Permit and Authorization Applications

OMB Control No. 0648-0084
Expiration Date: 09/30/2009

National Marine Fisheries Service
Marine Mammal and Endangered
Species Research and Enhancement
Permits – Justification for Collection
of Information
Background
Under section 104 of the Marine Mammal Protection Act of 1972 (MMPA) and section
10(a)(1)(A) of the Endangered Species Act of 1973 (ESA), NMFS may issue permits for
scientific research purposes or to enhance the propagation, survival, or recovery of
protected marine species. Under the Fur Seal Act of 1966 (FSA), NMFS may authorize
research on fur seals of the North Pacific pursuant to a permit.

Pre-application Guide (PAG)
The information obtained when filling out the PAG is necessary to determine what type
of permit/permit application is needed.

Completing an Application
Give Complete Information
We return incomplete applications with explanation or request additional information. If
we request additional information and do not receive it within 60 days, we may withdraw
the application. Applicable regulations: 50 CFR 216.33(c)(4) and 222.302(c)(1).

Project Information Page
File Number: Automatically generated by APPS. This number is necessary for
identification of the application in the APPS system/database, in the Federal Register
notices of receipt and issuance or denial, during correspondence with the applicant, and
to identify the permit administrative record. This number is also used as the permit ID
number when issued.
*Project Title: Necessary for identification of subject matter/type of permit application.
Applicable regulations: 50 CFR 216.33(a) and 222.308(b)(1).

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*Project Status: Automatically generated by APPS. Indicates a new permit is requested.
Previous Federal or state permit #: Not required. If entered, this information provides
permit analysts with the applicant’s previous permit number to determine compliance
with a previous permit’s terms and conditions.
*Permits Requested: Automatically generated by APPS. This is necessary to determine
the appropriate permit to issue and the required regulatory and statutory processing and
issuance requirements, and applicable permit restrictions.
*Where will the activities occur?: Permits must specify locations of authorized take or
import/export. Necessary to determine if work will be conducted in U.S., and therefore,
whether a permit is needed. This information is also necessary for considering impacts to
protected species and for conducting the appropriate environmental analyses under
NEPA, MMPA, and ESA. Applicable regulations/statutes: 50 CFR 216.36(a)(1)(iii), and
MMPA section 104(b)(2)(B); 50 CFR 222.308(b)(6)(i) and (iv), and 222.308(d)(2).
*Research Timeframe and Sampling Season/Project Duration: Permits must specify
the period during which the permit is valid. Permits are valid for five years unless a
shorter time period is requested. This information provides a basis to determine (1)
whether it is likely that the objectives will be met during the time allotted with the
available resources; (2) when the permit is needed (i.e., the start date); (3) impacts to the
affected species during sensitive periods such as nursing and breeding; and (4) potential
cumulative impacts that may arise from multiple permit holders working on the same
species, in the same location, and at the same time. Applicable regulations/statutes:
50 CFR 216.35(b), 216.36(a)(iv), and MMPA section 104(b)(2)(C); 50 CFR
222.308(b)(5)(i) and (b)(6)(iii).
*Abstract: NMFS is required to publish notice of receipt of an application in the Federal
Register for a 30-day public comment period. To ensure that an accurate summary of the
application is published, applicants are requested to include a short abstract of the
request. Applicable regulations/statutes: 50 CFR 216.33(d) and MMPA section
104(d)(2); and 50 CFR 222.303(b).

Project Description Page
*Project Purpose: Hypothesis/Objectives and Justification
The applicant must provide the objectives of their proposed activity, give a hypothesis
(for research), explain how the activities will ensure survival of the species (for
enhancement), and provide justification for the sample size and for requesting takes of
protected species. This information is required to determine (1) if the applicant is
proposing bona fide scientific research, (2) if the proposed enhancement activities are
necessary and consistent with a species’ recovery plan, (3) ensure the sample size is
appropriate to complete the objectives and not unnecessarily adversely impact the target
species, (4) whether the activities can be accomplished with a non-protected species.
The applicant must also explain the role of Co-investigators to ensure that we can assess

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their qualifications for the activities to be conducted and that the personnel are reasonable
in number. For threatened and endangered species, additional justification is required,
such as how the activity will contribute to the objectives of the species’ recovery plan and
other specific information required pursuant to the MMPA, ESA, and their implementing
regulations. Applicable regulations/statutes: 50 CFR 216.34(a)(3) and 216.41(b);
222.308(b)(4-5), 222.308(b)(10), and 222.308(c)(4), and statutory requirements (MMPA
104(c) and ESA section 10(a)(1)(A)).
*Project Description: This section requires the applicant to precisely describe the
activities they are proposing. Special exception permits must specify the number and
kind of species authorized to be taken, the location of take, and the manner of take.
Section 104(b) of the MMPA requires permits to specify the number and kind of marine
mammals authorized to be taken, the manner and location of the taking, and the period of
validity for the permit. Section 104(c)(1) of the MMPA requires permits to specify the
methods of capture, supervision, care and transportation and requires that the taking is
consistent with the purposes of the MMPA. Section 104(c)(3) of the MMPA requires
applicants for scientific research permits to submit information indicating that the taking
is required to further a bona fide scientific purpose. NMFS must determine that the
proposed method of taking is humane and will not present any unnecessary risks to the
health and welfare of marine mammals; and that the proposed activity by itself or in
combination with other activities, will not have a significant adverse impact of the
species or stock. Applicable regulations: 50 CFR 216.34(a)(1-7), 216.36(a)(1)(i-ii), and
section 216.41.
Regulations under the ESA require the applicant to provide a detailed description of how
the species will be used in order to determine whether the permit will operate to the
disadvantage of the species, and whether the permit will further a bona fide and necessary
research or enhancement purpose. Detailed protocols for transporting animals must also
be provided. Applicable regulations: 50 CFR 222.308(b)(4)(ii), (b)(5-7), and (c-d).
Import/Export requirements: NMFS must determine that marine mammals or their parts
to be imported are taken humanely and in compliance with the Acts. To satisfy this
requirement NMFS needs to know the country in which the taking will occur, how the
taking will be conducted, and the marine mammal management program/legal authority
of the country of taking. Any marine mammal part imported must not have been
obtained as a result of lethal take inconsistent with the Acts unless authorized by the
Office Director. An exception to certain restrictions in the Acts is provided if the import
or export is necessary to benefit the health or welfare of the protected species concerned.
Section 104(c)(9) of the MMPA states, "No marine mammal may be exported for the
purpose of public display, scientific research, or enhancing the survival or recovery of a
species or stock unless the receiving facility meets standards that are comparable to the
requirements that a person must meet to receive a permit...". The applicant is required to
submit information regarding exporting live marine mammals to ensure that (1) all
applicable laws are met, whether it is U.S. or foreign and (2) that protected species taken
(including held captive) in a foreign country are not taken or held in an inhumane manner
because of less-protective laws of a foreign country. Applicable regulations: 50 CFR

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part 14; 50 CFR 216.33(b), 216.34(a)(7), 216.35(c-d), 216.36(a)(1)(iii), 216.37(d), and
216.41(c)(1)(v).
NMFS must conduct a NEPA analysis for each permit issued, which requires a
description of the proposed action in order to determine the effects such action will have
on the target and non-target species and the environment. As required, NMFS must
request consultation under section 7 of the ESA regarding impacts to threatened and
endangered species, which also requires detailed a description of the proposed action in
order to determine whether the activity will jeopardize the existence of the listed species
or adversely modify critical habitat. Applicable regulations: 50 CFR 216. 33, NEPA
CEQ regulations, and 50 CFR part 402 (interagency consultations).

Project Supplemental Information Page
*Status of the Affected Species: Permits must specify the species authorized to be taken
and must be issued in accordance with the appropriate statutes and regulations. This
information is needed for assurance that the applicant is aware of the status of species for
which they are applying to take or import/export, and that the applicant is aware of the
requirements under the appropriate Acts, including requirements for consultation under
section 7 of the ESA. NMFS must determine that for enhancement purposes, the species
or stock identified in the application is in need of enhancement for its survival or
recovery and only animals and parts necessary for enhancement are taken. NMFS must
also determine that any requested import or export will not result in taking of marine
mammals beyond that authorized by the permit. Applicable regulations: 50 CFR
216.33(c)(2)(iii), 216.34 (a)(3) and (7), 216.36 (a)(1)(i), 216.41(b)(5) and (6), 222.308
(b)(6)(i and iv), and 222.308(c)(5) and (d)(1).
In addition, the applicant should be made aware that applicable import/export
requirements must be met with regard to the Convention on International Trade in
Endangered Species of Wild Fauna and Flora (CITES) pursuant to U.S. Fish and Wildlife
Service regulations.
*Attach a Literature Review File and Attach a References File: The applicant must
demonstrate whether the proposed activities are different from or build upon past
research; whether the activities are unnecessarily duplicative and thus may operate to the
disadvantage of the species; or whether the activities are necessary and would contribute
to the conservation of the species. This information will be used with other components
of the application to determine that the proposed activity will further a bona fide
scientific research or enhancement purpose. Applicable regulations: 50 CFR 216.3,
216.41(b)(1) and 222.308(c)(4).
*Lethal Take: This information is necessary to ensure that prohibitions and restrictions
on the lethal take of protected species are taken into consideration. Under the MMPA, if
lethal take is proposed, the applicant must demonstrate that non-lethal methods are not
feasible. For depleted, endangered, or threatened species, the results must directly benefit
that species or fulfill a critically important research need. The taking must be humane

