ESA-Research-Enhance-Application

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 QUESTIONS? .......................................................................................................................... 2
WHEN FILLING OUT YOUR APPLICATION:............................................................................................................... 2

APPLICATION INSTRUCTIONS ...................................................................................3
PROJECT INFORMATION ........................................................................................................................................... 3

PROJECT DESCRIPTION ............................................................................................................................................. 4

PROJECT SUPPLEMENTAL INFORMATION ........................................................................................................... 15

PROJECT LOCATIONS.............................................................................................................................................. 19
TAKE TABLE............................................................................................................................................................ 20

ANTICIPATED EFFECTS ON THE ENVIRONMENT ................................................................................................ 23
PROJECT CONTACTS ............................................................................................................................................... 25

SUBMIT APPLICATION ........................................................................................................................................... 29

ADDITIONAL INFORMATION .................................................................................. 29
WHAT IS THIS APPLICATION NOT FOR? ............................................................................................................... 29
WHEN SHOULD YOU APPLY? ................................................................................................................................. 29
WHAT IS THE PROCESS FOR GETTING A PERMIT? .............................................................................................. 29

WHAT IS THE PROCESS FOR REQUESTING A MODIFICATION TO A PERMIT? .................................................... 30

APPLICABLE LAWS AND REGULATIONS ............................................................. 30
PAPERWORK REDUCTION ACT STATEMENT .................................................... 31

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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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Smalltooth sawfish

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Sturgeon (Atlantic and shortnose)

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Sea turtles (in-water)

Please see our webpage on programmatic permitting
to determine if your methods qualify and when to
submit your application on the appropriate cycle.

Need help or have questions?

Visit our ESA scientific research permit web page, see
Additional Information on page 28, or contact us at
[email protected].

When filling out your application:
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Your application must be a stand-alone
document, readable to a layperson.

If you do not follow these instructions, your
application will be returned.

We will not consider your application if you
have overdue reports.

You will need to enter this information in our
online permit system, APPS
https://apps.nmfs.noaa.gov/.

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Entering your
application in APPS
Save your application every
20 minutes or you will lose
information!

An * indicates a required field.

Consider using these
instructions as a template to
draft your application in Word.
Then cut and paste into APPS.
Special characters may be
either lost or migrated
incorrectly.

Refer to Chapter 2 for how to
navigate APPS.

Your application will remain in
draft mode until you submit.
Attachments cannot be larger
than 20MB – contact us if you
need to attach larger files.

1 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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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. For example:
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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.
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 PAG. If the options are incorrect, please contact us at [email protected].

*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. Refer to Additional Information on page 28 for details
about when to apply and consult our programmatic permitting 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 10 years.
*Sampling Season/Project Duration (up to 1,000 characters): Describe the annual
season(s) of work including the months and frequency (i.e., when and how many times per
year, how frequently will you conduct your activities?). If year-round, 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 (common names).
Take activities (e.g., capture, sampling, tagging), import, or export
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Where your activities will occur and where animals or samples will be imported or
to where they will be exported.
Requested duration of the permit.

Project Description

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

We recommend you provide the information in this order:

1. Discuss the need for the research and the research questions you want to
answer.
2. Briefly summarize published findings related to
your research.
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If you previously held or worked under a permit,
use literature citations from that work to discuss
how you previously met your objectives; and
Use other published literature on the subject.

3. Describe how this study is different from, builds
upon, or duplicates past research.

4. If proposing novel procedures, include a discussion
on results from pilot studies or studies on other
species, if available.
5. Identify your objectives or hypotheses based on
the above information.

Bona fide research

The information you provide in
your application must
demonstrate that the proposed
activities would further a bona
fide and necessary or desirable
scientific purpose, taking into
account the benefits
anticipated for the target
species.

6. Discuss why your project must involve ESA-listed species (e.g., explain why
similar results could not be obtained by using an alternative non-endangered or
captive surrogate).

