Endangered Species Scientific Research & Enhancement Per

OMB No. 0648-0084; Expires XX/XX/XXXX

National Marine Fisheries Service

Endangered Species Scientific Research and
Enhancement Permit Application
TABLE OF CONTENTS

INTRODUCTION..............................................................................................................2
NEED HELP OR HAVE OTHER QUESTIONS? ................................................................................................... 2
WHEN FILLING OUT YOUR APPLICATION: .................................................................................................... 2

APPLICATION INSTRUCTIONS ..................................................................................3
PROJECT INFORMATION .............................................................................................................................. 3
PROJECT DESCRIPTION ............................................................................................................................... 4
PROJECT SUPPLEMENTAL INFORMATION ...................................................................................................13
PROJECT LOCATIONS .................................................................................................................................16
TAKE TABLE..............................................................................................................................................17
ANTICIPATED EFFECTS ON THE ENVIRONMENT .........................................................................................20
PROJECT CONTACTS ..................................................................................................................................21
SUBMIT APPLICATION ...............................................................................................................................24

FREQUENTLY ASKED QUESTIONS.........................................................................24
WHAT IS THIS APPLICATION NOT FOR? .......................................................................................................24
WHEN SHOULD I APPLY? ...........................................................................................................................24
WHAT IS THE PROCESS FOR GETTING A PERMIT? ........................................................................................24
WHAT IS THE PROCESS FOR REQUESTING A MODIFICATION TO A PERMIT? .................................................25

ADDITIONAL INFORMATION ...................................................................................26
PAPERWORK REDUCTION ACT STATEMENT...............................................................................................26

OMB No. 0648-0084; Expires XX/XX/XXXX

Introduction

This application is for requesting an Endangered Species Act (ESA) scientific
research or enhancement permit to take 1, import, or export National Marine
Fisheries Service (NMFS) protected species, including:
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Sawfish (largetooth and smalltooth)
Sea turtles (in-water)
Sturgeon (Atlantic and shortnose)

What is this application not for?
Research or enhancement activities on:
• Sea turtles on land or in rehabilitation
• Marine mammals
• Pacific marine and anadromous fish (e.g., steelhead, eulachon, salmon)
• Protected species parts (only involving importing, exporting, or receiving
parts)

Need help or have other questions?

We recommend you visit our ESA scientific research permit web page, see the FAQ
on page 24, or contact our office (301-427-8401).

When filling out your application:
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Refer to Chapter 2 for guidance on how to use APPS.

Save your application every 20 minutes or you will lose information!
You do not have to complete your application in one session. Your
application will remain in draft mode until you submit.
An * means it is a required field.

You may want to use these instructions as a template to draft your
application in a Word doc and then cut and paste into APPS. However, note
that special characters may be either lost or migrated incorrectly.
Attachments cannot be larger than 20MB – contact us if you need to attach
larger files.

Your application must be a stand-alone document that describes all proposed
activities and is readable to a layperson.

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A take under the ESA means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or
attempt to do any of the preceding.
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If you do not follow these instructions, your application will be returned and
you will be asked to resubmit a new application that includes the information
required.
We can only consider those activities that you describe in your LOI.

We will not consider your application if you have overdue reports for your
most recent permit or LOC.

Application Instructions
Project Information

File Number: This number is generated by APPS and cannot be changed. To
facilitate processing, reference this File No. in correspondence with our office.

*Project Title (up to 255 characters): Provide a concise title that includes
activities, species (or taxa if multiple species), location, and purpose of the research.
For example:
• Vessel surveys, sampling, and tagging sea turtles in the Gulf of Mexico to
characterize population structure, forging ecology, and movement patterns.
*Project Status: The project status (New or Renewal) is automatically selected
based on your answers in the APPS pre-application guide (PAG). Do not change this
field.
Previous Federal or State Permit #: If applicable, enter your most recent and
closely related NMFS permit number. Otherwise leave blank.

*Permits Requested: One or more permits will be listed based on your answers in
the APPS pre-application guide. If the options are incorrect, please contact us at
301-427-8401.
*Where Will the Activities Occur? One or more general locations will be listed
based on your answers in the APPS pre-application guide. .

*Research Timeframe: Enter the desired start and end dates of the entire project
in the following format: MM/DD/YYYY. IMPORTANT: Refer to the FAQ on page 26
for details about when to apply and consult our programmatic consultation web
page. The start date must be after the date you submit the application and should
consider how long it may take to process your request, at least 6 months. Permits
may be requested for up to a 10 year period only if the project fits within the scope
of an ESA Section 7 programmatic biological opinion. All other permits may be valid
for up to 5 years.
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*Sampling Season/Project Duration (up to 1,000 characters)
Describe the annual field season(s) including the primary months and frequency of
fieldwork (i.e., how many field days per year and how frequently will you conduct
your activities?). If this includes year-round research, indicate when activities are
most likely to occur and how frequently.
*Abstract (up to 2,000 characters): provide a short summary that must include:
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Purpose of the research or enhancement.
Species that may be taken, imported, or exported.
Proposed take activities (e.g., capture, sampling, tagging), import, or export
Where your activities will occur and where animals or samples will be
imported or to which they will be exported.
Requested duration of the permit (see FAQ).