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and any permanent removal of a marine mammal from the wild must be consistent with
any applicable quota established by the Office Director. The applicant must demonstrate
that the take of marine mammals will not likely have a significant adverse impact on the
species. For endangered marine mammals, the applicant must demonstrate that the
activity will be conducted consistent with the purposes and policies set forth in section 2
of the ESA. Under the ESA, the applicant must describe how the species will be used
and must demonstrate that the permit, if granted and exercised, will not operate to the
disadvantage of the species and therefore must justify the lethal take of listed species.
The applicant must also demonstrate that for ESA-listed species, whether the permit will
further a bona fide and necessary or desirable scientific purpose or enhance the
propagation or survival of the endangered species. Applicable regulations/statues: 50
CFR 216.34(a)(1),(3), and (4); 216.41(b)(2 - 4) and (c)(1)(v); MMPA section
104(c)(3)(B); and 50 CFR 222.308(b)(4)(ii), (b)(6)(v), (c)(2), and (c)(4).
*Anticipated Effects on Animals and Measures to Minimize Negative Effects: This
information is necessary to: (1) assess the environmental impacts of the proposed
activity and conduct the appropriate level of analysis under NEPA, (2) determine whether
the proposed activity is humane and does not present unnecessary risks to the health and
welfare of marine mammals, (3) determine whether the proposed activity will have a
significant adverse impact on the species or other components of the marine ecosystem,
(4) determine the effects of the proposed activities on ESA-listed species and whether the
permit, if issued, will operate to the disadvantage of such species, (5) determine whether
appropriate monitoring will be conducted to adequately assess the effects of the permitted
activities, and (6) prepare an initiation package and request consultation under section 7
of the ESA, as applicable. Applicable regulations: 50 CFR 216.33(c)(v) and (d)(i and
iv), 216.34(a)(1) and (4), 216.41(b)(4), and 222.308(b)(11), (c)(2) and (c)(5).
*Resources Needed to Accomplish Objectives and Disposition of Tissue Samples:
Applicants are required to demonstrate whether their expertise, facilities, and resources
are adequate to accomplish successfully the objectives and activities stated in the
application. If a live animal will be held captive or transported, the applicant’s
qualifications, facilities, and resources must be adequate for the proper care and
maintenance of the marine mammal. Applicants are also required to indicate how they
will dispose of, how they will store, or to where they will transfer remaining samples
after analyses are completed. Applicable regulations: 50 CFR 216.34 (a)(5) and (6);
216.37(c); 50 CFR 222.308(b)(5)(ii), (iii), (v); 222.308(b)(6) and (c)(9-10).
*Public Availability of Product/Publications: MMPA regulations require that research
results obtained under the authority of a special exception permit are published or
otherwise made available to the scientific community in a reasonable period of time.
This information is also used to determine that the proposed activity is for bona fide
research purposes. Applicable regulations: 50 CFR 216.41(c)(ii) and 222.308(c)(4).

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Captive Information
Applicants are required to address the following questions, as applicable.
(a) Why removal from the wild is necessary and why animals cannot be obtained
from captive or rehabilitated stock.
NMFS regulations allow for the use of stranded rehabilitated marine mammals for
special exception purposes in lieu of taking animals from the wild, which protects
wild stocks from impacts of removing individuals from the population. Any
permanent removal of a marine mammal from the wild must be consistent with
any applicable quota established by the Office Director. Applicants must justify
the need for use of an endangered species and whether an alternative species can
be used. Applicable regulations: 50 CFR 216.27(b)(4), 216.41(b)(3), and
222.308(b)(4).
(b) The name and location of the rehabilitation facility where animals will be tested.
The applicant must provide the location where the take will occur (see other
Location sections in this document for location justification and regulatory
citations). NMFS also needs this information to ensure authorization needed
under 50 CFR 216.27(c) has been obtained as it relates to the disposition of
rehabilitated marine mammals for special exception permit purposes. NMFS also
needs this information to determine a rehabilitation facility’s compliance with
their Stranding Agreement and applicable NMFS guidelines. This question is not
applicable to non-mammal ESA-listed species (research on sea turtles in
rehabilitation would require a USFWS permit; no other non-mammal ESA-listed
species is rehabilitated).
(c) The name and location of the captive facility holding the subject animals and,
where possible, the identity of specific animals.
The applicant must provide the location where the take will occur (see other
Location sections in this document for location justification and regulatory
citations) and the age/sex and species (see Project Description justification and
regulatory citations). This information is also used for marine mammal inventory
purposes.
(d) A copy of any license or registration issued by the Department of Agriculture,
Animal and Plant Health Inspection Service (APHIS), any outstanding variances
granted, and the most recent APHIS inspection report.
The APHIS is responsible under the Animal Welfare Act (AWA) for captive
marine mammals and has established regulations and standards, "Specifications
for the Humane Handling, Care, Treatment, and Transportation of Marine
Mammals" (9 CFR Part 3, Subpart E). Information regarding the appropriate
licensure or registration, variances, and standing with APHIS is used to determine
if the applicant’s facilities are adequate for the proper care and maintenance of a
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marine mammal. For any research involving captive marine mammals, the
applicant must provide supporting documentation. If marine mammals are on
public display incidental to research or enhancement, they must be held consistent
with AWA requirements and standards. APHIS does not regulate activities
involving fish, invertebrates, or reptiles. Applicable regulations: 50 CFR
216.34(a)(6); 216.41(a)(2), (b)(6)(v), (c)(1)(vi).
(e) The proposal submitted to the appropriate Institutional Animal Care and Use
Committee (IACUC) established under the AWA, the IACUC approval, and any
comments and recommendations of the IACUC.
This information is used to support a determination that the permitted activities
will be conducted in a humane manner. Applicable regulations/statutes: 50 CFR
216.34(a)(1) and MMPA section 104(b)(1)(B).
(f) A written statement from the responsible veterinarian or expert certifying that the
facilities, methods of care and maintenance, and methods of transport will be
adequate to ensure the well-being of the animals and, for marine mammals, will
comply with all care and transport standards established under the AWA.
This information is used to determine if the applicant’s qualifications, facilities,
and resources are adequate for the proper care and maintenance of protected
species. For any research involving captive marine mammals, the applicant must
provide supporting documentation. If marine mammals are on public display
incidental to research or enhancement, they must be held consistent with AWA
requirements and standards. For ESA-listed species, the applicant must provide a
statement from a licensed veterinarian or recognized expert verifying methods of
transport and maintenance are adequate to provide for the well-being of the
animals. Applicable regulations: 50 CFR 216.34(a)(6); 216.41(a)(2), (b)(6)(v),
(c)(1)(vi); and 222.308(b)(7)(vi).
(g) For ESA-listed species: Describe the care and maintenance of the animals,
including a complete description of the facilities where they will be maintained,
how they will be maintained, and the qualifications of husbandry staff.
Under the ESA, a complete description of how listed species will be maintained in
captivity is required to ensure the applicant’s qualifications and facilities are
appropriate for the proper care and maintenance of the species. This information
is also needed to determine whether the permit would further a bona fide and
necessary scientific purpose or enhance the propagation or survival of the affected
species, and to determine that the resources are adequate for the applicant to
successfully accomplish the objectives stated in the application. For scientific
research involving captive marine mammals, the applicant must submit
supporting documentation. For enhancement permits involving marine mammals,
the proposed captive maintenance must contribute directly to the survival or

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recovery of the species. Applicable regulations/statutes: 50 CFR 222.308(b)(8)
and 216.41(a)(2) and (b)(6)(iv) and MMPA section 104(c)(4).
(h) Whether a captive breeding program will be established and, if so, justification.
This information is used to describe the proposed action as it relates to research or
enhancement and to determine whether proposed breeding is consistent with a
recovery plan. Applicable regulations: 216.41(b)(6) and 222.308(b)(9).
(i) Indicate the disposition of captive animals at the termination of research or
enhancement activities. This information is necessary to determine if the subject
animals would be euthanized or released to the wild; or whether the animals
would be transferred to another disposition (e.g., public display), or kept in a
long-term research or enhancement program, and to permit accordingly. Any
marine mammals held in captivity under an enhancement permit must be returned
to the wild as soon as feasible; justification for other disposition must be
provided. Captive marine mammals may not be released to the wild unless
authorized by a scientific research or enhancement permit. Applicable
regulations/statutes: 50 CFR 216.35 (e), 216.41(c)(2) and MMPA section
104(c)(4)(B); and 50 CFR 222.308(b)(9) and (c)(9).
(j) If release of captive animals to the wild is proposed, state the length of time the
animals will be held, no matter how temporary, and describe the protocols for the
release, including mitigation and monitoring protocols.
This information is necessary to ensure there will be no disease transmission
between released animals and the wild population; that genetic exchange has been
taken into consideration; and that the animals have necessary skills to survive in
the wild. Such information is necessary to ensure that the permitted activity: (1)
is humane and does not present any unnecessary risks to the health and welfare of
marine mammals; (2) will not have a significant adverse impact on the species or
stock; and (3) will not operate to the disadvantage of an ESA-listed species.
Release of captive marine mammals must be conducted pursuant to a scientific
research or enhancement permit. Applicable regulations: 50 CFR
216.33(e)(4)(ii), 216.34(a)(1) and (4), 216.35(e), and 222.308(c)(2).

Project Locations
Permits must specify locations of authorized take or import/export. Necessary to
determine if work will be conducted in U.S., and therefore, whether a permit is needed.
This information is also necessary for considering impacts to protected species and for
conducting the appropriate environmental analyses under NEPA, MMPA, and ESA.
Applicable regulations/statutes: 50 CFR 216.33(a), 216.36(a)(1)(iii), and MMPA section
104(b)(2)(B); and 50 CFR 222.308(b)(6)(i) and (iv), 222.308(d)(2).

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Take Information
Applicants are required to enumerate the number of protected species, by species/stock,
age, sex, location, and manner in the form of a table. This table is used to verify the
number of animals requested to be taken as described in the narrative portion of the
project description and is used to create the take table for the permit, once issued. Further
justification and the applicable regulations are included above under “Project
Description.”

National Environmental Policy Act (NEPA) Considerations
In addition to information contained in other sections of the application as noted, the
questions posed in this section of the application are necessary considerations under
NEPA. These questions address such things as whether new or novel techniques will be
used and adopted by others (i.e., if a precedent will be set); whether there is risk from
hazardous substances or infectious agents; what impacts may occur to unique or protected
geographic areas, including refuges, sanctuaries, or critical habitats; whether the work
could cause loss or destruction of scientific, cultural, or historic resources; and whether
there could be introduction or spread of non-indigenous or invasive species as a result of
the permitted activity. Applicable regulations: NEPA CEQ regulations.