7. Discuss how your project will 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.
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8. If your goals are to directly enhance the survival or propagation of an ESA-listed
species, explain how your project will achieve these goals.
9. Take Number Rationale: Explain how you determined your sample size or take
numbers and why they are needed to meet the objectives.
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For example, did you base your numbers on previously reported 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 show whether the sample size is sufficient to provide statistically
significant or otherwise robust results.

Your take numbers should be realistic based on your future research plans as
well as your previous experience. We will examine reported take numbers from
your annual reports and compare those to the take numbers you are requesting
in your new application.
Discuss whether the same individual animals may be taken more than once
a year.

o If individual animals can be identified in real time, indicate the
number of times known individuals may be intentionally taken in a
year (e.g., recapture for instrument retrieval, multiple biopsy samples
per year, repeat surveys in the same area for identifiable individuals).
Explain why multiple takes of the same individual are needed to meet
your objectives.

*Project Description (up to 64,000 characters)

Please see our webpage on programmatic permitting to determine if your methods may fall
under an existing programmatic ESA Section 7 biological opinion with expedited
processing. If you wish to have your work covered by a programmatic opinion, please
ensure your described methods fit within its scope. Please contact us if you have questions.
Overview
Provide a brief overview of a typical day in the field or laboratory facility and the suite of
activities you intend to perform on each animal during an encounter or capture event.
Discuss the order in which you’ll perform the different methods. Include where your work
will happen, especially if different projects occur in different locations.
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Methods
Describe your methods. Your narrative description must match your APPS take table (see
Take Table section below).
You must provide:
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Clear descriptions of all methods (i.e., each take action and procedure in your
APPS Take table). See Table 1 below for guidance on what details to include.
A brief statement of each method’s or suite of
method’s purpose (i.e., how the activities relate to
meeting your objectives).

Identify the size and life stages of animals for
which you are requesting take.

o 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.

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o For sturgeon and sawfish, use the size
classes in the sidebar. Within each life
stage, define your target size range.

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.?
If you will intentionally target compromised
animals, explain the criteria you would use and
describe the conditions of the animals.

If you have multiple projects, it is helpful to name
them by project number or title and include
project names in the Details column of the Take
Table.

Fish Life Stages

Atlantic sturgeon

o ELS (early life stages; eggs to
larvae (<60mm Total Length
[TL])
o Juveniles (< 1000 mm Fork
Length [FL])
o Sub-adults (1000-1300 mm FL)
o Adults (> 1300 mm FL)
Shortnose sturgeon

o ELS (early life stages; eggs to
larvae (<60mm TL)
o Juveniles (< 450 mm FL)
o Sub-adults (450-600 mm FL)
o Adults (> 600 mm FL)
Smalltooth sawfish

o Neonate/Juvenile (< 2,200 mm
total length)
o Sub-adult/Adult ( ≥ 2,200 mm
total length)

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It is also helpful to reference take table lines in the narrative that correspond to the
take actions and procedures.

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Discuss whether animals of the same species (i.e., conspecifics) may be taken (e.g.,
harassed, captured) during your work.

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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.

Data analysis: Provide a brief description of how data and/or samples will be
analyzed.

Opportunistic research: If there are species in the same taxa that are not your
main research focus, but that you would study if opportunistically captured, include
a discussion of them in this section. Describe how the research would fit within
your objectives and which methods you would use to study these species. Include
rows for these species in your take table.
Mitigation measures that are inherent to your methods may be included in this
section or in the Effects and Mitigation section below.

Figures and photographs that illustrate your methods. You can attach them on the
Project Supplemental Information page.
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Cite references for the methods where applicable, but do not substitute a literature
citation for a complete description of the methods. You can attach a Literature Cited
on the Project Supplemental Information page. References must be made available
upon request.