Project Description

*Project Purpose: Hypothesis/Objectives and Justification (up to 64,000
characters)

For research permits, the information you provide in your application must
demonstrate that the permit, if issued, would further a bona fide and necessary or
desirable scientific purpose, taking into account the benefits anticipated for the
target species.
We recommend you provide the information in this order:

1. Identify and discuss the research question(s) or purpose of your project.
2. Briefly summarize published findings related to your research.
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If you previously held or worked under a research or enhancement
permit, use literature citations that support how you previously met
your objectives; and/or
Use other published literature on the subject.
Describe how this study is different from, builds upon, or duplicates
past research.
If proposing novel procedures, include a discussion on results from
pilot studies or studies on other species, if available.
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3. Discuss why your project must involve ESA-listed species (e.g., explain why
similar results could or could not be obtained by using a surrogate or captive
species).
4. Discuss how your project will, as applicable:
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Contribute to the objectives identified in the species’ recovery or
conservation plan or otherwise respond to recommendations of a
scientific body charged with management of the species;
Contribute significantly to understanding the basic biology or ecology of
the species; and/or
Contribute significantly to identifying, evaluating, or resolving
conservation problems.

5. If your goals are to directly enhance the survival or propagation of an
ESA-listed species, explain how your project will achieve these goals.
6. Identify your objectives or hypotheses based on the above information.

7. Take Number Rationale: Clearly explain how you determined your sample
size/take numbers and how they are needed to meet the objectives.
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For example, did you base your numbers on previous encounter rates
or abundance estimates for your study area and the number of
surveys to be conducted?
If appropriate for your study, include a power analysis or other
sample size estimation to clearly demonstrate the sample size is
sufficient to provide statistically significant or otherwise robust
results.

Indicate the number of times known individuals will be intentionally
taken in a year (e.g., recapture for instrument retrieval, multiple
biopsy samples per year, or repeat surveys in the same area for
identifiable individuals). Explain why multiple takes are needed to
meet your objectives.

*Project Description (up to 64,000 characters)
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Please see our webpage on programmatic permitting to determine if your
methods may fall under an existing programmatic ESA Section 7biological
opinion. If you wish to have your work covered by a programmatic opinion,
please ensure your described methods fit within its scope or contact our
office.
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Provide a brief overview of a “day on the water” and the suite of activities
you intend to perform on each animal during an encounter or capture event
including where your work will happen, especially if different projects occur
in different locations.
For proposed studies on sturgeon species, provide the water body (i.e.
specific river, bay, ocean basin) for each suite of methods described.

Methods

Describe your methodologies. Your narrative description must match your APPS
take table (see Take Table section below). Every procedure listed in the take table
must be described in the Project Description. It is helpful to reference take table
lines in the narrative that correspond to the take actions and procedures. If you
have multiple projects, it is also helpful to name them by project number or title and
include project names in the Details column of the take table.
You must provide:
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A clear description of all methods (i.e., procedures) for each species, by
Distinct Population Segment (DPS) where applicable. See examples in Table
1 below.
A brief statement of each method’s purpose (i.e., how the activity relates to
meeting your objectives).

Figures and photographs that illustrate your methods (e.g., tags and
instrument attachments, nets and net deployment). You can attach them on
the Supplemental Information page.
Indicate if you will intentionally take a known animal more than once
per day and/or year as driven by your objectives and study design (e.g.,
active acoustics, recapture for instrument retrieval or multiple biopsy
samples per year).

If recapturing animals, indicate under what circumstances they will be
immediately released without processing or fully or partially processed (i.e.,
what will be done to them on recapture).
Discuss whether non-target animals of the same species (i.e., conspecifics)
may be taken (e.g., harassed, captured) during your work.
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List out the suite of procedures that will be performed on only a subset of
animals and explain how you will decide which animals will receive which
procedures. Is this based on sex, life stage, body size, body condition, health
or appearance, needed sample size, etc?

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Note: You must demonstrate that the annual Expected Take numbers
requested for your activities do not exceed the number authorized for the
original capture authority, such as the cited biological opinion’s incidental
take statement.

If animals will be captured under another legal source (e.g., bycaught in
commercial federal fishery) prior to research or enhancement, cite the
specific legal authority by name, title, or permit number for the capture of
these animals. Clarify which activities you are requesting to perform after
the capture and how they will occur in relation to the other legal action.
Example citations: “ESA Section 7 biological opinion for the Gulf of Mexico and
South Atlantic spiny lobster fishery (NMFS 2009)” or “ESA Section 10 Permit
No. XXXXX”.

Sea Turtle Aerial and Vessel Surveys: Only request take for observations
or monitoring surveys with no intent to contact or capture animals if:
1. The encounter will last more than 5 minutes, and
2. For in-water work, you will approach animals within 50 yards.

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Contact us if you need help determining if your survey requires a permit.

Describe the size and life stages of animals for which you are requesting take.
You may attach a table indicating which ages and sex will receive each
procedure if needed (e.g., complex studies or multiple projects).
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For sea turtles, indicate the minimum size in straight carapace length
of the animals you expect to capture and for each procedure you are
requesting.
For sturgeon:
o Include total length for each age class proposed (e.g., size
ranges designating juvenile, sub-adults and adult life stages)
o Make sure you have indicated in the Objectives section above
the purpose of working with each life stage/size.
o In the details of the Take Table, define the size range of the
targeted life stage.

Cite references for the proposed methods where applicable, but do not
substitute a literature citation for a complete description of the methods.
References must be made available upon request.
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Mitigation measures that are inherent to your methods may be included in
this section, or in the Effects and Mitigation section below.