Project Contacts
This section is necessary for identification and contact purposes. A Permit Holder is
ultimately responsible for all activities of individuals operating under the permit. A
Responsible Party must be named if the applicant is an organization. Special exception
permits are not transferable. The Principal Investigator and Co-investigators share
responsibility in the absence of the Permit Holder. These persons will be named on the
permit as responsible for the authorized activities and are subject to enforcement actions.
Personnel involved in the authorized activities must be reasonable in number and limited
to those individuals who perform a necessary function and support personnel included for
purposes of training or as back up. Applicable regulations: 50 CFR 216.33, 216.35(i),
216.41(a), 216.41(c)(1)(iii-iv), and 222.308(b)(3).
Qualifications and Experience: Necessary to determine whether the individuals
operating under the permit are qualified to successfully accomplish the objectives,
conduct bona fide research or enhancement activities, carry out the specific types of take,
and properly care for and maintain captive animals (as applicable). Individuals
conducting activities authorized under a permit must possess qualifications
commensurate with their duties and responsibilities, or must be under the direct
supervision of a person with such qualifications. Persons who require state or Federal
licenses to conduct activities authorized under the permit must be duly licensed.
Applicable regulations: 50 CFR 216.34(a)(5-6), 216.35(f-h), 222.308(b)(6)(vi),
222.308(b)(8)(v), and 222.308(c)(11).

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Submit Application (Authentication and Certification)
Applicants must authenticate their identity by signature and certify that the information in
the application is accurate, under penalties of the ESA and MMPA. Permits must be
applied for in good faith. Applicable regulations: 50 CFR 216.33(a), 216.33(e)(4)(i),
222.302(a), 222.303(f)(1), 222.308(b)(12-13), and 222.308(c)(1). Also required by 18
U.S.C. 1001.

Requesting a Modification

Modification Request Questions
This information is necessary to identify what type of modification is being requested and
what processing steps are involved. The selections made on this screen dictate what fields
are available for applicants to edit on the screens that follow. Applicants are required to
provide information consistent with that required for a new permit (e.g., hypothesis,
methods, effects and mitigation), and the justification for requiring this information from
applicants is the same as described above, as applicable to the modification being
requested. Applicable regulations: 50 CFR 216.39 and 222.306.

Reports
Section 104(c) of the MMPA requires "...any person authorized to take or import a
marine mammal for purposes of scientific research, public display, or enhancing the
survival or recovery of a species or stock [to] furnish to the Secretary a report on all
activities carried out by him pursuant to that authority." Permit holders are required to
submit reports in accordance with the requirements established in their permits. Reports
are of several types and may be submitted annually or on occasion. For scientific
research and enhancement permits, the annual report is a summary of all research and
enhancement activities conducted during the preceding year. Annual reports are
necessary for NMFS to determine that the permit holder is abiding by the conditions of
the permit, to track numbers of animals taken and review the effects of the authorized
take on the species. Reports are also necessary to determine whether the permitted
research or enhancement activities met stated objectives and determine whether the
research findings were be published or otherwise made available to the public or
scientific community. Applicable regulations: 50 CFR 216.27, 216.38, 216.45,
222.301(h) and 222.308(b)(11).

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National Marine Fisheries Service
Marine Mammal and Endangered
Species Research and Enhancement
Permits

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National Marine Fisheries Service Marine Mammal and
Endangered Species Research and Enhancement Permits

BACKGROUND........................................................................................................................................... 3
WHEN TO APPLY .......................................................................................................................................... 4
PROCESSING ................................................................................................................................................ 4
PRE-APPLICATION GUIDE (PAG) ................................................................................................................. 5
GENERAL GUIDANCE FOR FILLING OUT AN APPLICATION .............................................................................. 6
APPLICATION LAYOUT.................................................................................................................................. 7
COMPLETING AN APPLICATION USING APPS ................................................................................ 8
GIVE COMPLETE INFORMATION ................................................................................................................... 8
PROJECT INFORMATION PAGE...................................................................................................................... 8
PROJECT DESCRIPTION PAGE .................................................................................................................... 10
PROJECT SUPPLEMENTAL INFORMATION PAGE ........................................................................................... 14
CAPTIVE INFORMATION PAGES ................................................................................................................... 19
PROJECT LOCATIONS AND TAKE INFORMATION PAGES ................................................................................ 20
TAKE INFORMATION PAGES ........................................................................................................................ 22
NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) CONSIDERATIONS PAGE ................................................. 29
PROJECT CONTACTS PAGE ......................................................................................................................... 29
SUBMIT APPLICATION PAGE ....................................................................................................................... 33
AUTHENTICATION AND CERTIFICATION....................................................................................................... 34
PROJECT STATUS................................................................................................................................... 35
REQUESTING A MODIFICATION ....................................................................................................... 37
MODIFICATION REQUEST QUESTIONS ........................................................................................................ 39
MODIFICATION TYPES................................................................................................................................ 40
SUBMITTING YOUR MODIFICATION REQUEST.............................................................................................. 43
ADDITIONAL INFORMATION ............................................................................................................. 44
PAPERWORK REDUCTION ACT STATEMENT ................................................................................................. 44

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Background
This chapter describes how to use APPS to apply on-line for Marine Mammal Protection
Act and Endangered Species Act scientific research and enhancement permits for
National Marine Fisheries Service (NMFS) protected species, including:
• Cetaceans;
• Pinnipeds (excluding walrus);
• Sea turtles (in water);
• Shortnose sturgeon;
• Smalltooth sawfish; and
• White and black abalone.
Under section 104 of the Marine Mammal Protection Act of 1972 (MMPA) and section
10(a)(1)(A) of the Endangered Species Act of 1973 (ESA), NMFS may issue permits for
scientific research purposes or to enhance the propagation, survival, or recovery of
protected marine species. Under the Fur Seal Act of 1966 (FSA), NMFS may issue
permits for research on fur seals of the North Pacific.
Additional state laws or regulations more restrictive than the MMPA or ESA may also
apply to your activities and you are responsible for securing any necessary state permits
or authorizations.
Possession of a permit is a privilege. NMFS must evaluate issuance of permits in
consideration of its duties to protect and recover listed species.
Permits may be issued for up to five years and will include conditions necessary to
mitigate and monitor the impacts of the proposed activities.

Please note, not all MMPA and ESA permit applications are currently available on
APPS. You will need to use separate application instructions and apply by mail if you
require the following permits/authorizations:
• MMPA General Authorization (GA)
• MMPA Commercial/Educational Photography Permit
• MMPA Public Display Permit
• MMPA Incidental Harassment Authorization (IHA)
• MMPA Incidental Take Letter of Authorization (LOA)
• MMPA Pre-Act Parts Authorization
• ESA Section 10(a)(1)(B) Incidental Take Permit
For more information on applying for these permits, click the “Permit Types” link in the
APPS Features box, use the Pre-Application Guide in APPS (see below), or visit
http://www.nmfs.noaa.gov/pr/permits/types.htm.

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Overview
When to Apply
Target Species
Non-ESA listed marine
mammals

Non-ESA listed marine
mammals

Non-target species
No ESA-listed species or
designated critical habitat
will be adversely affected
by the research activities
ESA-listed species or
designated critical habitat
may be adversely affected
by the research activities

ESA-listed species (marine
mammals and other taxa)

When to apply
At least 6 months prior to
when you want to begin
research/enhancement
activities
At least one year prior to
when you want to begin
research/enhancement
activities
At least one year prior to
when you want to begin
research/enhancement
activities

Processing
Once we receive a complete permit application, it is subject to a mandatory 30-day
public comment period. We concurrently send the application to the appropriate NMFS
Regional and Science Center Offices, subject matter experts, and the Marine Mammal
Commission for review and comment as applicable.
All permits must be analyzed under the National Environmental Policy Act (NEPA).
An environmental assessment (EA) or environmental impact statement (EIS) is necessary
if proposed research or enhancement activities:
•
are the subject of public controversy based on potential environmental
consequences,
•
have uncertain environmental impacts or unknown risks,
•
may result in cumulatively significant impacts, or
•
may have an adverse effect upon endangered or threatened species or their
habitats (note: any harassment or take of these species is considered an adverse
effect).
If an application does not contain sufficient information on the environmental impact of
the proposed activity to determine whether an EA/EIS is necessary, or if the information
is insufficient to complete such analyses, the application may be returned to the applicant
or processing will be prolonged.

4

As applicable, NMFS must request consultation with the following agencies on the
potential effects of certain proposed activities, as listed below:
Agency
NMFS Endangered Species Division
NMFS Office of Habitat Conservation
NOAA National Ocean Service
U.S. Fish and Wildlife Service

Subject of Consultation
ESA-listed species and designated critical
habitat
Essential Fish Habitat (EFH)
National Marine Sanctuaries
ESA-listed species and designated critical
habitat

Issues that arise during these consultations will prolong the permit process.

Pre-application Guide (PAG)
Refer to Chapter 1 for guidance on filling out the PAG, which is required prior to
applying for a permit using APPS. Upon completing the PAG, the “Results” page will
indicate the type of NMFS permit required. Please note the Questionnaire No. for future
reference.
You have the option at this point to start an application or cancel. If you select cancel,
you will have to complete another PAG before starting your application. If you are
satisfied with the results of the PAG, click the link to start an application.
If you have questions about the results of the PAG or about completing your application,
please call the Permits Division at 301-713-2289.

5

General Guidance for Filling out an Application
Refer to Chapter 2 (“How to Use the System”) for basic instructions for using APPS,
including system requirements, creating a new account, using the “portfolio” page,
detailed navigation guidance, and information on saving and submitting your application.
APPS will assign your application a file number. Please reference this file number in
correspondence about your project (e.g., in email subject headings). When starting from
your portfolio, clicking on the link of your application file number under the “File
Number” column will take you to the application.
General guidelines
•

Data is not saved automatically. APPS will display a warning message and will
time out after 20 minutes without any activity. To avoid loss of data, save the
application before the system times out. Save frequently using the “Save” link at
the top of your application. You will also be prompted to save each page when
you click on the navigation links. Select “Save” to save new data, or “Cancel” to
continue on to the next screen without saving.

•

You do not have to complete an application in one session. You may save the
application as a draft as long as you save before logging off or before the system
“times out” and logs you off due to inactivity. The draft application may be
accessed later from your portfolio and will remain in draft mode until you
complete the required fields and submit the application.

•

An asterisk (*) marks a field that is required.

•

Some text boxes have character limits, which includes spaces.

•

You may cut and paste from other documents (e.g., Word), but special characters
and formatting will be lost.

Navigation guidelines
•

Do not use your web browser’s navigation buttons. Doing so may cause you
to lose information. Use the navigation links “< Previous” or “Next >” or the
breadcrumbs at the top of the APPS screen, as described below and in Chapter 2.

•

Two options are available to navigate through the application sections:
o Breadcrumb links (represented by the title of each major section of the
application) allow you to jump to other pages in the application without
having to complete the required information prior to leaving a page
(i.e., you can skip a section and come back to it later).