Table 1. Guidance on Describing Commonly Used Methods
When describing your methods, include the following information, as applicable:
Take action/
procedures
Active acoustics
(all)

Active acoustics
(for behavioral
response studies)

Method Description Guidance

Sound source (e.g., echosounder, underwater speaker, acoustic deterrent
device)
Beam width
Water depth, or depth range if applicable
Frequency (bandwidth)
Maximum source level (specify metric SELcum or SPL RMS)
Maximum received level
Distance of source to target and non-target animals (including marine
mammals)
Signal duration and duty cycle
Number of exposures/trials in a day and whether you will target the same
animal(s) more than once
Duration of each sound exposure and maximum total duration of sound
emission per 24-hr 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 include all of the details above in the Active Acoustics section. If
working with a variety of sound sources, be sure to include these details for
a “typical” playback scenario as well as a worst-case scenario (e.g. source
level, received level, duty cycle, frequency, maximum exposure duration,
etc.).
Make sure to consider all functional hearing groups, including target and
non-target exposures. We strongly recommend consulting the NMFS 2018
User Spreadsheet and accompanying instructions for impacts to marine
mammals. Be sure to specify if your source is impulsive (direct from
source) or non-impulsive (playback via speaker).

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Take action/
procedures
Administer
drugs or other
substances (e.g.,
stable isotopes,
bone marking,
anesthesia)

Aerial and vessel
surveys
(manned)
For encounters 5
minutes or longer
(see p. 7 for
details)
Aerial surveys
using unmanned
aircraft systems
(UAS)

Auditory
brainstem
response or
evoked potential

Method Description Guidance
Name of each drug/chemical and its purpose, including for
reversal/recovery
For captive fish: Euthanasia drugs and protocols
Dosage of each drug/chemical
Delivery method and route (e.g., intramuscular, intravenous, subcutaneous,
topical, immersion)
Location of administration on body
Duration of each drug
Post drug administration monitoring
Optional: you may include a drug table with the information requested
above
Number of surveys per year
Type and size of survey aircraft and/or vessel
Number of aircraft and/or vessels to be operated at the same time
Type of survey (e.g., line transect, photogrammetry)
Minimum altitude/approach distance
Air/vessel speed
Protocols for breaking track to ID and/or capture species
Duration spent with group or individual per day
Number of surveys per year
Type and size of UAS and/or vessel
Number of aircraft and/or vessels to be operated at the same time during an
encounter
Type of survey (e.g., line transect, photogrammetry)
Minimum altitude
Air speed
Protocols for breaking track to ID species
Duration spent with group or individual per day
Type of UAS – fixed wing or vertical takeoff and landing (VTOL)
Payload components – what is the UAS carrying and for what purpose (e.g.,
camera, sensor)?
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)?
Type of sounds emitted (e.g., pips, clicks, tones)
Maximum source level
Whether animal will be transported to a facility (complete the Transport
Section in Take Table)
Distance and position of speaker relative to animal to target animal
Signal duration, duty cycle, and frequency of sound emitted
Total duration of sound emission (including total exposure duration within
a 24-h period)
Handling/restraint methods (including anesthesia/sedation, see above)
Type of measurement equipment (suction cup or needle electrodes and
location on animal)
Handling duration
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Take action/
procedures
Captive
experiments

Method Description Guidance
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:
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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).

Capture and
restraint

For fish species: Provide justification if a captive breeding program will be
established in accordance with the species conservation plan or recovery
plan. If requested by NMFS, indicate if you are willing to participate in a
captive breeding program. If not, describe how you will prevent breeding.
Type of capture (e.g., hand, gill net [drift or anchored], trawl, seine) and gear
description (e.g., net dimensions and mesh size)
Deployment methods (e.g., boat type, net set, tow or soak times)
Configuration, duration, and monitoring of net sets (how often net set is
checked)
Number and roles of personnel
Numbers of animals captured at a time
Number of animals processed at a time
Dimensions and type of holding container/manner of restraint
Anesthesia/sedation (see Administer Drugs above)
Manner of release
Duration of restraint/holding from capture to release
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).
For sea turtles: Identify an on-call veterinarian and nearby permitted
rehabilitation facility available for emergencies