Table 1. Guidance for Commonly Used Methods
When describing your methods, you must include the following specific information,
as applicable:
Take action/
procedures
Active acoustics

Administer
drugs or other
substances (e.g.,
stable isotopes,
bone marking,
anesthesia)
Aerial and vessel
surveys
(manned)

Example details to include in methods

Sound source (e.g., sidescan sonar, underwater speaker, acoustic
deterrent device; actual source vs. playback; stationary vs. mobile)
Source depth in water column
Frequency (bandwidth)
Maximum source level (specify metric SELcum or SPL RMS)
Maximum received level for target and non-target species and how
this was determined
Distance of source to target and non-target animals (including marine
mammals)
Signal duration and duty cycle
Duration of sound exposure to an individual animal as well as total
potential duration of exposure within a 24-h period
How many sound source types might be used within a 24-h period
Ambient sound level, when known
Post playback monitoring (monitoring distance and duration)
Please provide propagation loss models, when available
Name of each drug/chemical and its purpose
Name of any drug reversal or emergency response drugs
Dosage of each
Delivery method and route (e.g., intramuscular, intravenous,
subcutaneous, topical, immersion)
Location of administration on body
Duration of anesthesia or sedatives
Personnel that would administer drug (e.g., veterinarian or
veterinary technician; and if they possess any required state licenses)
Post drug administration monitoring
Type of survey craft/ vessel and size
Type of survey (e.g., line transect, photogrammetry)
Number of platforms (aircraft and vessel) to be operated at the same
time
Number of surveys per year
Minimum altitude/approach distance
Air/vessel speed
Protocols for breaking track to ID species
Duration spent with group or individual/day

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Take action/
procedures
Auditory
brainstem
response or
evoked potential

Captive
experiments

Capture and
restraint

Example details to include in methods
Type of measurement equipment (suction cup or needle electrodes
and location on animal)
Type of sounds emitted (e.g., pips, clicks)
Maximum source level
Distance and position of speaker relative to animal to target animal
Signal duration, duty cycle, and frequency of sound emitted
(including total exposure duration within a 24-h period)
Would different sound types be played within 24-h period
Handling/restraint methods (including anesthesia/sedation, see
above)
Handling duration
Data collection and analysis method
Whether animal will be transported to a facility (complete the
Transport Section in Take Table)
In addition to describing the procedures of the experiment on the
animals, describe their care and maintenance, including a complete
description of the facilities where they will be maintained. This
includes but is not limited to:
• Dimensions of the pools or other holding facilities
• Number, sex, and age of animals by species to be held in each
tank/enclosure
• Water supply, amount, quality, power supply, and backup
redundancy
• Diet, amount and type
• Sanitation & quarantine practices.
Indicate the final disposition of animals after completion of
experiments (e.g., for sturgeon: continued maintenance, euthanasia
or transfer to another permitted facility, if appropriate).
Type of capture (e.g., hand or net (gill [drift or anchored], trawl,
seine) and gear description including dimensions and mesh size
Deployment methods (e.g., boat approach and net set, tow or soak
times)
Configuration, duration, and monitoring of net sets (how often net set
is checked)
Numbers of animals captured at a time
Number of animals processed at a time
Anesthesia/sedation (see drug administration)
Dimensions and type of holding container
Number and roles of personnel (must be adequate to perform all
activities without harming excess captured animals; else the
animals must be released immediately)
Additional equipment or personnel necessary for capturing and
handling excess numbers
Duration of restraint/holding from capture to release
Sea turtles: Identify an on-call veterinarian and nearby permitted
rehabilitation facility available for emergencies
Manner of release
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Take action/
procedures
Export/import
samples

External
instruments (a
table is helpful for
multiple tag
types)

Example details to include in methods
Sample type (e.g., blood, muscle, gonad)
Where are samples going: person and country
Where are samples coming from: high seas or origin country
Designated port of entry/import or export
How sample/animal is taken in foreign country or on the high seas
and legal take authority
Type of storage/shipping, including preservatives, etc.
Analysis
Re-import/export or retain/archive if samples remain after analysis
Type of instrument
Location on body
Dimensions
For turtles: tag frontal area and shape per Jones et al. (2013) 2 .
Mass in air or water
For fish: Percentage of body mass
Minimum size of animal to receive each tag type
Maximum footprint/maximum number of tags/animal
Method of attachment (e.g., remote suction cup; restraint and
adhesives; monofilament line)
Disinfection/sterile preparation for carapace drilling site and gear
For remote deployment or detachment: number of attempts per
animal/day, minimum approach distance and angle, method of
detachment
Pain management if required (see Administration of Drugs)
Will it be coated with antifouling paint?
Duration of attachment procedure, curing time
Duration of instrument retention on animal
Release mechanism or recapture to remove
Type of data collection (e.g., archival requiring retrieval)
How will you determine which animals receive which tags or more
than one tag?
Post-tag monitoring

2 Todd Jones, T., Van Houtan, K. S., Bostrom, B. L., Ostafichuk, P., Mikkelsen, J., Tezcan, E.,
Carey, M., Imlach, B., Seminoff, J. A. and Rands, S. (2013), Calculating the ecological impacts
of animal‐borne instruments on aquatic organisms. Methods Ecol Evol, 4: 1178-1186.
doi:10.1111/2041-210X.12109
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Take action/
procedures
Internal
instruments (e.g.,
stomach
temperature pills,
telemetry tags)