6

•

APPS navigation links (“< Previous,” “Reset,” or “Next >”) on the right side of
the pages require you to go to each screen in a sequential order, and you are
required to enter all information prior to leaving a page.

Application Layout
New applications will open in draft or editing mode. You will navigate through a series
of screens to enter information in the following sections of the application:
1) Project Information, Project Description, and Project Supplemental Information
– this section requires specific information about your project, such as the duration and
timing of your work, hypothesis/justification, description of methods, and other
information.
2) Location and Take Information – this section requires information about the places
you are requesting to work, the numbers and types of protected species you expect to take
or import, and the methodologies you will use to conduct your research or enhancement
activities.
3) NEPA – this section requires information about how your activities would result in
impacts on the environment, including the physical and biological aspects of the
environment.
4) Project Contacts – this section requires information on the Applicant/Permit Holder,
Principal Investigator, Co-investigators, or others that will be working under the permit.
5) Submit – this section allows you to view your completed application and submit it to
the Permits Division for review and processing. APPS will run checks before you can
“Submit” an application to ensure you have completed all required screens or data fields.
You will go through steps to authenticate your identity and certify the contents of your
application prior to submitting it, which requires you to provide a signature to the Permits
Division.

7

Completing an Application using APPS
Give Complete Information
Please provide complete and specific information according to the instructions in this
document. APPS will not allow you to submit an application if one of the required fields
is not filled out. The Permits Division cannot process applications that do not
include all of the required information. We will return incomplete applications with
explanation or request additional information. If we request additional information and
do not receive it within 60 days, we will withdraw your application. Please note the
following:
•

Your application must be a stand-alone document and must clearly describe all
proposed activities even when you reference published literature.

•

When a question does not apply, please indicate “Not Applicable” or “N/A” and
provide a brief explanation as to why the question is not applicable.

•

Please avoid the use of technical jargon when possible because your application
will be available to the public for review.

•

You are encouraged to contact the Permits Division at 301-713-2289 with
questions in advance of submitting your application.

Project Information Page
File Number
This number is automatically generated by APPS and cannot be changed. Use this
number in correspondence about your application.
*Project Title (enter up to 255 characters)
Describe the project as concisely and descriptively as possible. Include the species (or
taxa if multiple species), the study’s geographic range, and purpose. For example:
•

“Characterizing the Population Structure, Forging Ecology, and Movement
Patterns of Green Sea Turtles in the Gulf of Mexico.”

Note: If working on a draft application, we strongly recommend you enter a project
title before logging out of the system.
*Project Status
Project status (“New” or “Renewal”) is automatically selected based on your answers in
the pre-application guide (PAG). Do not change this field.
8

Previous Federal or state permit #
If applicable, please enter your most recent NMFS permit number. If you have/had more
than one permit, enter the permit most closely related to this application.
Note: State permit numbers are only applicable for Pacific marine and
anadromous fish applications.
*Permits Requested
One or more items will be listed based on your answers in the PAG. If the options listed
are incorrect, please call the Permits Division at 301-713-2289 for assistance.
*Where will the activities occur?
One or more general locations will be listed based on your answers in the PAG. If a
location is incorrect, please call the Permits Division at 301-713-2289 for assistance.
Note: You will have the opportunity to provide more specific location
information on subsequent pages.
*Research Timeframe
Enter the proposed start and end dates of the entire project in the following format:
MM/DD/YYYY. Please review the “When to Apply” section above and provide realistic
dates based on processing time.
•

The start date must not be prior to the date you successfully submit the
application.

•

The end date must be within five years of the start date.

•

You may enter more specifics on your project dates/field seasons under
“Sampling Season/Project Duration” (see below).

*Sampling Season/Project Duration (enter up to 1,000 characters)
Describe the annual sampling season(s) and the duration of the project. Include the
months of the year and frequency of fieldwork/sampling (e.g., how many times per year
and how frequently will you sample?).
If your research extends beyond five years, or is a continuation of previously authorized
research, enter information here about when the research began and when you expect it to
end.

9

*Abstract (enter up to 2,000 characters)
Provide a brief summary (approximately 200 words) of the proposed research and/or
enhancement project. We will publish this summary in the Federal Register Notice of
Receipt that initiates the 30-day public comment period. The summary should include
concise statements of the following information:
•

Purpose of the research or enhancement activity;

•

Target species (common and scientific names);

•

Type of take activities (e.g., capture, biopsy sampling), import and/or export;

•

Numbers of animals to be taken for each activity or number of animals from
which specimens will be imported and/or exported, by species or taxa (over a
specified time, e.g., per year);

•

Numbers and kinds of non-target species, including those listed under the ESA,
that may be taken incidentally;

•

Specific geographic location(s), including locations from which animals or
specimens will be imported or to which they will be exported, if applicable; and

•

Requested duration of the permit (e.g., five years).

After you have completed this page, save and click “Next >” or click the “Description”
breadcrumb at the top of the APPS page to move to the next page.

Project Description Page
*Project Purpose: Hypothesis/Objectives and Justification (no text limit)
Answer the following questions:
•

What are your objectives?

•

What is the expected significance of your proposed activities?

•

For research, what is the hypothesis being tested?

•

For enhancement, how will your activities enhance the survival or recovery of the
species in the wild?

Describe how your proposed work is different from, builds upon, or duplicates past
research or enhancement activities.

10

Describe why your work cannot be accomplished without taking marine mammals or
protected species.
Justify your sample size. Include a power analysis or other sample size estimation to
determine whether the sample size is sufficient to provide statistically significant or
otherwise robust results appropriate for your research study.
Justify your need to sample specific sex, age class, sub-populations, etc.
For each species, demonstrate how your research activity would contribute to the basic
knowledge of the biology or ecology of the species, or how your activity will identify,
evaluate or resolve conservation problems.
Explain the role of each Co-investigator (CI).
As applicable, also address the following:
For ESA-listed and MMPA-depleted species:
•

Why must your study involve ESA-listed or depleted species? Discuss the use of
possible alternatives (e.g., surrogate non-ESA listed species).

•

How will your project contribute to the objectives identified in the species’
recovery or conservation plan? Please be sure to identify specific priorities of
these plans.

•

Does your project have broader significance than your individual goals? For
example, does your project respond to recommendations (other than those listed
in a recovery or conservation plan) of a scientific body charged with management
of the species? If so, describe.

•

If there is no recovery or conservation plan, how will your project otherwise
contribute to conservation and/or recovery of the species?

•

How will your research directly benefit the species or fulfill a critically important
research need?

•

How will your enhancement activities contribute to maintaining or increasing
distribution or abundance, enhance the health or welfare of the species, or ensure
the survival or recovery of the species in the wild?

•

Will captive maintenance for enhancement maintain a viable gene pool, increase
productivity, provide necessary biological information, or establish animal
reserves?
ƒ How does the benefit of removing animals from the wild into captivity
outweigh alternatives that do not require removal from the wild?

11

ƒ

What plans are in place for returning animals and any offspring to the
wild? If animals are going to remain in permanent captivity,
additional justification is required.

*Project Description (no text limit)
This section should clearly describe the methods you will use, the number of animals you
will take, and the locations in which you will take them. This section should provide the
reader with a clear picture of what will systematically happen during a typical day/field
season of research or enhancement activities.
Note: Background information and literature review will be requested in a later
section.
Describe the number of individuals, by species, sex, age class, manner, and location
in which you will take1 animals and animal parts/specimens over a specified period
(annually or per field season if less than one year).
If you will take the same animals in more than one manner, list the number of animals
and all procedures that you would conduct.
•

Example: capture, blood sample, biopsy, and flipper tag 25 adult male and 25
adult female (non-pregnant and non-lactating) individuals annually during nonbreeding season.

If individuals will be taken more than once (e.g., recapture for instrument retrieval or
multiple tagging attempts), indicate the frequency and type of take activity per individual
per year or per field season if less than one year.
Provide detailed methods for each take activity, including but not limited to
descriptions of the following:
• Platform types (vessel or aircraft description)
• Aerial and vessel survey type and routes (attach figure if possible)
• Approach distances (by aerial, vessel, or ground)
• Approach techniques (speed, direction in relation to animals)
• Photo-identification (techniques and analysis)
• Capture techniques (hand, net [type and mesh size], cage [type and dimensions])
1

By regulation, a take under the MMPA means to harass, hunt, capture, collect, or kill, or attempt to harass,
hunt, capture, collect, or kill any marine mammal. This includes, without limitation, any of the following:
The collection of dead animals, or parts thereof; the restraint or detention of a marine mammal, no matter
how temporary; tagging a marine mammal; the negligent or intentional operation of an aircraft or vessel, or
the doing of any other negligent or intentional act which results in disturbing or molesting a marine
mammal; and feeding or attempting to feed a marine mammal in the wild.
Under the ESA, a take means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or
attempt to do any of the preceding.

12

•
•
•
•
•
•

Handling/restraint (methods and number of persons to restrain, maximum time)
Sedation/anesthesia (type, route/site, dosage, duration, reversal/other drugs)
Marking (flipper and PIT tagging, branding, bleach/other temporary marking)
Instrumentation (attachment method, types of sensors, dimensions, weight, battery
life, duration of attachment)
Biological sampling (type, volume/size, site, analysis, shipment, storage)
Acoustic sampling (passive recording or auditory evoked potential) or acoustic
playbacks (frequency, source level, signal duration, duty cycle, and energy
output).

Please make sure your methods are detailed enough for us to evaluate potential effects.
Refer to Appendix VIII for guidance on what level of detail is required.
Cite references for the methods where applicable, but do not substitute a literature
citation in lieu of a complete description of the methods.
On the “Supplemental Information” page, you may attach files containing figures or
photographs to illustrate your methods (e.g., tags and tag attachment, nets and net
deployment). See below for instructions on attaching files.
Include the purpose of each take activity (including the purpose of specific samples
taken). How do these take activities relate to meeting your objectives?
Indicate the estimated number and type of non-target species that you may affect each
year, and the manner in which you may affect them during your research. This includes
but is not limited to marine mammals, ESA-listed species, sea birds, sharks, plants, etc.
If you were to encounter a non-target species in the same area of your study but you do
not expect to affect them in any way, please describe why and any actions you will take
to prevent impacts (e.g., not in area during time of study; would not approach closer than
100 meters; would halt operations until non-target species moved out of study area).
Describe how your proposed activities coincide with or avoid sensitive biological periods
such as reproductive seasons and maternal care of both target and non-target species.
For import and export activities, answer in detail the following:
•

How will the animals or specimens/parts to be imported be taken in the country of
origin?