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Take action/
procedures
Export/ import/
receive samples

Method Description Guidance
Type of activities:
● Export samples collected under the requested permit or received from
other legal sources
● Re-import exported samples
● Import samples from foreign countries
● Receive samples from other U.S. legal sources
Sample type (e.g., skin/blubber, blood, muscle, DNA)
U.S. or foreign sources of samples:
● Authorized persons or collections, including your own research;
● Animals in captivity (samples from routine husbandry procedures or
under separate authorization);
● Animals in foreign countries stranded alive or dead or that died during
rehabilitation;
● Animals killed during legal subsistence harvests; or
● Animals killed incidental to legal commercial fishing operations
How the sample or animal was originally taken
The legal authority for the original take for imported/received samples
Sample preservation, storage/shipping/analysis
What country are samples being exported to?
Where are samples being imported or received from: high seas, name and
affiliation, or country
Designated port of entry/import or export
See also Disposition of Tissue Samples below

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Take action/
procedures
External
instruments
(e.g., instruments
attached with
epoxy, suctioncup, wire, etc.; a
table is helpful for
multiple tag
types)

Method Description Guidance
Type of instrument
Type of data collection (e.g., archival requiring retrieval)
Instrument dimensions:
• Mass in air or water
• For turtles: tag frontal area and shape per Jones et al. (2013) 2
• For fish: Percentage of body mass
Minimum size of animal to receive each instrument type
Maximum footprint/maximum number of tags per animal
Criteria for determining tag types and number of tags on an animal (e.g.,
body condition, life stage)
Whether tags will be coated with antifouling paint
Attachment method (e.g., remote suction cup by pole; restraint and
adhesives; monofilament line)
Disinfection/sterile preparation for carapace drilling site and gear
For remote deployment or detachment:
• number of attempts per animal per day,
• minimum approach distance and angle,
• include total number of attempts needed for all work if requesting
multiple procedures (e.g., tag and skin sample) on same animal during
same encounter
Pain management if required (see Administration of Drugs)
Location on body
Duration of procedure, including curing time
Duration of instrument retention
Release mechanism or recapture to remove
Post-tag monitoring

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:10.1111/2041210X.12109
2

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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

Method Description Guidance
Type of instrument
Instrument dimensions
Mass in air
Percentage of body mass for all tags combined
Criteria for determining tag types and number of tags per animal (e.g., body
condition, life stage)
Minimum size of animal to receive an internal instrument
Use of local anesthetic or anesthesia/sedation (see Administer drugs)
Cleaning/sterile preparation
Insertion method (describe e.g., surgical implant, injection, stomach tube)
and any applied coating on the tag
Location within body
Duration of procedure
Duration of instrument retention
How instruments are voided
Type of data collection (e.g., archival requiring retrieval)
Post-tag monitoring
For sea turtles: include a veterinary-approved protocol for stomach pills
Type of tissues
Equipment (e.g., needle, punch, scalpel)
Size or volume of sample (diameter and depth or total volume)
Equipment sterilization or disinfection
Location on body
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 per day (i.e., success rate)
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)
Number of samples per animal per capture event and per year
Sampling intervals (e.g., for serial blood samples)Sample preservation and
storage
For sea turtles: include a veterinary-approved protocol for laparoscopy,
tumor removal surgery

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

Non-intrusive
sampling (e.g.,
photography;
diagnostic
imaging;
collecting voided
feces, urine, fish
eggs or milt; skin
swabs)
Remotely
Operated
Vehicles (ROVs)

