticide consultations, review of modifications to EPA’s models is ongoing.  These tools are being made available to the public during review of the BEs and BiOps, and EPA will consider any comments the public may have during this review process through finalization of the BiOps. Unless specified below (i.e., for the Pesticides Water Calculator), these models/tools and their outputs should be considered provisional and subject to revision following the completed QA/QC process including consideration of public comment. EPA anticipates completing the QA/QC process before any regulatory decision is made regarding these chemicals

A brief description of tools and models that are used to estimate exposures and risks in aquatic and terrestrial habitats are provided below. Also provided are tools that are used to characterize effects using available toxicity data.

Aquatic Tools and Models:

Pesticides Water Calculator (PWC)

The Pesticide Water Calculator (PWC), an update to the Surface Water Concentration Calculator (SWCC), is used to estimate pesticide concentrations in water bodies that result from pesticide applications to land for the three pilot chemicals. The PWC is designed to simulate the environmental concentration of a pesticide in the water column and sediment and is used for regulatory purposes by the USEPA Office of Pesticide Programs (OPP). The PWC uses PRZM version 5.0+ (PRZM5) and the Variable Volume Water Body Model (VVWM), replacing the older PE5 shell (last updated November 2006), which used PRZM3 (Carousel et al., 2005) and EXAMS (Burns, 2003). This updated model can be found on the Models for Pesticide Risk Assessment web page.

Note: this model has undergone a complete QA/QC and is not a provisional model.

Pesticide Water Calculator (PWC) ESA Automation Tool, v. 1.01 beta (XLSX) (1 pg, 46 K) Free Viewers

The PWC ESA Automation Tool is a spreadsheet that has been built to assist in developing the inputs necessary to run the ESA Batch feature available in the new version of the PWC. Each row below row 2 represents a PWC run. The user enters the appropriate information in the columns that have headers in black (columns A-T and AB-PN). The red columns will fill in automatically once the user copies the functions contained in row 3 to the rows being created. Row 1 provides guidance on the information required for some of the column input values. For instance, Column D is the Koc flag, which should be entered as either True or False. Additional instructions and information regarding data processing can be found in the “ReadMe” worksheet within the workbook.  The tool has been updated to include field and waterbody inputs for hydrologic unit code (HUC) Region 19 (Alaska).

A new version of the PWC ESA Automation tool is provided (Dated January 10, 2017). Changes made to the previous version posted in April 2016 are captured at the bottom of the “Read me” page of the tool and include the following: incorporation of baseflow estimates and capped watershed sizes for HUC 13 and HUC 16 at the largest HUC. 

Note. This is a pre-release beta version of the Pesticide Water Calculator tool. It has not yet been subject to review and results should be considered provisional and subject to revision.

PWC ESA scenarios (zip file) (1 pg, 297 K) Free Viewers

For aquatic exposure assessments, input scenarios are used to represent a finite set of combinations of soil, weather, hydrology, and management/crop use conditions that are expected to maximize the potential for pesticides to move into surface water. For aquatic modeling of the three pilot chemicals under ESA, scenarios were developed for:

  • 11 general crop classes:
    • o corn;
    • cotton;
    • soybean;
    • wheat;
    • pasture/hay;
    • other crops [e.g., clover, fallow field, sod/grass for seed];
    • orchards and vineyards;
    • other trees [e.g., managed forests];
    • other grains [e.g., barley, buckwheat, canola, rye, sugarcane];
    • other row crops [e.g., peanuts, sugar beet, sunflower, tobacco]; and
    • vegetables and ground fruit)
  • 12 nonagricultural uses:
    • adulticide;
    • developed commercial areas,
    • developed open space [e.g., recreational areas];
    • golf;
    • impervious;
    • unspecified land cover [e.g., nurseries];
    • rangeland;
    • residential;
    • right-of-way;
    • wide area use [WAU]; and
    • Christmas tree orchards)

These categories are based on the USDA National Agricultural Statistics Survey (NASS) Cropland Data Layer (2010-2014). These scenarios are grouped by HUC2 region and crop class. One representative scenario is selected for each HUC2-crop combination based on runoff potential, and 30 years of representative weather (from the Solar and Meteorological Surface Observation Network [SAMSON]) are used based on the station within each HUC2 with the median cumulative precipitation. 

The zip file below contains the scenarios used for aquatic modeling of the three pilot chemicals.  The scenario files are named using the following convention: crop_group_nameESAHUC2.  For example, the corn scenario for HUC2 Region 1 has been named CornESA1.scn.  If multiple weather stations are identified for a particular HUC2 region, an “a” or “b” is added to the scenario name.