Intrusive
sampling (e.g.,
blood, digital fecal
extraction,
laparoscopy,
lavage, muscle,
scute, skin,
swabs); remote or
under restraint

Marking (e.g.,
bone mark (OTC,
fluorescent),
flipper tag,
Floy/dart tags,
paint, PIT tag,
shell etching)

Example details to include in methods
Type of instrument
Dimensions
Mass in air or water
Percentage of body mass for all tags combined
Size of animals (including minimum size) to receive an internal
instrument
Location within body
Cleaning/sterile preparation
Insertion method (e.g., surgical implant, injection, stomach tube) and
any applied coating on the tag (e.g., antibiotic)
Local anesthetic or anesthesia/sedation (see Administer drugs) if
applicable
Duration of insertion procedure
Duration of instrument retention
How stomach pills are voided
For sea turtles: include a veterinary-approved protocol for stomach
pills
Type of data collection
Type of tissues
Size or volume of sample (diameter and depth or total volume)
Location on body
Number of samples per animal per capture event and per year,
sampling intervals (e.g., for serial blood samples)
Sampling equipment description and disinfection
If restrained: cleansing/disinfection of site; left open or wound
closure
If remote: collection method (e.g., pole sampling), minimum approach
distance, number of attempts per animal
Minimum size of animal to receive each procedure
Pain management or sedation (drugs and dosages as above)
Whether animal will be transported to a facility for temporary
holding (see Transport information in Take Table below)
For sea turtles, include a veterinary-approved protocol for
laparoscopy, tumor removal surgery, and bone biopsy
Sample storage and analysis
Type of mark
Location on body
Method of application
Cleaning and disinfection procedures
Duration of mark
Dimensions of tag or mark
Size of animals to receive tags including minimum size
Sizes of PIT and flipper tags for sea turtles -Total number and
combination of tags or marks on each animal
For turtles:
-Veterinary-approved protocol for PIT tagging turtles <16 cm SCL
-Type of paint (non-toxic only)
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Take action/
procedures
Non-intrusive
sampling (e.g.,
behavioral
observations;
diagnostic
imaging;
collecting voided
feces, urine, fish
eggs or milt;
photogrammetry)
Remotely
Operated
Vehicles (ROVs)

Example details to include in methods
Approach method
Sampling method (e.g., X-ray; genetic tissue from fin)
Minimum approach distance
Frequency of observations/sampling/day
Duration of observations/sampling/day
Data or sample collection and analysis
Whether animal will be transported to a facility for temporary
holding (see Transport information in Take Table section)
For Unmanned Aircraft Systems (UAS), same details for aerial
surveys and also:
Type of UAS – fixed wing or vertical takeoff and landing
Payload components (e.g., camera, sensor) – what is the UAS carrying
and for what purpose?
Ground control station description (what it is, where it will be located
on shore or on vessel, number of stations, and how close the
station will be to animals)
Do you have the appropriate FAA permits/authorizations (including
pilot licenses)?
Encounter duration
Number of UAS operated at one time

For underwater ROVs, same details as for vessel surveys and also:
Description and size of ROV
Whether it is tethered or wireless, tether material and length
Deployment method, in relation to capture and release of animal, if
applicable
Describe any light sources
Whether there will be a live video feed monitored
Encounter duration

Non-target ESA-listed Sea Turtle and Fish Species: Discuss whether and how
non-target ESA-listed sea turtles or fish species may be incidentally captured or
otherwise affected. These are species that co-occur with your target species and
that could be harassed or taken during your work. Include these species, by DPS
where applicable, on separate rows, in the Take Table if you expect incidental take
(e.g., harassment or capture).

Non-target taxa (e.g., marine mammals, seagrasses) should be addressed in the
Effects and Mitigation section below.

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Project Supplemental Information

Attach a Supplemental Information File
You can attach up to 10 files in APPS to provide additional information.
• Preferred file formats: Microsoft Word, Excel, or PDF.
• The maximum file size allowed is 20 MB.
• Audio and video files (such as mp3, m4b, wav) cannot be uploaded. Please
contact us if you need assistance with these file formats.
• On the Location screen, you will be asked to attach a map.

Status of the Affected Species (up to 2,000 characters)
If choosing “range-wide” in the Stock/Listing Unit column in a row of the take table,
indicate which stocks or DPSs you are targeting.

*Mortalities (up to 2,000 characters)
If authorization for mortality 3 (euthanasia/intentional 4 or accidental/unintentional)
is proposed:
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What activities could result in mortality?

Briefly summarize mortalities that have occurred during the previous five
years of your permitted activities using the same or similar techniques;
include circumstances and cause of death, and how a similar outcome can be
prevented.
Explain why it’s not feasible to use other methods that won’t result in
mortality.

Specify the maximum number of animals of each species/DPS and age class
that could die or be euthanized annually or over the life of the permit.
Justify the number of mortalities.

For euthanasia of fish, indicate if it is for humane reasons (e.g., if working
with compromised/comatose animals) or euthanasia for directed lethal take.

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Caused by the presence or actions of researchers including but not limited to deaths or serious injuries
sustained during capture and handling, while attempting to avoid researchers or escape capture, or resulting
from infections related to intrusive procedures such as sampling or tagging.