Method Description Guidance
Type of mark
Dimensions of tag or mark
Total number and combination of tags or marks on each animal Location on
body
Method of application
Cleaning and disinfection procedures
Duration of mark
Whether mark would be reapplied, if lost
Size of animals to receive tags including minimum size
For turtles:
-Veterinary-approved protocol for PIT tagging turtles <16 cm SCL
-Type of paint (non-toxic only)
Minimum approach distance for remote data collection (PIT tag scanning,
underwater photography)
Sampling method (e.g., X-ray; topical swab)
Frequency of encounter?/sampling per day
Duration of encounter/sampling per day
Data or sample collection
Whether animal will be transported to a facility for temporary holding (see
Transport information in Take Table section)
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
unintentionally captured or otherwise affected. These are species that co-occur with your
target species and that could be harassed or taken during your work, but that you will not
opportunistically incorporate into your study.

Include these non-target species on separate rows in the Take Table if you expect take (e.g.,
unintentional harassment or capture). For ESA species designated by Distinct Population
Segment, specify the DPSs.
Other 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. Contact us if
you need assistance.
• 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 the specific DPSs you are targeting, their status under the MMPA and/or ESA, and
location. Otherwise, put N/A and choose the specific stock or DPS in the take table.
*Mortalities (up to 5,000 characters)
If authorization for mortality 3 (euthanasia/intentional 4 or accidental/unintentional) is
proposed:
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What activities could result in mortality and how?

What is the maximum number of animals of each species/DPS that could be
seriously injured, unintentionally die, or be euthanized annually and over the life of
the permit? For example, two serious injury/mortalities per year, not to exceed four
over the life of the permit.
Justify the number of mortalities requested.

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.

3 Caused by the presence or actions of researchers including but not limited to deaths or serious injuries

sustained during capture and handling, including predation or while attempting to avoid researchers or
escape capture, or resulting from infections related to invasive procedures such as sampling or tagging.

4 This includes euthanasia for humane reasons (e.g., if working with compromised/comatose animals).
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Euthanasia of captive fish:
o Under what circumstances is euthanasia conducted (e.g., directed research,
final disposition)?

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o How is it decided, conducted (including use of drugs), and who conducts it?

Euthanasia may not be requested for sea turtles. Euthanasia falls under the
authority of the Sea Turtle Stranding and Salvage Network.

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 Take Table actions (Take Actions, Observe/Collect Method (e.g., capture),
and Procedures) will affect individual target and non-target animals. You should
discuss the effects of mortalities in the Mortalities section above.

Cite the best available science (i.e., peer-reviewed literature or other published data
sources) and your experience (e.g., personal communication, annual permit reports).
References must be made available upon request.
Group together take actions with similar responses and describe, as applicable:
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Typical behavioral and physiological responses
Worst-case responses

% of animals that typically exhibit each response type
Average/estimated recovery time

Wound healing time (e.g., from invasive sampling or tagging)
Condition of animals on recapture/resight
Recovery from sedation and/or handling

Post-release behavior (immediate and long-term)

Time it takes to resume normal behavior after harassment
Tag retention and tag breakage

Anticipated drag costs for sea turtle transmitters and attachments

Effects on sensitive life stages (e.g., spawning adults)

Effects to nesting female sea turtles if working during the nesting period
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●

•
•

•

Habitat use for animals in resident populations (based on telemetry data, resightings, recaptures)

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 studies on other species, if available, and any results from testing, if
applicable.
Discuss the anticipated effects on the species or DPS, especially if mortalities or
reproductive effects are possible. On what is your determination based?

You may include mitigation and monitoring protocols here or in the Methods section
above. Do not restate those here if they are included above; simply reference the section
where the following information appears.
•

For invasive procedures, including biological sampling and instrumentation, describe
your steps to prevent infection. For example, describe if and how you will:
o Prepare the sampling site by cleaning and disinfecting the tissue (for captured
animals).

o Use single-use, sterile instruments (e.g., needles).

o Sterilize 5 other devices prior to use and in the field if contaminated including but
not limited to use of cold sterilization

•
•

o Administer prophylactic antibiotics to animals (include the drug, dosage, and
route of administration).