•

If samples will be obtained from dead animals, how did the animals die (e.g.,
subsistence hunt)?

•

What is the authorizing government agency for the legal collection of animals or
specimens in the country of origin? Be prepared to provide documentation
regarding the legality of the take in the country of origin for your annual reports.

13

•

What are the shipment/transport methods, including safe handling protocols?

•

What are the methods for sample preservation, analysis, and curation (for samples
not destroyed in analyses), including safety protocols for laboratory work?

•

If an import would be necessary for the protection or welfare of a live marine
mammal, discuss the circumstances involved and any alternatives considered.

For exports of living marine mammals from the U.S., the appropriate agency of the
foreign government must certify that:
•

The information in the application is accurate;

•

The laws and regulations of the foreign government involved allow
enforcement of the terms and conditions of the permit; and

•

The foreign government involved will afford comity to any permit
amendment, modification, suspension, or revocation decisions.

After you have completed this page, save and click “Next >” or click the “Supplemental”
breadcrumb at the top of the APPS page to move to the next page.

Project Supplemental Information Page
Attach a Supplemental Information File
If you do not have enough room to answer any of the questions in this or the other
sections, you may attach files to complete a section or sections. There are additional
areas in the application to attach maps, grant proposals, etc.
•

To attach a file, use the “click here to attach a supplemental file” link.

•

An MS Word file is the preferred format, but formats such as PDF, MS Excel,
Word Perfect, and ZIP files are also acceptable.

•

An attachment may not be larger than 10 MB and you may attach up to 10
files. If you have a larger document, reduce the size by removing material that is
not essential for the review of your application.

•

Once you have attached a file, the screen will display text indicating that a file is
attached. You may need to refresh the screen to see this after hitting “save.”

*Status of the Affected Species (enter up to 2,000 characters)
As applicable, indicate the status of each target species or stock as follows:

14

•
•
•

ESA - threatened or endangered
MMPA - depleted or strategic
Convention on International Trade in Endangered Species of Wild Fauna
and Flora (CITES) - Appendix I, I, or III

Species information is available at the following web sites:
http://www.nmfs.noaa.gov/pr/species/
http://www.fws.gov/
http://www.cites.org/
*Attach a Literature Review File
Attach a background literature review for your project by clicking on the “Click here to
attach a Literature Review file” link and follow the above instructions.
This document should provide a succinct review of relevant information published by
accredited scholars and researchers, including you, and should include appropriate
citations. Your purpose is to convey to the reader what knowledge and ideas have been
established related to your proposed research/enhancement, and what the strengths and
weaknesses are. If you have previously held a permit, discuss how your past findings
have contributed to the body of knowledge and how they relate to your proposed
objectives.
*Lethal Take (enter up to 800 characters)
If you do not expect to kill or seriously injure any animals, intentionally or
unintentionally, click the “Not Applicable” check box and leave the larger text box blank.
If intentional lethal take is involved, provide an explanation of why a non-lethal method
is not feasible or why lethal take is unavoidable. For ESA-listed or MMPA depleted
species, also describe how the results will directly benefit the species or fulfill a critically
important research need.
•

Provide methods of lethal take, number of animals to be taken per year, and
protocols for tissue collection, analysis, and carcass disposal if not previously
described in the “Project Description” section.

If unintentional mortality or serious injury2 is possible incidental to, or as a result of, the
proposed activities, indicate the following if not previously described in the “Project
Description” section:
•

Maximum number of animals from each species that could die or be seriously
injured per year and how you arrived at that number;

2

For marine mammals, serious injury is defined by regulation as any injury that will likely result in
mortality.
15

•

Potential ways that animals may die incidental to the proposed activities; and

•

Protocols for tissue collection, analysis, and carcass disposal.
Note: Unintentional mortality refers not only to a death during research, but also
to those that succumb at a later time (e.g., death due to effects of stress from
handling, adverse reactions to drugs, complications from a pre-existing condition,
or abandonment of dependent young).

*Anticipated Effects on Animals (no text limit; refer to Appendix VIII for guidance on
what level of detail is required)
•

What are the anticipated effects of each of the activities alone or cumulatively on
the behavior and physiology of the target animals? How will animals react to
your actions and what are the consequences of those reactions? Identify both
short- and long-term potential effects.
Note: If you have conducted this work previously, please clearly describe and
quantitatively summarize the types of reactions of animals from past research.
Include citations for any relevant references and be prepared to provide copies if
requested. Annual permit reports and other non-published works are acceptable
citations.

•

What are the anticipated effects on the population as a whole? On what is your
determination based?

•

Summarize any mortalities that have occurred during the previous five years of
research or enhancement activities conducted by you using the same or similar
techniques, including circumstances involved and cause of death.

•

Describe how conspecifics or non-target species in the study area may react to or
otherwise be affected by your activities (e.g., will you encounter them on your
way to or from the study site? How will you avoid harassment?).

*Measures to Minimize Negative Effects (no text limit; refer to Appendix VIII for
guidance on what level of detail is required)
•

For each activity, what measures will you take to minimize impacts to wildlife?
Provide information for both target and non-target species (e.g., plants, fish,
coral). Describe measures you will implement to ensure your activities are
conducted in a humane manner, with minimal disturbance, stress, and harm to the
subject animals. Are you proposing to use methods that will have the least
potential for pain and stress?

16

•

Indicate any short- and long-term post-procedure monitoring you would conduct
to evaluate the effects of your activities and/or to ensure animals have recovered.

•

What efforts will you make to collaborate or coordinate research with others in
your study area? Explain how this will occur and how it will minimize impacts.
For example, will it involve sharing resources, samples or data; timing surveys,
etc.?

•

If the proposed activities may cause stress, discomfort, pain, suffering, injury, or
mortality, you must explain why there are no feasible alternative methods to
obtain the desired data.
Note: Where an IACUC (Institutional Animal Care and Use Committee) is
required, include the signed approvals and comments. You may attach these files
using the “Attach a Supplemental Information File” link at the top of the “Project
Supplemental Information” page (see above). If the protocols have not been
approved, indicate the status. Applicants are encouraged to include the protocols
submitted to and approved by their IACUC in addition to approval letters in
support of their application.
For applications involving captive care of marine mammals, there is a separate
section to attach your IACUC documents.

Attach a References File
If your application contains citations to published work, you must include a list of
references. References contain bibliographic information that would allow a reader to
obtain a copy of the referenced work.
Note: Referenced materials must be made available to the Permits Division upon
request, as needed for evaluation of the application, or preparation of any
necessary ESA and/or NEPA analyses. Note that all documents referenced in
support of your application must be available to the public upon request. Do not
reference confidential documents, or other information you are not willing to
provide to the public at the time your application is submitted.
*Resources Needed to Accomplish Objectives (enter up to 800 characters and attach file
if necessary)
Explain how your expertise, facilities, and resources are adequate to successfully
accomplish the objectives and activities stated in your application.
Include the name and address of sponsors, cooperating institutions/researchers, or
contractors, if not listed as Co-investigators on the application, and clearly indicate their
role.

17

If the proposed take activities will be conducted by a contractor, provide a statement as to
whether a qualified member of your staff (include name(s) and qualifications) will
supervise or observe the taking. Attach copies of any relevant formal research proposals,
contracts, or letters of agreement that would demonstrate the financial or logistical
resources available to you to conduct and complete the proposed activities.
Indicate whether you have applied for, secured, or will apply for other federal, local, or
state permission to conduct your proposed work, and what those approvals include.
Note: You may add an attachment here for funding proposals, letters of
agreements, lists of cooperators and their roles, etc.
*Disposition of Tissue Samples (enter up to 800 characters)
If you will not collect, receive, possess, transport, or import/export tissue samples, click
the “Not Applicable” check box and leave the text box blank.
If this section is applicable, provide a description of the disposition of any parts or
samples remaining after the research or enhancement activities are complete. If you have
made arrangements with a museum or other institutional collection to ensure that
remaining tissues will be available for scientific research or enhancement purposes,
include information on where the samples will be stored, transferred, and
how/when/where they will be disposed. Include contact information for each of
researchers, laboratories, museums, and/or institutional collections that would receive
these tissue samples or specimens. If you will not retain or transfer samples, state
whether samples will be consumed in analysis or will be destroyed.
*Public Availability of Product/Publications (enter up to 800 characters)
Describe the end product(s) of your proposed research and how they will be made
available to the public.
After you have completed this page, save and click “Next >” or click the
“Location/Take” breadcrumb at the top of the APPS page to move to the next page.

18

Captive Information Pages
Based on your responses to the PAG, you may be required to provide additional
information on animals in captivity (permanent or temporary), including removing
animals from the wild into captivity and research or enhancement on captive or
rehabilitating animals. As applicable, address the following:
(a) Explain why removal from the wild is necessary and why you cannot obtain
suitable animals from captive or rehabilitated stock. (Enter up to 2,000
characters.)
(b) If the source stock is to be beached/stranded marine mammals undergoing
rehabilitation, indicate the name and location of the rehabilitation facility. (Enter
up to 1,000 characters.)
(c) If the source stock is from animals already in captivity (other than animals in
rehabilitation) indicate the name and location of the facility and, where possible,
identify the specific animals (by NOAA ID number if applicable) to be involved
in the proposed activity. (Enter up to 1,000 characters.)
(d) Include a copy of any license or registration issued by the Animal and Plant
Health Inspection Service (APHIS) of the U.S. Department of Agriculture, any
outstanding variances granted, and the most recent APHIS inspection report.
(You must attach a file here.)
(e) Include the proposal submitted to the appropriate Institutional Animal Care and
Use Committee (IACUC) established under the Animal Welfare Act (AWA), the
IACUC approval, and any comments and recommendations of the IACUC. (You
may attach a file here.)
(f) Provide a written statement from the responsible veterinarian or expert certifying
that the facilities, methods of care and maintenance, and methods of transport will
be adequate to ensure the well-being of the animals and, for marine mammals,
will comply with all care and transport standards established under the AWA.
(You must attach a file here.)
(g) For ESA-listed species: Describe the care and maintenance of the animals,
including a complete description of the facilities where they will be maintained.
This includes the dimensions of the pools or other holding facilities; the number,
sex, and age of animals by species to be held in each; the water supply, amount,
and quality; the diet, amount and type; sanitation practices; and qualifications and
experience of the husbandry staff.
(h) Indicate whether a captive breeding program will be established and, if so,
provide justification in accordance with the species conservation or recovery plan
as applicable for enhancement activities. For ESA-listed species, indicate if you
19

are willing to participate in a captive breeding program if requested by NMFS.
(You may enter up to 1,800 characters.)
(i) Indicate the disposition of captive animals at the termination of research or
enhancement activities. (You may enter up to 1,800 characters.)
(j) If release of captive animals to the wild is proposed, state the length of time the
animals will be held, no matter how temporary, and describe the protocols for the
release, including post-release monitoring protocols. Include in the release
protocol mitigation for the following:
ƒ Disease transmission between released animals and the wild population;
ƒ Potential genetic exchanges between introduced and endemic stocks;
ƒ Ability of the released animals to forage and protect themselves from
predators; and
ƒ Elimination of behavioral patterns acquired during captivity that could
prove detrimental to the released animals or the social structure of local
populations.