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This includes euthanasia for humane reasons (e.g., if working with compromised/comatose animals). Only
in rare instances may wild fish be sacrificed in directed research, unless there are clear, documented
conservation benefits outweighing the loss.
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If authorization to euthanize a wild fish for scientific research purposes,
explain how the research will directly benefit the species or fulfill a critically
important research need with a conservation benefit. (Note: Directed
research requiring euthanasia of captive sturgeon is an optional disposition
for such animals.)

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Note: For sea turtles, euthanasia may not be requested as part of an
application; euthanasia falls under the authority of the Sea Turtle Stranding
and Salvage Network.

Indicate how euthanasia will be decided, conducted, and who will conduct it.

What are the protocols for necropsy and carcass disposal? If necropsy
cannot occur, explain why.

*Effects and Mitigation (up to 64,000 characters)
Discuss how the Observe/Collect Method (e.g., capture), and Procedures, except
mortalities, in the take table will affect individual target and non-target animals.
Effects of mortalities only need to be discussed above in the Mortalities section.

Cite the best available science (i.e., peer-reviewed literature or other published
data sources) and your experience (e.g., personal communication), including results
from your own research. References must be made available upon request.
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Include in your discussion:
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Typical behavioral, physical, and physiological responses,
Worst-case responses,
% of animals that normally respond,
How long it takes for animals to recover, and
The time it takes wounds to heal.

Also, include an assessment of:
• Condition of animals on recapture/re-sighting
• Recovery from sedation and handling
• Post-release behavior (immediate and long-term)
• Habitat use for animals in resident populations (based on telemetry
data, re-sightings, recaptures)
• Healing from intrusive sampling
• Healing from intrusive transmitter deployments
• Anticipated drag costs for sea turtle transmitters and attachments
• Tag retention
• Effects to nesting female sea turtles if working during the nesting
period
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Bycaught non-target species: will they be released alive? Or is a certain
percentage expected to be unintentionally harmed or killed?

For novel procedures, discuss the most likely anticipated responses based
on literature from prior studies on other species, if available, and any results
from testing, if applicable.

Discuss the anticipated effects at the level of the species or DPS, especially
if mortalities or reproductive impacts are possible. On what is your
determination based?

You may include mitigation and monitoring protocols here, in the Project
Description section. Do not restate those here if they are included above; simply
reference the section where the following information appears.
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Describe your short- and long-term post-procedure monitoring protocols.

Explain why monitoring or mitigation is not feasible for specific procedures,
species, situations, etc., as needed.
For sea turtles: if veterinarian approval is required, attach the full protocol,
any veterinary comments/recommendations, and the signed approval. This
may include an approved Institutional Animal Care and Use Committee
(IACUC) 5 proposal.

Describe any mitigation you will take to avoid or minimize impacts to nontarget protected species (e.g., marine mammals, sturgeon, sea turtles, corals,
U.S. Fish and Wildlife Service species). Indicate which DPS(s), if applicable, of
the species that may be affected. Discuss whether and how they may be
incidentally harassed, captured, or otherwise affected. Identify if you require
take of these species.

Research Coordination
• Describe how you will collaborate or coordinate with other researchers in
your action area.
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List these researchers and explain how you will work together. For example,
will you share vessels, samples, or data? Will you coordinate the timing of
surveys to avoid disturbance or repeated captures of the same animals?

Attach a References File
Attach a bibliography only including references cited in this application.
Referenced materials must be made available upon request, as needed for
5

For sea turtle research: NMFS researchers are required to submit the NMFS IACUC-approved
protocols and assurance letter.
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evaluation of the application, or preparation of any necessary ESA or NEPA analyses.
If a link to your referenced material is available, add the link to your References File.
*Resources Needed to Accomplish Objectives (up to 2,000 characters and attach
files if necessary)
• Explain how your expertise, facilities, and resources (people, physical and
monetary) are adequate to accomplish your proposed objectives and
activities.
•

•

Attach copies of relevant formal research proposals, contracts, grant awards,
or letters of agreement that would demonstrate financial or logistical
resources.
Indicate the status of other international, federal, state, or local
authorizations you have applied for, secured, or will apply for.

*Disposition of Tissue Samples (up to 2,000 characters)
Indicate the disposition of any remaining samples after your project is complete.
•

•

State whether samples will be consumed in analysis, destroyed,
retained/archived, or returned to a facility/researcher.

If applicable, list the name and location of the person or institution that will
store/curate/receive samples. Indicate if you will retain legal custody of the
archived samples or if you wish to permanently transfer the samples once
your project is complete.

*Public Availability of Product/Publications (up to 800 characters)
Describe the end products of your proposed project and how they will be made
available to the public.

Project Locations

First, describe where you plan to work. Then, for each location, use the Take Table
to list the species you expect to encounter and the procedures you will conduct.
•

•

Add New Location: provide information about one or more study areas
• General area (ocean basin)
• State(s), as applicable.
Enter Location Details, as applicable:
• Waterbody: enter names of rivers, estuaries, bays, etc.
• Latitude and longitude of your study area
• River miles (Being Mile and End Mile)
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•
•
•

Limits of your study area (e.g., to the U.S. EEZ, to the edge of the
continental shelf, to 50m depth)
Names of land masses where research will occur (e.g., islands).

Attach File: Include a high quality map(s) to scale that clearly shows the
location of your proposed activity and any environmental areas of interest. If
possible, include a shapefile, Google Earth kmz/kml, or ASCII text file with
lat/long data and the associated basic metadata with your application.

