National Protected Species Toolbox (NPST)

Environmental change and anthropogenic impacts are a serious conservation and management concern for protected and other non-target megafauna species such as sea turtles, marine mammals, sharks, and seabirds.  In the United States, management actions and environmental policies are geared towards reducing impacts on critical species from fisheries bycatch, oil spills, and habitat and climate change.  Implementing the appropriate regulatory or management action requires data and appropriate data-analysis frameworks.  For example, under the Magnuson-Stevens Act, reference points are required to be estimated for all target and non-target species considered a part of the fishery.  Under the Endangered Species Act, analyses are needed to inform the question of whether proposed actions will jeopardize listed species.  Under the Marine Mammal Protection Act, limits to direct human-caused mortality and serious injuries must be estimated.

Common traits of many marine megafauna include slow life histories (long-lived, late-maturing, low-recruitment to adult stage), widespread distribution across political boundaries, and being poorly sampled by research surveys.  Also, some species are more vulnerable to environmental perturbations and may require more innovative and interventionist approaches, e.g., corals to promote recovery and prevent extinction. These factors result in data scarcities and present a challenge to established assessment methods used to manage exploited marine populations that are often data intensive.

Assessments of target fish stocks are conducted using a suite of analytical methods that can be applied in diverse management contexts and circumstances of data availability.  Many of these developments have been supported by research funding from NOAA (e.g., Advanced Sampling Technology Working Group, Assessment Methods Working Group program) and now contribute to the NOAA Fisheries Toolbox.  A similar “toolbox” comprising products and applications tailored to policies and data uncertainties for protected species would benefit management of protected and other highly migratory non-target species. Currently, products and applications developed through the Protected Species Toolbox Initiative are housed by the Office of Science and Technology (ST).

The ST-administered Toolbox initiative is a critical long-term research and development (R&D) investment in applied science, which in some cases may be available for immediate management application or transitioned over time for management actions.

Goals and Objectives of the NPST:

  • Produce, evaluate, and disseminate analytical products and applications to improve protected species assessments in support of regional and/or national management priorities.
  • Enhance partnership and coordination among science and management offices by jointly identifying research priorities for the Toolbox Initiative.
  • Investigate, understand, and predict intensity and magnitude of impacts on protected species populations from ecosystem change, human activities, and cumulative and aggregated stressors.
  • Strengthen scientific excellence and capacity by recruiting and training young researchers in cutting-edge techniques and novel approaches and through inter-disciplinary collaboration and produce products and applications for scientific or management use.

NPST Repository

Funded Projects:


Each thematic group is comprised of science and management teams and is individually led by two science center-based investigators.

  1. Coral Demographics (PIFSC, NCCOS and JIMAR), to develop spatially-explicit predictive maps for ESA-listed coral species occurrence, abundance, demographic patterns, and potential connectivity.
  2. Spatial Analysis (AFSC, SEFSC, SWFSC, and NWFSC), to develop or enhance existing spatial tools for various taxonomic groups (sea turtles, cetaceans, and pinnipeds) facilitating integration or effective use of different data streams (acoustics, fine-scale and broad-scale survey data, telemetry, photo-id) to generate improved protected species analytical models.
  3. Population Assessments (NWFSC, SWFSC, NEFSC, and SEFSC), to improve quality, transparency and national consistency in protected species population assessments and estimated population parameters (e.g. cetacean trend analysis, bycatch estimate calculation) and produce user-friendly interactive web tools to enable easy analysis and evaluation of different methods suggested above in management decision-making.


  • Development of quantitative tools for assessing effects of anthropogenic mortality for marine turtle populations (SWFSC and NWFSC) - Year 1
  • Development of quantitative tools for predicting protected species and fishery co-occurrence(SWFSC and NWFSC) - Year 2
  • Advancing development of a limit reference point estimator for sea turtles, and evaluating methods for applying local management to highly migratory species (SWFSC)
  • Development and evaluation of quantitative tools to assess the impact of anthropogenic impacts on marine turtle populations (NEFSC and SEFSC)
  • Developing ocean ecosystem indicators for marine turtle juvenile recruitment (PIFSC)
  • Development of quantitative and web-based tools for modeling marine animal movement and habitat use from satellite telemetry data (AFSC)
  • Deploying protected species tools via cloud computing (NWFSC)   

National Protected Species Toolbox Mini-Symposium

Scientists from NOAA Fisheries' Science Centers gathered at the NOAA Science Center in Silver Spring on November 18, 2015, to present some of the tools and applications they have been working on between 2013 and 2015. These emerging tools were developed as part of a national protected species toolbox initiative supported by Dr. Richard Merrick (NOAA Fisheries’ Chief Scientist) and spearheaded by the Office of Science and Technology, to produce quantitative analytical tools to improve protected species assessments and better analyze impacts from human activities. The mini-symposium served as an opportunity to strengthen scientific connections and collaboration between NOAA Fisheries science centers and internal and external partners. Over 70 external and NOAA participants attended the symposium via webinar and in person.

Presentation List

  1. Spatial prediction of fisheries bycatch — Brian Stock, Eric Ward and Tomo Eguchi (SWFSC/NWFSC) (Presentation )

  2. An integrative model of sea turtle growth based on recoveries and mark-recapture data —Brandon Chasco, Eric Ward and Tomo Eguchi (SWFSC/NWFSC) (Presentation )

  3. Quantitative tools to assess the impact of anthropogenic activity on sea turtle populations— Melissa Warden and Heather Haas (NEFSC) (Presentation )

  4. Advancing development of a limit reference point estimator for sea turtles, and of a local management approach for highly migratory species — Alex Curtis and Jeff Moore (SWFSC) (Presentation )

  5. A spatial risk assessment tool that connects oceanographic and demographic information to predict distribution and abundance for protected species — Paul Richards and Nathan Putnam (SEFSC) (Presentation )

  6. Crawl: An R package for modeling animal movement from satellite telemetry data — Devin Johnson (AFSC) (Presentation )

  7. Developing and deploying web-based tools to visualize marine animal movement data and explore abundance and trend of pinniped populations — Josh London (AFSC) (Presentation )

  8. Developing ocean ecosystem indicators for marine turtle juvenile recruitment — Kyle Van Houtan (PIFSC) (Presentation )

  9. Deploying protected species tools via cloud computing — Eli Holmes (NWFSC) (Presentation )

Science Communication and Coordination


Science Connect

Protected Species Toolbox

Protected Species Assessment Workshop