Project Locations and Take Information Pages
Overview
On the main “Project Locations and Take Information” page, you can describe your
location, add new locations, edit or delete existing locations, add or edit take information,
and view your defined locations.
The “Project Locations and Take Information” page will first prompt you to “Add New
Location” and this will allow you to provide more information about where you will be
working, based on the results of your PAG.
Once you have entered one or more locations, the lower part of the “Project Location and
Take Information” page will display them. You will then have the option of adding
another location, editing or deleting a location, or adding/editing the take information for
a location. You will use the “Take Information” page to describe the species you will
encounter and the procedures you will conduct at each location.
How to Add a New Location
Follow these sequential steps to add location information:
1) Add New Location : Click on this button to add a location and enter that location
information. This will take you to a “Project Location Information” page.

20

You must enter multiple locations if you will be working in different
places (e.g., multiple oceans or rivers). You will enter each location
separately and each will have an affiliated take table.

2) *Select the general area: Next, use the drop-down menu to choose a general area
where you will be working (this may be automatically populated based on
information in the PAG). You can only enter one general area at a time.
Note: If you are requesting to receive or import/export parts of animals, select
the “Parts” option as your location and enter country of import/location of
sample origin, and to where samples will be shipped/exported in the location
details section.
If you are requesting to work with captive animals, including those in
rehabilitation, select the “Captivity” option as your location and enter names of
captive facilities in the location details section. You will provide more details in
the “Captive Information” section, described above.
Please note that NMFS does not have jurisdiction in the territorial waters of
another country and therefore cannot authorize the take of protected species in
those waters. For U.S. citizens, activities beyond territorial waters are considered
to occur on the high seas and need coverage by a NMFS permit.
3) *Select the state(s): If applicable, this second drop down menu will be visible.
Choose all applicable states for the general area by holding down the Control key and
clicking on all applicable states.

If the correct geographic choices do not show up, please contact the
Permits Division at 301-713-2289.

4) Enter Location Details : Click this button. Enter information on this page as it
applies (disregard any non-applicable fields). Use the “Location Description” box
(up to 255 characters) to briefly describe your study for each take table. Information
on this page includes:
• Under “Waterbody,” enter names of rivers, estuaries, bays, etc.
• Latitude and longitude of your study area
• River miles (“Begin Mile” and “End Mile”)
• Limits of your study area (e.g., to the U.S. EEZ, to the edge of the
continental shelf, to 50m depth)
21

•

Names of land masses where research will occur (e.g., islands, rookeries)

5) Attach File: Click on this link to attach maps or other information to provide
detailed descriptions about the locations where you will be working. If you have
multiple study areas and species, identify species locations on a map. Formats such
as PDF files, MS Excel, MS Word, and Word Perfect are acceptable. The attachment
may not be larger than 10 MB. If you have a larger document and cannot reduce the
size, please fax this document to the Permits Division at 301-427-2521.
6) You may enter all the locations where you are requesting to work at one time, and
then go back to enter the takes associated with those locations; or, you can enter a
location and go straight to entering the takes for that location.
How to Edit or Delete a “currently defined” Location
1) Edit/Delete Location : From the “Project Locations and Take Information” main
page, click on this button to edit location information you entered or to delete a
location.
2) This will take you to the “Project Location Information” page. Here you can edit any
information previously entered on this page. Select “save” to save your changes.
3) Delete Location : Clicking on this button will delete the location specified on the
“Project Location Information” page. A pop up box will ask if you want to delete.
Click “OK” to delete and “Cancel” to cancel the deletion.

0 Deleting a location will also delete all associated takes (if
entered) with that location. You will get a warning message to
confirm that you want to delete a location.

Take Information Pages
Overview
•

Edit/Add Take
: You may access this button from the “Project Locations
and Take Information” main page or from the “Project Location Information”
page. Click on this button to go to the “Take Information” page. You may also
click on the “Next >” link from the “Project Location Information” page to get to
the “Take Information” page.

•

On this page you will enter the species to be taken, by age and sex class, the
number of individuals, methods (e.g., capture, intrusive procedures), and sample
dates (See Entering Take Information section below).
22

Note: All data fields in the take table require entries and the information must be
specific to the location listed at the top of the page. If you have more than one
location, each location will have a separate take table. Save your data often so
that information is not lost.
•

The “Take Information” page has three parts:
ƒ The top of the page identifies which location you are working on;
ƒ The middle has editing tools (buttons) that allow you to add, edit, delete,
copy, and re-organize take records in the take table; and
ƒ The bottom has the take table.

•

You will create a separate record row for each unique combination of species,
production type (wild or captive), life stage, take action, capture method, and
procedures.

•

The take table is a very large landscape format. Depending on the size of your
screen you may need to use the right and left scroll arrows to complete the table.

Take Table Editing Tools (Buttons)
Editing buttons above the take table appear in the following order:
1) Add More Lines : Clicking this button allows you to add more lines (rows) to
the take table. You can only add more lines if at least one row contains data.
2) Edit Selected Records : Use this to “unlock” or “unfreeze” selected rows in the
take table so that you can edit information you have previously entered and saved.
You must first put a check in (click on) the “Select” box at the far left of each row
you want to edit. Click on the Save button to save your edits.
3) Delete Selected Records : Clicking on this button allows you to delete selected
take rows from this location. You must first put a check in (click on) the “Select”
box at the far left of each row you want to delete. Click on the Save button to
save your edits.
4) Copy Selected Records : This tool allows you to copy selected take records to
the current location, another location within the same general area, or a location in
a different general area. You must first put a check in (click on) the “Select” box
at the far left of each row you want to copy.
Note: The “Copy Selected Records” function is useful if you are conducting the
same activities on multiple species (e.g., enter all the procedure information for
one species, copy that row, and then edit the record as needed).

23

5) Clicking on the Copy Selected Records button will open a new window. You
may choose to go to a new location (i.e., a separate take table) after you copy
the records or stay at the location you are in by selecting those radio button
options in the “Copy Take Records” pop up window.
a) If you copy the takes within the current location, you will make
duplicate copies of the selected rows. The copied records will appear
at the bottom of the take table. You must make some changes to the
copied rows or you will receive a “duplicate records” error message.
b) If you copy the takes to a new location (e.g., a state) within the
same general area (e.g., Atlantic Ocean), the information you have
entered will be saved, you will be taken to a new location information
page, and all the take information from the previous location will
already be entered. In order to distinguish the new location from other
locations, you must make sure that at least one of the location
descriptors is unique.
c) If you copy the takes to a new location in a new general area (e.g.
Atlantic Ocean to Pacific Ocean), you will be taken to a blank location
page. Once you enter the location information and click the
Edit/Add Take button, you will go to the “Take Information” page
and you will see all the takes you copied from the previous location.
d) If you copy the takes to another location you have already created,
you will be taken to that location page and all the take information you
copied from the previous location will already be entered. The records
will appear at the bottom of the take table.
6) Copy All Records : This function allows you to copy all take records to the
current location, a new location within the same area, a new location outside the
area, or to another location you already created. See the information in the “Copy
Selected Records” section above for more details about the options.
Note: You may choose to go to the new location after you copy the records or
stay at the location you are in by selecting those radio button options in the “Copy
Take Records” pop up window.
7) Re-number lines : Each line in the take table is numbered. If you delete one or
more records, click this button to re-number the remaining lines consecutively.
This tool also re-orders the rows alphabetically by species’ common name and
population name.

24

8) Edit Location : Clicking on this will take you back to the “Location
Information” screen for editing (effectively “unlocking” the location in the top
portion of the page).
9) Save : This button saves all edited or updated take information. Save often in
case of interruption or computer problems, and save before navigating to another
page.
10) Export to Excel : This button allows you to export your take table to Microsoft
Excel.
Entering Take Information
The take table represents annual takes for the duration of your project. The takes you
enter for this location are displayed in a table in the lower part of the page. If you have
not entered any take information, the table is blank (except for automatically entered
begin and end dates). You must enter at least one row for every location. Enter the
following information to add takes for each location in the application.
Note: The options that appear in the dropdown menus in the take table are based
on the species group (e.g., marine mammals) you indicated in the PAG, the
location that you have selected, and the individual species that you select. If you
are having difficulties, please first check that the previous fields were entered
correctly. See Appendix VII for a list of the options that appear in the take table
drop down menus.
Columns in the take table appear in the following order:
1) Select: Leave this box blank unless you need to copy, move, or delete the line
following the instructions above.
2) Line: Each line in the Take Information section is automatically numbered. If
you make changes to the take table (e.g., delete a line), you may renumber the
lines in consecutive and alphabetical order following the instructions above.
3) Species: Use the drop down list to select one species. Species are listed
alphabetically by common name and/or category (e.g., whale, sperm). If the
species you are looking for is not on the drop-down menu, double check your
location (species are populated based on location). If you are still having
problems, contact the Permits Division at 301-713-2289.
Note: For a complete list of species, click on the “Species Lists” link on the left
side of the “Project Location” page (you will have to navigate back to the “Project
Location” page).