Take Table

The take table represents the estimated number of animals you propose to take
annually during your research. Your permit and subsequent reports will also
include a similar table.
Columns you will fill out in the take table:

1. Select: Leave this box blank unless you need to copy, move, or delete the
row.
2. Species: Use the drop down list.

3. Listing Unit/Stock: Select the applicable ESA listing unit/stock. Choose
Range-wide if your location has multiple populations of the same species and
you cannot distinguish between them while in the field.
4. Production/Origin: Select from the drop-down list. Categories include
Wild, Captive, Rehabilitation Facility, or All.

5. Life Stage: Select from the drop-down list. You may enter take information
for more than one life stage (e.g., adult versus juvenile) on separate rows or
select a combination of life stages for one take category. Include specified
ages if they differ for each procedure in the Details column.
6. Sex: Select from the drop-down list. If your activity targets only one sex,
indicate which. If it targets both and they can be targeted separately, enter
separate rows for male and female; otherwise select Male and Female or
Unknown for immature life stages if applicable.

7. Expected Take: This represents a reasonable estimate of the maximum
number of individuals you will take, import, or export, annually.

For vessel surveys of sea turtles that do not involve capture but will
remain within 50 yards for more than 5 minutes, you will be required to
count every animal you approach within 50 yards, regardless of whether a
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behavioral reaction has occurred. Count 1 take per animal observed per day
when you know it is the same animal. If unable to identify the animal, count
each turtle seen as a new take.

For aerial surveys of sea turtles that will stay with animals for more
than 5 minutes flown at an altitude lower than 700 ft. 6, count 1 take per sea
turtle observed per day, regardless of the number of passes over the same
animal.

8. Take Action: The “take action” is a generalized overview of how animals
will be taken by your activities over the course of the year. If more than one
action is proposed for your project, you must enter the takes on separate
rows. For example, if some animals will be captured and sampled while
others will only be harassed.
9. Observe/Collect Method: Select the method of observation (e.g., survey,
vessel) or collection/capture. Select only one observe/collect method per
row. If multiple methods are proposed, you must provide take information
in separate rows for each observe method.

10. Procedures: You will open a separate pop-up window with a speciesspecific list of activities. Hold down the Control key to select all activities to
be performed concurrently.

a. Choose “Other” if a proposed activity is not listed. In the Details box
(see below), briefly describe what the “Other” activity is. For example,
Other = carapace swabs.
b. You must select ‘Transport’ if you will temporarily hold and perform
experiments on wild animals (e.g., acoustics, imaging, feeding studies)
in a facility.
c. If some animals will only get a subset of procedures, list this subset
on a separate row in the take table. An animal may be counted only
against one take row per capture/encounter event.

11. Transport: You must select ‘transport’ from the procedure list to enable this
section. You are required to provide the below information about the
transport and holding of animals when prompted.
a) Mode(s) of transportation: Describe the vehicle or other platform used to
transport animals.

6 We are looking for data to establish minimum thresholds for when take is likely to occur from aerial
surveys.
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b) The name of the transportation company, if applicable, and the
qualifications of the common carrier to transport live animals: If a contractor
or other entity will do the transportation, enter information in the box.
Otherwise, click on N/A.
c) Maximum length of time from capture to arrival at destination: How long
will the animals be in transport?
d) Description of the container (e.g., cage, tank) used to hold the animal
during transit: Include the material of the container and its dimensions.

e) Any special care procedures (e.g., moisture, medicines) to be administered
during transport: How will the animals be cared for during transport?
f) A statement as to whether the animals will be accompanied by a
veterinarian or some similarly qualified person: If so, give the name,
affiliation, contact information for each person.

g) Destination: Use the drop down list to select the destination. If your
destination is not on the list, click on the “New Facility” button to add it. If
the animals will be taken to a laboratory or aquarium, provide details of the
location. If the animals will be released in another waterbody, provide
details of the location.

h) How will the animals be contained at the destination facility? Describe the
containment system for the animals, quarantine procedures, and effluent
treatment.
i) The final disposition of the animals: Describe, for example, whether the
animal will be released into the wild or retained in permanent captivity.

12. Begin Date: Populated with the Begin Date you entered on the Project
Information page. You may change the date to coincide with a specific
project time shorter than the overall duration of the permit. You cannot
enter a date that is earlier than your original Begin Date.
13. End Date: Populated with the End Date you entered on the Project
Information page. You may change the date to coincide with a specific
project time shorter than the overall duration of the permit. You cannot
enter a date that is later than the End Date you previously entered.

14. Details: You may enter up to 255 characters in this text box to provide
details on each take table row. This is especially useful for clarifying age
class, takes, intentional repeated takes, specific activities, or projects.
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Anticipated Effects on the Environment

1. Will you be working in or near areas with unique environmental
characteristics or important scientific, cultural or historical resources?
Examples include:
•
•
•
•
•
•
•
•
•
•
•
•
•
•

Animals used for subsistence
Archaeological resources
Critical Habitat of ESA-listed species
Essential Fish Habitat including wetlands, coral reefs, sea grasses, and
rivers
Federally recognized Tribal and Native Alaskan lands, cultural or natural
resources, or religious or cultural sites
Marine Protected Areas
Minority or low-income communities
National or State Parks
National Marine Sanctuaries and National Monuments
National Historic Landmarks
Sites listed in or eligible for listing in the National Register of Historic
Places
Wild and Scenic Rivers
Wilderness Areas
Wildlife Refuges

a. If yes, please list those areas. As applicable, mention if you will need to or
have already obtained permission (licenses, permits, authorizations) to
work in these areas.
b. How would your activities affect such resources? What measures will
you take to ensure your work does not cause loss or destruction of such
resources?