Note: These scenarios are pre-release beta versions, which have not yet been subject to review. PWC results generated using these scenarios should be considered provisional and subject to revision.

This file has been updated to include scenarios for HUC 19 (Alaska).

Note: These scenarios are pre-release beta versions, which have not yet been subject to review. PWC results generated using these scenarios should be considered provisional and subject to revision.

PWC Postprocessor, v. 1.0 beta (XLSX)(1 pp, 2.26 MB)(1 pg, 39 K) Free Viewers

The PWC Postprocessor is a spreadsheet that has been built to assist in analyzing the results from the multitude of PWC runs conducted for the draft BEs.  The tool allows the user to compare EECs to aquatic thresholds, summarize EECs by HUC2 and bin combination, and make effects determinations for all listed species associated with aquatic habitats.  The tool also allows the user to evaluate individual PWC runs conducted in support of the draft BEs. Before running the tool, the user should store all of the PWC runs and the summary file in a single directory.  Additionally, the user should check the ErrorSummary file and ensure that no errors occurred during the PWC batch run. Additional instructions and information regarding data processing can be found in the “ReadMe” worksheet within the workbook.

A new version of the PWC Postprocessor is provided (Dated January 10, 2017). Changes made to the previous version posted in April 2016 are captured at the bottom of the “Read me” page of the tool and include species and habitat bin updates. 

PWC Non-ag Postprocessor, v. 1.0 beta (XLSX) (1 pp, 10.8 MB) Free Viewers

The PWC Non-ag Postprocessor is a spreadsheet that postprocesses the residential, impervious, and rights-of-way time series generated in the PWC and allows for the generation of the 1-in-10 year and 1-in-15 year EECs.  For some of the pilot chemicals, non-agricultural uses (e.g., applying to gardens, lawns, around commercial buildings, etc.) have been modeled using multiple PWC scenarios which represent the variety of surface types that could occur in a nonagricultural setting (e.g., turf, impervious, right-of-way).  The time series for the individual runs are normally combined afterwards to generate a time series and 1-in-10 or 1-in-15 year statistics to represent the non-agricultural use.  This spreadsheet automates this process.  Additional instructions and information regarding data processing can be found in the “ReadMe” worksheet within the workbook.  Note: This tool should be run prior to using the PWC Postprocessor so that the results can be incorporated into the analysis.

A new version of the PWC Non-ag Postprocessor is provided (Dated November 7, 2016). Changes made to the previous version posted in April 2016 are captured at the bottom of the “Read me” page of the tool and include species and habitat bin updates. 

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Terrestrial Tools and Models:

Terrestrial Effects Determination (TED) tool, v. 1.0 beta (XLSX) Revised March 2016(1 pg, 1.21 MB) Free Viewers

In order to improve efficiency and expand EFED’s modeling capabilities to other, non-dietary routes of exposure for terrestrial organisms, the TED tool was developed. This tool integrates T-REX, T-HERPS, the earthworm fugacity model, TerrPlant and AgDRIFT. In addition to dietary based exposures, the tool also estimates pesticide doses to animals exposed via drinking water, dermal and inhalation routes. The TED tool estimates concentration-based and dose-based pesticide exposures relevant to assessing risks of direct effects to listed species and indirect effects through declines in prey or impacts to habitat. Exposures are compared to relevant thresholds and endpoints and are used to estimate the distance from the edge of the field to which risk extends and the duration of time that residues are at levels representing a concern for effects to individual listed species. A description of the methods employed by this tool is provided in Attachment 1-7.

A new version of the TED tool is provided (Dated December 22, 2016). Changes made to the previous version posted in April 2016 are captured at the bottom of the “Read me” page of the tool and include correction of errors described in the public comments and species updates. 

Note: This is a pre-release beta version of the Terrestrial Effects Determination Tool. It has not yet been subject to review and results should be considered provisional and subject to revision.

Integrated Terrestrial Investigation Model (TIM, v. 3.0 beta) and Markov Chain Nest Productivity Model (MCnest, v. 2.0 beta) (zip file) (1 pg, 704 K) Free Viewers

TIM has been integrated into the MCnest model to provide risk estimates associated with declines in survival and fecundity of birds exposed to pesticides. The models represent exposures on treated sites (e.g., agricultural fields and orchards) and adjacent areas receiving spray drift. A full description of TIM is available online. A full description of the basic MCnest model is also available online. The integrated version of TIM and MCnest replaces the T-REX portions of exposure used in the basic MCnest model.