25

4) Listing Unit/Stock: Depending on the species selected in the previous field, this
field will display those listing units or stocks that are in the location in which you
are working. Use the drop-down list to select a “Listing Unit/Stock.” Choose
“Range-wide” if, for example, your location has multiple stocks of the same
species and you cannot distinguish between them while in the field; or, for
example, if you are importing specimens from locations worldwide. Do not select
“Range-wide” for ESA-listed species whenever possible.
5) Production/Origin: Use the drop-down list to select a “Production/Origin.”
Available categories include “wild” and “captive,” and for marine mammals,
“rehabilitation facility.” If you will be entering take information for more than
one type of Production/Origin, you will need to enter a separate row for each one.
6) Life Stage: Use the drop-down list to select the applicable life stage. 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.
7) Sex: Use the drop-down list to select a sex. 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.”
8) Expected Take: This represents the number of animals you expect to take or
import, annually. Enter the number of animals you expect to capture, observe,
etc. for the “Take Action” you select. For actions where a number is difficult to
determine (e.g., abalone spawning, import/export of parts), contact the Permits
Division at 301-713-2289.
9) Indirect Mortality: This column is inactive. You may enter indirect mortality
numbers associated with all take actions by choosing “Unintentional Mortality”
as a separate “Take Action” on a separate row in the take table.
10) Takes Per Animal: Indicate the number of times an individual will be subject to
the take actions, etc., annually. See Appendix VIII for more guidance.
11) Take Action: Use the drop-down list to select the type of action. The “Take
Action” is a generalized overview of how animals will be taken. Select only one
action. If more than one action is proposed, you must enter the takes on separate
rows.
12) Observe/Collect Method: Use the drop-down list to select the method of
observation (e.g., survey, vessel) or capture (e.g., net). Select only one
observe/collect method per row. If various methods will be used, you must
provide take information in separate rows for each observe/capture method.
Note: You can use the Copy Selected Records button to duplicate takes within
this location (see above for directions).

26

13) Procedures: This field is where you provide specific information on the research
or enhancement activities that will be conducted. A separate pop-up window will
appear with a species-specific list of activities. Hold down the Control key to
select all activities to be performed concurrently. Choose “Other” if your
proposed activity is not listed. In the “Details” box (see below), briefly describe
what the “Other” means.
Note: The procedures list includes both intrusive activities such as “insert
ingestible telemeter pill” and non-intrusive activities such as “observations,
behavioral,” “photo-id,” and “acoustics, passive recording.”

Refer to Appendix VII for a complete listing of “Take Actions,”
“Observe/Collect Methods” and “Procedures” by species groups.

14) Run: For fish species, use the drop-down menu list to select an appropriate run,
as applicable. Otherwise, select N/A.
15) Transport : If you will be transporting live animals during your research or
enhancement activities and chose “transport” as a “Procedure,” clicking on this
button will allow you to enter information about the transport. Click on the this
button to enter or edit the information.
In the “Transport Information” window, you have the option to select a transport
location from information you previously entered. If you have not previously
entered transport information or you need to enter a new transport record, click on
the “click here” link to go to the “Transport Information” window. All of the
fields on this page are required.
a) *Mode(s) of transportation: Describe the mode of transportation. Include a
description of 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 animal(s) 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.

27

e) *Any special care procedures (e.g., moisture, medicines, aeration) 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 species 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, classroom, 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 fish
will be released, sacrificed, or deposited in a museum collection (e.g., “Retain
alive for six months, then release”; “Sacrifice for tissue analysis.”).
j) When you have completed all nine fields, click the Save button to save the
information and go back to the “Transport Information” box. When you have
entered all the transport information for your application, save and return to the
“Take Information” page.
16) Begin Date: This field is populated with the “Begin Date” you entered on the
“Project Information” page. The take table represents annual takes within the
overall project duration. You may change the date to coincide with a specific
project time shorter than the overall duration of the project. You cannot enter a
date that is earlier than the “Begin Date” you entered on the “Project Information”
page.
17) End Date: This field is populated with the “End Date” you entered on the
“Project Information” page. The take table represents annual takes within the
overall project duration. You may change the date to coincide with a specific
project time shorter than the overall duration of the project. You cannot enter a
date that is later than the “End Date” you entered on the “Project Information”
page.
18) Details: You may enter up to 255 characters in this text box to provide details on
each take table row. For example, if you chose “instrumentation, external” as a
procedure, use this box to describe what type of instrument you will be deploying
(e.g., satellite tags).

28

19) When finished entering and saving take information, either click on “Next >” to
take you back to the location page for any final location editing or adding new
location and take information; OR, go to the breadcrumbs on top of the page and
click on “NEPA.”

National Environmental Policy Act (NEPA) Considerations Page
You are required to answer all five questions on this page. Please answer each question
completely. “Yes” or “no” are not sufficient answers and your application will be
considered incomplete. When you are finished, click the “Next >” link.
1) Will your activities involve equipment (e.g., scientific instruments) or techniques
that are new or may be considered experimental or controversial? If yes, are they
likely to be adopted by other researchers in the future?
2) Do your activities involve collecting, handling, or transporting potentially
infectious agents or pathogens (e.g., biological specimens such as blood)? Do your
activities involve using or transporting hazardous substances (e.g., toxic
chemicals)? If yes, provide a description of protocols you will use to ensure humans
are not infected or injured.
3) Do any of your activities occur in or near unique geographic areas such as state or
National Marine Sanctuaries, Marine Protected Areas, Parks or Wilderness Areas,
Wildlife Refuges, Wild and Scenic Rivers, designated Critical Habitat for
endangered or threatened species, Essential Fish Habitat, etc.? If yes, would any
aspect of your activities impact the physical environment, such as by direct
alteration of substrate (e.g., by bottom trawling, net setting, anchoring vessels or
buoys, erecting blinds or other structures, disrupting nesting bird habitat)?
4) Could your work affect sites listed in or eligible for listing in the National Register
of Historic Places? Could your work cause loss or destruction of scientific, cultural,
or historic resources (e.g., archeological resources)? If yes, list the sites and explain
how they might be affected or why they would not be affected.
5) Could any of your activities, intentionally or not, involve the transport any
materials, biological or otherwise, from one area to another (e.g., transporting
animals or tissues, discharging ballast water, working in sensitive remote areas)? If
yes, explain the types of activities. Describe all 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).

Project Contacts Page
On this page you will enter information about the people who will be responsible for
overseeing the project and others who will be working under the permit. As the person
entering the application, you will automatically be assigned the following roles:
29

Applicant/Permit Holder, Principal Investigator, and Primary Contact. See the
directions below for how to change who is assigned to these roles.
The following table and Appendix II explain the differences between the personnel roles.
Note: The Applicant, Principal Investigator, and Primary Contact can be the
same person.
Able to
make
changes to
application
Yes
Applicant/Holder
Responsible
Party
Yes

Principal
Investigator
Primary Contact
Co-Investigator
Other personnel
(e.g., Research
Assistants)

Must be
named in the
permit
application
Yes
Yes (only if
Holder is an
entity)

CV, resume, or list
of qualifications
required
Yes
No (If they are
participating in the
research they should
also be listed as a
Co-investigator)

Receive
automatic
emails from
APPS
Yes

Can request
modifications
and submit
annual reports
Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes
No

Yes
Yes

No
Yes

Yes
No

Yes
No

No

No

No

No

No

To change the person assigned to the Applicant/Permit Holder, Principal Investigator,
Responsible Party, and Primary Contact roles, click the Change button next to the
name. This action will open the “Contact Search” window. To prevent duplicate entries,
you MUST ALWAYS search the database for the person before entering a new
contact.

30

Use the following steps to search:
1) Enter the person’s last name.
2) Click Search for Contact .
3) If the person is listed in the search results, click the Select button to add them to your
application.
4) If too many entries are returned, you may enter additional information about the
person, and click Search for Contact again.
5) If the search did not find the person you want to add, click Create New Contact .
6) You will be prompted to enter the person’s contact information. Enter all required
information and save when you are finished.
Note: If you remove yourself as a contact you will no longer have access to the
application.
A project must have a Responsible Party when the Applicant/Permit Holder is an
organization, institution, or agency. The Responsible Party is an official who has the
legal authority to bind the organization, institution, or agency and is ultimately
responsible for all activities of any individual operating under the authority of the permit.
Note: The Responsible Party is most often used when there is a likelihood of
staff changes. For example, permits cannot be transferred from one individual to
another. If the Permit Holder changes, NMFS has to issue a new permit.
However, the Responsible Party role can be transferred to another individual.
Long-term research projects held by public agencies tend to encounter staff
changes and in many cases, NMFS has assigned the Permit Holder role to the
agency. It is up to the applicant to decide if this is appropriate for their project.
To add a Responsible Party, follow the steps above.
In addition to the roles described above, you must add Co-investigators to the
application if the Principal Investigator will not always be present during the permitted
activities. Co-investigators are individuals who are qualified and authorized to conduct
or directly supervise activities conducted under a permit issued for scientific research or
enhancement purposes without the on-site supervision of the Principal Investigator.
Use the following steps to add a Co-investigator:
1) Click on the Add Personnel button.
2) The Contact Search box will open
3) Follow the instructions above for searching and adding a new contact.
4) Once you select a person, click on the Save Personnel button before adding another
Co-investigator.
5) Repeat this process until you have added all Co-investigators.

31

Qualifications and Experience
You are required to submit information about the qualifications and experience of the
Principal Investigator and all Co-investigators. This information can be in the form of a
resume, CV, or simple summary. The documentation you submit must demonstrate the
individual’s qualifications to conduct the activities (e.g., blood sampling) proposed on the
target species and include a list of relevant publications.
To attach documentation, such as a resume:
1) Click the Add CV button next to the person’s name.
2) A pop-up window will appear that allows you to attach a file.
Note: If the person’s CV is already in the APPS system, you will see a file name
under “Selected File;” however, we ask that you still attach your version
because it may be more recent than the one we have on file.
3) Click Browse and locate the file.
4) Click Attach and wait for the file to upload.
5) When finished, click the Cancel button to close the pop-up window.

Resumes and CVs are considered part of an application’s public record and are
available to reviewers and the public. Refer to the Additional Information at the end of
this chapter. Please do not include personal information such as:
• Home address/phone number
• Date of birth
• Social security number
• Nationality
• Marital status
• Salary
As the Applicant, it is your responsibility to notify your Co-investigators that their names
and resumes will be available to the public. When you submit your application, all Coinvestigators will receive an automatic email saying that they have been named on
your application.