Describe your short- and long-term post-procedure monitoring protocols.

Explain if and why monitoring or mitigation is not feasible for specific procedures,
species, situations, etc., as needed.

5 Sterilization destroys or eliminates all forms of microbial life and is carried out by physical or chemical
methods (CDC 2008). Disinfection eliminates many or all pathogenic microorganisms, except bacterial
spores, on inanimate objects usually by liquid chemicals (CDC 2008).
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•

•

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) 6 proposal.

Describe any mitigation you will take to avoid or minimize impacts to non-target
protected species (e.g., marine mammals, sturgeon, sea turtles, corals, U.S. Fish and
Wildlife Service species). Discuss whether and how they may be unintentionally
harassed, captured, or otherwise affected. Identify if you require take of these species.
For ESA species designated by DPS, specify the DPSs. Identify if you require takes of
these species.

Research Coordination
● Describe how you will coordinate with other permit holders in your action area.
o List their names and affiliations.

●

o Explain how you will work together. For example, will you share vessels or
coordinate the timing of surveys to avoid repeated takes of the same
animals?

Will you collaborate with other permitted researchers to share data? If so, list their
names and affiliations and explain your collaboration plans.

Attach a References File
Attach a bibliography of references cited in this application. Referenced materials must be
made available upon request, as needed for evaluation of the application and preparation
of 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 4,000 characters and attach files if
necessary)
● Explain how your expertise, facilities, and resources 7 are adequate to accomplish
your proposed objectives and activities.

sea turtle research: NMFS researchers are required to submit the NMFS IACUC-approved protocols
and assurance letter.
7 Expertise includes a summary of the cumulative experience of you and your personnel. Facilities include
such things as your existing infrastructure or laboratories. Resources include financial (e.g., current funding
and/or history of securing funding); material (e.g., sampling equipment, UAS, boats); and other resources
(e.g., collaborative partnerships that can be drawn on to support your work).
6 For

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●

●

List relevant proposals, contracts, grant awards, or letters of agreement that would
demonstrate your resources. If funding is not yet secured, provide a history of
funding over the past 5 years. Copies must be made available upon request.
Indicate the status of other international, federal, state, or local authorizations and
permits you have applied for, secured, or will apply for.

*Disposition of Tissue Samples (up to 4,000 characters)

Outline what will be done with the biological samples during your research or
enhancement and after your project is complete, as follows:

1. If you are performing your analyses in-house, state whether the samples will be
consumed, destroyed, or curated.
2. If you are sending samples to another entity:
●

●

List the name, affiliation, and location of any person or institution that will
receive, analyze, or curate samples. 8

Include the sample type and purpose of transfer (type of analysis and/or
curation). State whether samples will be consumed in analysis, destroyed,
curated, or returned.

3. If samples will remain after the completion of your research, indicate if you will
retain legal custody of the curated samples or if you will permanently transfer
custody of the samples.

*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, follow the guidance below to 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 in each location.
•

Add New Location: provide information about one or more study areas
o General area (ocean basin)
o State(s), as applicable.

8 Persons

or institutions authorized to receive samples for analysis or curation related to the objectives of
your permit are known as Authorized Recipients.
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•

•

Enter Location Details, as applicable:
o Waterbody: enter names of rivers, estuaries, bays, etc. This is required for
sturgeon research.
o Latitude and longitude of your study area
o River miles (Begin Mile and End Mile)
o Limits of your study area (e.g., to the U.S. EEZ, to the edge of the continental
shelf, to 50m depth)
o 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, import, or export
annually during your research.

Sea Turtle Vessel
Surveys

For surveys that do not involve
capture, but will remain
within 50 yards for more than
5 minutes:
•

Columns you will fill out in the take table in APPS:

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 or DPS. Only 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.