The integrated TIM/MCnest model was designed in Matlab 2013b and requires the Matlab Compiler Runtime (MCR) to be installed on your computer.  MCnest will not run without the MCR.  Due to its size, we are not hosting the MCR on our website.  Download it free of charge from the Mathworks websiteExit The required version is the Windows 64-bit MCR for Matlab release 2013b.

A species library is available for use with the integrated TIM/MCnest model. This library includes life history parameters for 13 species of listed birds that are included in the refined avian risk assessment (Appendix 4-7). The metadata for these parameters are included in supplemental information 2 of Appendix 4-7.

Note: This is a pre-release beta version of the integrated TIM/MCnest model. This model and the species library have not yet been subject to review and results should be considered provisional and subject to revision.

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Effects Tools:

Data Array Builder (DAB), v. 1.0 beta (zip file) (1 pg, 258 K) Free Viewers

The DAB generates ecotoxicity data arrays, or graphic representations of effects data, based on formatted ECOTOX data reports and user-entered registrant-submitted studies. Once the data have been inserted into the workbook and formatted according to the tool’s instructions, the DAB allows sorting of the data by user-defined taxonomic group, effect type, and endpoint and generates dot plots presenting the data. The user can also create summary plots by effect type that show the range of values and median concentration for each type of effect. Additional details regarding data processing can be found in the “ReadMe” worksheet within the workbook.

Note: This is a pre-release beta version of the Data Array Builder. It has not yet been subject to review and results should be considered provisional and subject to revision.

Species Sensitivity Distribution (SSD) toolbox, v. 1.0 beta (zip file) (1 pg, 6 MB) Free Viewers

The SSD toolbox allows the user to fit distributions to acute toxicity data available for tested species that fall within the same group (e.g., fish, birds, invertebrates). It combines a variety of algorithms to support fitting and visualization of simple SSDs. The current version of the tool supports five distributions, including:

  • normal;
  • logistic;
  • triangular; 
  • gumbel; and
  • burr.

When any of the first four distributions are chosen, the data are first common-log transformed (log10). When the burr distribution is chosen, the data are fit on their measurement scale. The tool also supports fitting distributions using four different methods (maximum likelihood, moment estimators, graphical methods, and Markov Chain Monte Carlo). From these distributions, direct and indirect effects mortality thresholds (1/million chance of mortality and 10% mortality) are calculated. Median threshold values are estimated along with the 95th percentile confidence intervals. Guidance on how to use the tool is provided in the User’s Guidance document. Technical details on the methodology employed in this tool are provided in Attachment 1-5.

The SSD Toolbox was designed in Matlab 2013b and requires the Matlab Compiler Runtime (MCR) to be installed on your computer.  The SSD Toolbox will not run without the MCR.  Due to its size, we are not hosting the MCR on our website.  It can be downloaded free of charge from the Mathworks  Exitwebsite.  The required version is the Windows 64-bit MCR for Matlab release 2013b.

A new version of the SSD Toolbox is provided (Dated August 29, 2016) that has improved functionality. The underlying mechanics of the tool remain unchanged.   

Note: This is a pre-release beta version of the SSD Toolbox. It has not yet been subject to review and results should be considered provisional and subject to revision.

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Weight of Evidence (WoE) Tools

In order to conduct the Step 2 Weight of Evidence (WoE) analyses in a transparent, consistent and efficient manner, tools were developed to automatically generate WoE matrices for each of the listed species and designated critical habitats evaluated as part of the draft BEs for chlorpyrifos, diazinon and malathion. These tools integrate available life history information for species, overlap analyses, toxicity data and exposure estimates relevant to the species and critical habitat in order to make risk and confidence calls for different lines of evidence (i.e., mortality, growth, reproduction, behavior and sensory effects). A zip file containing the WoE tools is available for chlorpyrifos (ZIP) (1 pp, 17 MB), diazinon (ZIP) (1 pp, 16 K) and malathion (ZIP) (16 pp, 16 MB). Each zip file contains the following files:

  • 4 species template files (Species Animal Template, Species Plant Template, Species Aquatic Animal Template, and Species Aquatic Plant Template)
  • 5 root files (TED tool “Base” file, TED tool “alt” file, TerrWoE, AquaWoE and the data matrix template)
  • 1 Read Me file

The brief “Read Me” file contained in the zip file provides information on how files need to be organized and opened in order to create a WoE matrix using a unique species ID number.  Attachment 4-1 provides additional information on how these tools are organized and the types of information used in the matrix generation.

New versions of the WoE tools are provided (Dated January 12, 2017). Changes made to the previous version posted in April 2016 include correction of errors described in the public comments and species and habitat bin updates. 

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