32

You may also add personnel who perform other roles (Research Assistants,
Veterinarians, Tissue Sample Disposition) to the application.
To add other personnel:
1) Click on the Add Personnel button.
2) The Contact Search box will open.
3) Follow the instructions above for searching and adding a new contact.
4) Once a person is added, APPS defaults their “role” to Co-investigator.
5) To change the role, click on “Co-Investigator.”
6) Another window will open with a list of roles. Choose the role you want.
7) Click Save.
8) Once the role has been assigned, click on the Save Personnel button before adding
other personnel.
When you are finished, click the “Next >” link to go to the Submit Application page.

Submit Application Page
Before you can submit your application, you must authenticate your identity and certify
that all information in the application is correct. After you click the
Click Here to Submit Application button, an authentication screen will appear.

33

Authentication and Certification
1) Print the following screen and have the Applicant/Permit Holder or Responsible Party
sign and date the page (for personnel definitions refer to Appendix II). If the Principal
Investigator (PI) differs from the Applicant/Permit Holder or Responsible Party then the
PI must also sign and date the page. Signatures will remain on file in the Permits
Division for five years or until you apply for a new permit, whichever comes first.

To print on one page make sure your text size is set to “smaller.”
In Internet Explorer go to “View” then “Text Size” and choose
“smaller.”
2) After you have signed and dated the page, please fax it to the Permits Division at
301-427-2521.
3) Once you have faxed your authentication page, save your application and log off
APPS.
4) A permit analyst will email or call you to confirm receipt of the signature page within
1-2 business days.

34

5) After you are notified that your signature was received by the appropriate office, you
may log into APPS and submit your application by clicking on the
Click Here to Submit Application button. The following certification screen will
appear:

6) You must read and accept the certification statement before your application can be
submitted. If you choose not to accept the statement, your application will not be
submitted and your request cannot be processed.
7) Once submitted, you will receive an automatic email saying that you have
successfully submitted your application.

Project Status
Once an application has been submitted, the “Project Status” page will track the progress
of the application. This screen will display which analysts have been assigned your
application and where your application is in the review process. From the “Project
Overview” page, click on the “Application Preview” link. From this page you can access
the “Status” page. Click on the “+” next to “Status” to open that page (see below).

35

Application Preview Screen

36

Requesting a Modification
This section of APPS allows the Applicant, Principal Investigator, and Primary Contact
to request changes to the issued permit.
Note: The Director, Office of Protected Resources, may amend or modify
scientific research and enhancement permits in response to or independent of a
request from the Permit Holder. Amendments and modifications are subject to
additional analyses under NEPA and the ESA.
Requests to modify the following permit specific conditions may require a new 30-day
public review and comment period:
•
•
•
•
•

changing the species to be taken or imported/exported;
increasing the number of animals to be taken or imported/exported;
changing or adding locations;
changing methods; and
extending the expiration date.

Other requests such as changing personnel or allowing a film crew to accompany the
researchers may be authorized without public review.
To begin, log in to your portfolio and open the submitted or issued permit that you would
like to modify by clicking on the “file number” link. At the top of the page, you will see
a series of links including “Request a Modification.” Click on this link to open the “New
Modification Request” page (see below).

37

New Modification Request Page

38

Modification Request Questions
1) What changes are you requesting? (Select all that apply)
On the first page of the “New Modification Request” window, you must check the type(s)
of modification(s) you are requesting. You have the following list of options:
• Edit/Add Location
• Edit/Add Take Information
• Edit Personnel
• Permit Extension for a year or less
• Authorization to allow a film crew to accompany researchers
• Change Study Objectives/Hypotheses
• Other
Your selections will dictate which fields are available for you to edit on the screens that
follow. For example, if you select “Edit/Add Take Information” you will only be able to
modify the take table. If you decide that you need to change other parts of the permit,
you will have to return to this screen and check those options.
2) Provide a Title for your request (up to 255 characters)
Describe the modification as concisely and descriptively as possible. Be sure to enter a
modification title before logging out of the system.
3) Describe your request (no text limit)
A request to modify an issued permit should address the pertinent sections of these
instructions relevant to the requested change. Your request should include the
following information, as applicable. See corresponding sections of application above
for information required under each category below. Disregard those that do not apply to
your modification request.
•
•
•
•
•
•
•
•
•
•
•
•

Brief narrative summary
Research timeframe and sampling season/project duration
Literature review
Purpose: hypothesis/objectives and justification (also include a report of takes
used annually to date when requesting a take increase)
Project description (include specifications for changes in methods or gear,
such as tags)
Status of the affected species (if requesting a change in species)
Lethal take (intentional or unintentional)
Anticipated effects on animals
Measures to minimize negative effects
Resources needed to accomplish objectives
Captive information
References
39

•
•

For personnel changes, include qualifications/experience in each take activity
For filming authorizations, include who (names and roles of crew), what,
when, where, why, how, and products that will be developed.

Notes: If requesting a change in authorized take, please make sure to select
“Edit/Add Take Information” and edit your take table within APPS. Do not
provide a separate take table when attaching a file.
For changes in field equipment or study areas, we highly recommend that you
attach figures, maps or illustrations drawn to scale.

4) Attach a file (Optional):
If you need to attach figures, maps, or other supporting documents please attach a file.
To open the attachments window, click on the “Select File” button. Within the
attachments window, you will click on the “Browse” button, and then navigate to the
directory containing the file you wish to attach. After locating the file, click the “Attach”
button. You can attach more than one document from this window. When you have
finished attaching files, click the “Cancel” button to return to the modification request
form. If you are making substantial or complex changes to your permit, your attachment
should contain enough detail in order for reviewers to understand your request.
Click “Next >” to proceed.

Modification Types
Edit/Add Location
If you selected this option, you will see the “Modification Locations and Take
Information” screen. Currently defined locations are displayed in the lower half of the
screen. For instructions on adding locations and take information, see the “Project
Locations and Take Information” section above. There is no limit to how many locations
you can add.
To increase your action area by adding states to your action area, click on the “Change
area or state” button.
To add a new location, click on the “Add new location” button.
To edit or delete an existing location, select the location and click on the “Edit/Delete
location” button.
When you have completed changes to the location information, and if you have no other
edits, you can submit your modification request. Click the “Next>” link at the top right

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of the screen. You should now see the “Submit Modification Request” screen. You are
encouraged to preview your modification before submitting.
Edit Take Information
This option allows applicants to request a modification to the take table. Some of the
typical types of modification requests include the addition of new methods, an increase in
the number of animals taken, and the addition of new species. You may edit any part of
the take table. See the “Take Table” section above for instructions on required
information in the table.
When requesting an increase in the number of animals to be taken, make sure that you
request the total number of animals to be taken (i.e., the number of takes you are
currently authorized plus your proposed increase). Please note that requests for increases
in take of species/stocks currently authorized by the permit must demonstrate valid
justification, including a reporting of how many authorized takes you have used.
Requests that do not provide this information may be considered incomplete. Provide
justification in the “Describe your request” text box or by attaching a supporting
document.
To request to remove/delete existing take records, first check the “Select” box to the left
of the record you wish to delete, then click the “Delete selected records” button near the
top of the page. A pop-up notice box will appear that indicates that the record will still
appear in the table but is marked for deletion.
To request to modify existing take records, first check the “Select” box to the left of the
record you wish to modify, then click the “Edit selected records” button near the top of
the page. The take table should refresh with an editable copy of the original record with
the next consecutive version number. For example, if you selected line number 2 to edit,
the copied record should be line number 2, version A. Then, make the changes you
would like to the record.
When you have finished entering the edits, additions, and deletions you want to request,
click the “Save” button and then the “Next>” link. You will be taken to the “Location”
page where you can then proceed to another location for which modifications are needed
or submit your application.
Edit Personnel
Refer to the “Project Contacts” section above for instructions on editing personnel
information. The process for searching and adding contacts for modifications is the
same. When using the search function, be sure to exhaust your search (i.e., start out with
a generic search before getting too specific so that duplicate contacts are not created).
To request removal of a contact, check the box labeled “remove” to the right of the
contact’s role.

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Note: To add personnel you must attach a CV or resume for each person.

Resumes and CVs are considered part of an application’s public record and are
available to reviewers and the public. Refer to the Additional Information at the end of
this chapter. Please do not include personal information such as:
• Home address/phone number
• Date of birth
• Social security number
• Nationality
• Marital status
• Salary
As the Applicant, it is your responsibility to notify your Co-investigators that their names
and resumes will be available to the public. When you submit your modification, all Coinvestigators will receive an automatic email saying that they have been named on
your application.

Permit Extension for a year or less
If you wish to apply for a permit extension, check this box and include your proposed
extended expiration date and justification in the description of your request.
Authorization to allow a film crew to accompany researchers
If you wish to apply for an authorization to allow a film crew to accompany you during
research, check this box and provide information on who will accompany you (i.e.,
production company, names and roles of the crew), where and when filming would occur,
and the purpose of the filming (e.g., documentary on humpback whales).
Change Study Objectives/Hypotheses
If you wish to modify the study objectives/hypotheses, check this box and include the
new objectives/hypotheses the description of your request.
Other
If you check this box, please explain the modification in the description of your request.

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Submitting Your Modification Request
After moving through all of the applicable windows, you may submit your request using
the “Next >” links or click the “Submit” link near the top of the page. A window should
appear that suggests you review your request before submitting. IMPORTANT: You
must click the Click Here to Submit Modification button on this page to submit your
application. Once submitted, you will receive an automatic email saying that you have
successfully submitted your application. A permit analyst will contact you regarding
your submitted application.
Call the Permits Division at 310-713-2289 if you need assistance.

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Additional Information
Under section 104(c) of the MMPA and section 10(a)(1)(A) of the ESA, persons may be
authorized to take marine mammals and threatened and endangered species, respectively,
for purposes of scientific research or enhancing the survival of the species. Interested
persons are required to submit an application in accordance with the Acts and the
implementing regulations at 50 CFR part 216, subpart D, and 50 CFR part 222. These
instructions for applying for a research or enhancement permit are drawn from, but do not
substitute for, ESA regulations and MMPA regulations. These regulations are available
at the following web site: http://www.gpo.gov/. MMPA section 104 is available at:
http://www.nmfs.noaa.gov/pr/pdfs/laws/mmpa104.pdf. ESA section 10(a)(1)(A) is
available at: http://www.nmfs.noaa.gov/pr/pdfs/laws/esa_section10.pdf.

Paperwork Reduction Act Statement
The information requested in this application is required and is used to determine whether
the activities described in the application are consistent with the purposes and policies of
the Acts and their 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 Conservation and Education 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 amendments, 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 Control No. 0648-0084
Expiration Date: 09/30/2009

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