•

•

Count every animal you
approach within 50 yards,
regardless of whether a
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.

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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 on the same row.
6. Sex: Select from the drop-down list. If your
activity targets only one sex, indicate which.
Otherwise select Male and Female.

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

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, create separate take rows for animals
that will be captured and sampled versus animals
that will be harassed only.

Sea Turtle Aerial
Surveys

For surveys that will stay with
animals for more than 5 minutes
and flown at an altitude lower
than 700 ft.:
•

Count 1 take per sea turtle
observed per day, regardless
of the number of passes over
the same animal.

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 species-specific list of
activities. Check the boxes to select all activities to be performed concurrently on
the same animals.
a. Choose “Other” if a proposed activity is not listed. In the Details box (see
below), briefly describe what the “Other” means. 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.
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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.

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 and design 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
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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: Enter up to 255 characters to provide details on each take table row. This
is especially useful to clarify age class, takes, intentional repeated takes, specific
activities, or projects.

*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? Yes or no.
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. (up to 1,200 characters)
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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? (up to
1,200 characters)
c. For marine mammal activities in Alaska or Washington, how will you ensure
your project does not adversely affect the availability (e.g., distribution,
abundance) or suitability (e.g., food safety) of marine mammals for subsistence
uses? (up to 800 characters) Enter Not Applicable.

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. (up to 2,000 characters)
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

3. Invasive Species

a. 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. Yes or no.

b. 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. (up to 1,200 characters)

4. Biological Specimens

a. Will your activities involve collecting, handling, or transporting potentially
infectious agents or pathogens, such as biological specimens (animals,
blood, tissues)? Yes or no.

b. Will your activities involve using or transporting hazardous substances, such
as toxic chemicals? Yes or no.
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c. 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.
(up to 1,200 characters)

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? Yes or no.

If yes:
a. Briefly describe the equipment or techniques and provide any information about
the use of these in your study area and/or with other taxa and what is known
about their impacts. (up to 1,200 characters)
b. Discuss the degree to which they are likely to be adopted by others for similar
activities or applied more broadly. (up to 800 characters)

Project Contacts

The person entering the application in APPS will automatically be assigned the following
roles: Applicant/Permit Holder, Principal Investigator (PI), 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 the last name in the APPS search box.

4. Include a table with the names of the PI and Co-Investigators (CIs), and the specific
procedures they will oversee or conduct (see example Table 3). 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 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
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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.
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 modifications (e.g., personnel changes), and submits reports. The
Primary Contact may also serve other roles on the permit (e.g., Applicant/Permit Holder,
PI, CI).
The Applicant/Permit Holder or Responsible Party, PI, and Primary Contact will
have access to APPS to enter and edit the application, submit reports and
modification requests, and will receive automatic emails from APPS.

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 must 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.

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. RAs do not need to be named in the application or permit.
A Veterinarian (for sea turtles only) who is licensed to practice on sea turtles must be
identified for each sea turtle permit application. A veterinarian must be named: 1) for
emergencies in an on-call capacity, and 2) to directly perform or supervise certain
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methods, including surgery and drug administration. More than one veterinarian may be
listed to fulfill these roles.

Unmanned Aircraft Systems (UAS) Pilots are persons who have their FAA-certification to
fly unmanned aircraft systems and experience piloting UAS. A CI or the PI with taxa specific
(e.g., sea turtles) experience may be qualified to serve in this role. In other cases, you may
designate someone as a UAS Pilot who is tasked with only that role and does not have taxa
specific experience.
Personnel for Unmanned Aircraft Systems (UAS)