2. Discuss if your activities have the potential to impact the physical or
biological environment, in particular coastal and marine environments.
Impacts can be positive or negative. Examples of potential impacts include:
•
•
•
•
•
•
•

Altering substrate while anchoring vessels and buoys.
Using bottom trawls or other types of nets.
Erecting structures.
Ingress and egress of researchers.
Injuring or killing benthic organisms (e.g., seagrass, corals).
Altering the physical or chemical characteristics of water (e.g., oil
spills)
Affecting a species’ abundance or distribution.
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3. Does your project involve activities known or suspected of introducing or
spreading invasive species, intentionally or not? Examples include
transporting animals or other biological specimens, discharging ballast
water, and using boats/equipment at multiple sites.

Describe measures you would take to prevent the possible introduction or
spread of non-indigenous or invasive species, including plants, animals,
microbes, or other biological agents.

4. Will your activities involve collecting, handling, or transporting potentially
infectious agents or pathogens, such as biological specimens (animals, blood,
tissues)?

Will your activities involve using or transporting hazardous substances, such
as toxic chemicals?
If yes to either question, describe the protocols you will use to ensure that
public health and human safety are not adversely affected, such as by spread
of zoonotic diseases, chemical injuries, or contamination of food or water
supplies.

5. Do your activities involve equipment (e.g., scientific instruments) or
techniques that are new, untested, or have unknown or uncertain impacts on
the biological or physical environment?
If yes:
a. Briefly describe the equipment or techniques and provide any
information about the use of these in your study area, other areas,
and/or with other taxa.

b. Discuss the degree to which they are likely to be adopted by others for
similar activities or applied more broadly.

Project Contacts

As the person entering the application, you will automatically be assigned the
following roles: Applicant/Permit Holder, Principal Investigator, and Primary
Contact.

1. You may need to change or add personnel. See Chapter 2 for directions on
how to change who is assigned to these roles.
2. Use the guidance below to help you decide who should have what role.
3. To prevent duplicate entries, ALWAYS search APPS for the person before
entering a new contact. Start with entering only the last name in the APPS
search box.
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4. Include a table (see example Table 2) listing the names of the PI and CIs, and
the specific procedures they will oversee or conduct. Attach the table on
the Supplemental Information page.
5. As you add personnel, check whether each person already has a
Qualifications Form (QF) in APPS. It will appear next to their name once
you add them to your Contacts page. If there is not a QF in APPS, then
attach one for the PI and each CI. See “Qualifications and Experience section
below.

Descriptions of Personnel Roles
A project must have a Responsible Party if the Applicant/Permit Holder is an
organization, institution, or agency. The Responsible Party or Applicant/Permit
Holder is an official who has the legal authority to bind the organization, institution,
or agency and is ultimately responsible for the activities of any individual operating
under the authority of the permit. A resume does not need to be provided for this
person unless they will also serve as the PI or a CI.

The Principal Investigator (PI) is the individual primarily responsible for the take,
import, export, and any related activities conducted under the permit. There can
only be one PI on a permit. The PI:
•
•
•

Must have qualifications, knowledge, and experience relevant to the activities
authorized by the permit
Must be on site during activities conducted under the permit unless a CoInvestigator is present to act in place of the PI
May also be the Applicant/Permit Holder and Primary Contact.

The Primary Contact is the person primarily responsible for correspondence
during the application review process and after a permit is issued. Typically this
person administers the permit, requests amendments/modifications (e.g., personnel
changes, filming requests), and submits reports. The Primary Contact may also
serve other roles on the permit (e.g., Applicant/Permit Holder, PI, CI).
Co-Investigators (CIs) are individuals who are qualified and authorized to conduct
or directly supervise activities conducted under a permit without the on-site
supervision of the PI.
• You may add CIs to the application if the PI will not always be present during
the permitted activities.
• CIs can also be added or removed once a permit has been issued.
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Research Assistants (RAs) are individuals who work under the direct and on-site
supervision of the PI or a CI. RAs cannot conduct permitted activities in the absence
of the PI or a CI.
Authorized Recipients (ARs) are persons or institutions authorized to receive
samples for analysis or curation related to the objectives of your permit as
discussed in the Disposition of Tissues section. Permit holders may designate ARs
at their discretion with a letter.

Qualifications and Experience
The PI and each CI must have a QF. Previously we accepted CVs, resumes, and
biosketches, but often these did not include sufficient information about the
person’s field experience. The QF is designed to give us the information we need.
Once you fill out a QF and attach it to your profile in APPS you won’t have to again,
unless your skills or experience change. Each contact should only have 1 QF file in
his/her profile; personnel may replace their existing file with an updated version as
they gain new experience.
Persons authorized as the PI or CIs must have qualifications corresponding to their
duties. Note, if the PI or a CI will be supervising but not performing specific
procedures, each person must have sufficient cumulative experience to oversee the
project, personnel (e.g., other CIs, research assistants, veterinarians), and
procedures. If you do not provide sufficient information, we will not authorize the
person(s) to conduct the research or enhancement activities.