To fly UAS, you must have: 1) someone with experience working with the target species in
the wild, and 2) someone who is FAA-certified to conduct or oversee UAS flights with
approximately 5 hours of flight experience. These may be satisfied by one or more persons,
depending on the qualifications of your team. The following scenarios describe the
personnel roles for UAS that you may request based on their qualifications.
Table 2. UAS Personnel
Scenario 1: Species expert who is also an FAA-certified UAS pilot
If the person has:
They may be named as:
PI or CI to supervise and operate UAS.
Experience working with the subject
No separate UAS Pilot required to be named
species/taxa in the wild and UAS
experience with an FAA UAS certification on the application.
Scenario 2: Species expert (PI or CI) accompanied by an FAA-certified UAS pilot
If the person has:
They may be named as:
Experience working with the subject
PI or CI to supervise UAS. A separate UAS
species/taxa in the wild, but no UAS
Pilot must be named for the UAS operation.
experience
UAS pilot to operate the UAS or directly
oversee operation as the remote pilot in
UAS experience and FAA UAS certification
command. The UAS pilot must be
but no taxa specific experience
supervised by the PI or a CI with taxa
specific experience.
Note: Other personnel who are not FAA-certified may manually operate the UAS (e.g., for
training purposes) provided the FAA certified pilot designated on the permit directly oversees
the UAS operation.

Qualifications and Experience
The PI and each CI must complete a Qualifications Form (QF). Previously we accepted
CVs, resumes, and biosketches, but often these did not include sufficient information about
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the person’s field experience to demonstrate they were qualified in the proposed take
activities. You can download a blank QF from the Contacts page in APPS or from any of our
permitting web pages.
Once you fill out a QF and attach it to your profile in APPS, you won’t have to do it again,
unless your skills or experience change. Each contact should only have 1 QF file in their
profile; it will apply to all permits they are affiliated with. They may replace the QF 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,
they must demonstrate 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).

In addition, you must submit a table (see Table 3) defining the PI and CI roles and
activities (i.e., supervising or conducting specific procedures) to be performed. Attach this
table on the Supplemental Information screen
Table 3. 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
Jane Doe, Ph.D.,
Co-Investigator
Institution C, City,
State
John Doe, Ph.D.,
University D, City,
State
Bob Jones, City,
State

Activities
Supervise and perform all
activities under the permit

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

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 supervised by the PI
or a CI
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Submit Application

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

Additional Information
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 you apply?

For projects within the scope of existing programmatic consultations, the following
timelines apply.
Species

Atlantic and shortnose sturgeon
Sea turtles
Smalltooth sawfish

Application
Due
August 1
April 1
August 1

Decision
(Issue or Deny)
January 31
September 30
January 31

If your project falls outside the scope of a programmatic consultation, submit your
application 1 year in advance of the proposed research.

What is the process for getting a permit?

1. Follow these instructions and contact the Permits and Conservation Division at
[email protected] or 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.
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.
b. Concurrently, we will send your application to subject matter experts in partner
institutions and federal and state agencies for review.
c. We will determine whether or not your proposed research requires an ESA
Section 7 consultation. Your research may fall under a programmatic
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consultation. If it does not follow under a 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.
a. We will draft the permit and supporting documentation (including National
Environmental Policy Act analyses, responses to public comments, and
documentation of ESA issuance criteria).
b. The documents will be reviewed by various NMFS offices including a legal
review.
c. 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.
d. 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 permitting 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.

Applicable Laws and Regulations

Under ESA 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. 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.
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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.

Paperwork Reduction Act Statement

A Federal agency may not conduct or sponsor, and a person is not required to respond to,
nor shall a person be subject to a penalty for failure to comply with an information
collection subject to the requirements of the Paperwork Reduction Act of 1995 unless the
information collection has a currently valid OMB Control Number. The approved OMB
Control Number for this information collection is 0648-0084. Without this approval, we
could not conduct this information collection. Public reporting for this information
collection is estimated to be approximately 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 information collection. All responses to this
information collection are required to obtain a permit pursuant to the ESA, NEPA, and their
implementing regulations. Send comments regarding this burden estimate or any other
aspect of this information collection, 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; email [email protected].

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