In addition, you must submit a table (see Table 2) defining the roles and activities to
be performed for the PI and each CI listed in the application.
Table 2. Example Personnel Roles
Name/Affiliation
Role
John Smith, Ph.D., Principal Investigator
University A, City,
State
Jane Smith,
Co-Investigator
Institution B, City,
State
Jane Doe, D.V.M.,
Co-Investigator and
Institution C, City, Attending Veterinarian
State

Activities
Supervise and perform all
activities under the permit

All activities excluding
anesthesia during captures and
UAS
Oversee and conduct captures,
and anesthesia of sea turtles

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Jane Doe, Ph.D.,
Institution C, City,
State

John Doe, Ph.D.,
University D, City,
State
Bob Jones, City,
State

Co-Investigator

Oversee and conduct captures,
anesthesia, and surgical
implantation of sonic tags in
fishes
Collect skin biopsy samples and
create cell lines

Co-investigator
UAS pilot

UAS pilot

Submit Application

See Chapter 2 for how to submit your application and check on its status.

Frequently Asked Questions
What is this application not for?

Research or enhancement activities on:
• Sea turtles on land or in rehabilitation
• Marine mammals
• Pacific marine and anadromous fish (e.g., steelhead, eulachon, salmon)
• Protected species parts (only involving importing, exporting, or receiving
parts)

When should I apply?

Generally, applications for scientific research or enhancement should be submitted
at least 1 year before your project begins. For projects within the scope of existing
programmatic consultations, the following timelines apply.
Species

Application Due

Decision (Issue or Deny)

Atlantic and shortnose sturgeon

August 1

January 31

Sea turtles
Smalltooth sawfish

April 1
August 1

September 30
January 31

What is the process for getting a permit?

1. Follow these instructions and contact the Permits and Conservation Division
at 301-427-8401 with any questions.
2. Submit your application via APPS.
a. A permit analyst will review your application and contact you if
additional information is needed.
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3. Address any questions within 60 days or your application will be withdrawn.
a. Once we consider your application complete, we will publish a notice
in the Federal Register, which starts a mandatory 30-day public
comment period.
a. Concurrently, we will send your application to subject matter experts
in partner institutions and federal and state agencies for review.
b. We will determine whether or not your proposed research requires
an ESA Section 7 consultation. Your research may fall under a
programmatic consultation. If it does not follow under the
programmatic, we will need to request consultation to assess impacts
to ESA-listed species. The ESA consultation can take up to 6 months.

4. Address any questions received during the comment period.
c. We will draft the permit and supporting documentation (including
National Environmental Policy Act analyses and documentation of
MMPA and ESA issuance criteria).
d. The documents will be reviewed by various NMFS offices including a
legal review.
e. For individual consultations, a Biological Opinion will be issued if
ESA-listed species may be taken and adversely affected to determine if
the activity will jeopardize the species or adversely modify critical
habitat.
f. The Office Director will decide whether to issue or deny your permit.

What is the process for requesting a modification to a permit?

If your permit falls under a programmatic consultation, you may need to submit
your modification request as part of the application cycle. See our programmatic
consultation web page for information on when to submit different types of modification
requests.
Use APPS to submit your modification request. You’ll need to provide a description
of your proposed changes and include all the necessary details for those changes, as
applicable. Use these application instructions as a guide. For example, changes to
your objectives will require that you discuss all the points in the Project Purpose
section. Additions to personnel require Qualifications Forms and descriptions of
their roles.

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Additional Information

Under Section 10(a)(1)(A) of the ESA, persons may be authorized to take threatened
and endangered species for purposes of scientific purposes or enhancing the
survival or propagation of the species. Interested persons are required to submit an
application in accordance with the ESA and the implementing regulations at 50 CFR
Part 222. These instructions for applying for a research or enhancement permit are
drawn from, but do not substitute for, ESA regulations. Read ESA Section
10(a)(1)(A). Under NEPA, Federal agencies must assess the effects of federal
actions on the environment. Under Section 7 of the ESA, Federal agencies must
ensure that the permitted activities will not jeopardize the continued existence of
listed species or result in adverse modification of critical habitat.

Paperwork Reduction Act Statement

The information requested in this application is required and used to determine
whether the activities described in the application are consistent with the purposes
and policies of the ESA and its implementing regulations.
Public reporting burden for this collection of information is estimated to
average 50 hours per response, including the time for reviewing instructions,
searching existing data sources, gathering and maintaining the data needed, and
completing and reviewing the collection of information. Send comments regarding
this burden estimate or any other aspect of this collection of information, including
suggestions for reducing this burden, to the Chief, Permits and Conservation
Division, Office of Protected Resources, F/PR1, NOAA/National Marine Fisheries
Service, 1315 East-West Highway, Silver Spring, MD 20910.

All permit documentation, including the application, permit and modifications,
reports, inventory information, and any other associated documents are considered
public information and as such, are subject to the Freedom of Information Act.

Notwithstanding any other provision of the law, no person is required to respond to,
nor shall any person be subject to a penalty for failure to comply with, a collection of
information subject to the requirements of the Paperwork Reduction Act, unless
that collection of information displays a currently valid OMB Control Number.
OMB No. 0664-0084
Expiration Date: xx/xx/xxxx

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Questions or Problems? Contact the NMFS Permits and Conservation Division: 301-427-8401