4.4.9.3 endangered and threatened species · the endangered species act (esa) (87 stat. 884, as...

4.4.9.3 Endangered and Threatened Species

4.4.9.3.1. Introduction

4.4.9.3.2. Section Objectives

4.4.9.3.3. DOT Policy

4.4.9.3.4. Legal Basis

Abstract of Law/Regulation

Other Related Regulations

4.4.9.3.5. General Methodology Analysis and Evaluation

State Endangered and Threatened Species

Federal Endangered and Threatened Species

Procedures for Federal Actions

Procedures for Non-Federal Actions

4.4.9.3.6. Interagency Coordination and Agreements

4.4.9.3.7. Project Development and Construction Guidance

Project Scoping Stage

Preliminary Design (Phases I-IV)

Final Design (Phases V & VI)

Construction Considerations

4.4.9.3.8. Operations Guidance

Emergency Procedures

NYSDOT-Issued Permits

Location-Specific Considerations

4.4.9.3.9. Flow Charts

State Endangered and Threatened Species Process

Federal Section 7 Endangered and Threatened Species Process – FHWA as Federal

Action Agency

Federal Section 7 Endangered and Threatened Species Process – Federal Action

Agency Other Than FHWA

4.4.9.3.10. Local Projects Guidance

4.4.9.3.11. Appendices

A. Legal Citation

B. Scope of Services

C. Definitions

D. References

E. Contacts

F. Sample Statements

G. FHWA ESA Section 7 Process (Issued via EB 17-024)

H. Coordination Regarding Waterbodies Supporting S1 or S2 Mollusks (Issued via

EB 18-010)

https://www.dot.ny.gov/divisions/engineering/environmental-analysis/manuals-and-guidance/epm/repository/4.4.9.3_AppG_FHWA_ESA_Section_7.pdf

https://www.dot.ny.gov/portal/pls/portal/mexis_app.pa_ei_eb_admin_app.show_pdf?id=12436

https://www.dot.ny.gov/divisions/engineering/environmental-analysis/manuals-and-guidance/epm/repository/TEM%204.4.9.3%20APPENDIX%20H.pdf

https://www.dot.ny.gov/portal/pls/portal/MEXIS_APP.EI_EB_DOC_DETAILS.show?p_arg_names=doc_id&p_arg_values=12762

ENDANGERED AND THREATENED SPECIES

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August 2011 TEM 4.4.9.3

4.4.9.3.1 Introduction

Federal and state laws protect certain species of plants, fish, and wildlife that are listed orproposed for listing as endangered or threatened, as well as their designated critical habitat. Toensure compliance with these laws, and to secure project approval, staff should determine if anaction will affect a protected species or its habitat, assess the severity of those effects, and ifnecessary, incorporate measures to address impacts.

This involves: 1) determining whether or not the action requires endangered/threatened speciesreview; 2) reviewing the U.S. Fish and Wildlife Service county list and the NY Natural HeritageProgram (NYNHP) database as an initial screening for applicable projects; 3) determining thetype and significance of the Natural Heritage record; 4) conducting a habitat assessment and fieldsurvey to determine the likelihood of occurrence of an endangered or threatened species in theproject area; 5) determining the potential effect of the project on a listed or proposed species; 6)evaluating avoidance, minimization and mitigation measures; and 7) agency coordination asnecessary. This process should be completed prior to Design Approval.

State and federal agencies play important roles in the regulatory process. Agencies havingregulatory responsibility for endangered and threatened species are:

NYS Department of Environmental Conservation (NYSDEC) (state listed species) U.S. Fish and Wildlife Service (USFWS) (federally listed non-marine species) National Marine Fisheries Service (NMFS) (federally listed marine species) Federal Action Agency for the proposed action (federally listed species)

Table 1. Endangered / Threatened Species Agency Coordination by NYSDOT Region

State Listed Species:NYSDEC coordination

Federally listed Species:USFWS and Federal Action

Agency coordination

Federally listed Species:NMFS and Federal Action

Agency coordination

NYSDOTRegion

All regions All regions 1, 8, 10, 11

Throughout this discussion, the term "Services" will be used to generically refer to both USFWSand NMFS. However, this is not meant to imply that all actions discussed herein are taken bythe Services jointly.

4.4.9.3.2 Section Objectives

This section outlines procedures for compliance with state (State Endangered and ThreatenedSpecies Subsection) and federal (Federal Endangered and Threatened Species Subsection)endangered species regulations.


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4.4.9.3.3 DOT Policy

It is the policy of NYSDOT to avoid and minimize to the greatest extent practicable, all impactson endangered and threatened animal and plant species and the habitat on which they depend.

4.4.9.3.4 Legal Basis

Abstract of Law/Regulation

Federal Endangered Species Act

The Endangered Species Act (ESA) (87 Stat. 884, as amended; 16 U.S.C. 1531 et seq.) waspassed to protect and recover imperiled fish, wildlife and plant species and the ecosystems uponwhich they depend.

Section 9 of the act prohibits the taking of any federal endangered animal species by any entity,public or private, regardless of federal agency involvement. This prohibition generally has beenapplied by regulation to threatened species as well, unless there are special rules that provideexemptions, or some other alternative approach (see 50 C.F.R. Parts 17 and 227). Theprohibition does not apply to plant species, except that it is illegal under Section 9(a)(2) toremove an endangered plant from federal land, or to take an endangered plant in knowingviolation of State law.

Section 7 of the ESA requires federal action agencies to use their legal authorities to promote theconservation objectives of the ESA and to consult with the USFWS and NMFS, as appropriate,to ensure that effects of actions they authorize, fund, or carry out will not jeopardize thecontinued existence of listed species. For the purpose of this consultation, the ESA requires theaction agency to provide the best scientific and commercial data available concerning the impactof the proposed project on listed species or designated critical habitat. The consultation processis divided into informal and formal consultation. The type of consultation required is dependenton the proposed action’s level of impact. Actions that may affect species that are proposed forlisting are coordinated through the similarly-structured “conference” process.

Informal consultation determines the likelihood of adverse effects on a listed species or criticalhabitat. Informal consultations:

identify the nature and extent of the effects of federal (agency) actions on listed species andcritical habitat;

identify adverse effects and suggest ways to avoid them;

resolve project conflicts or differences of opinion between USFWS/NMFS and the actionagency or applicant as to the nature and extent of adverse effects;

provide the action agency with opportunities for carrying out conservation activities pursuantto Section 7(a)(1); and

help monitor cumulative effects on a species or ecosystem.


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Formal consultation determines if an agency’s proposed action is likely to jeopardize thecontinued existence of a listed species or destroy or adversely modify critical habitat. It alsodetermines the amount or extent of anticipated incidental take in an incidental take statement.The USFWS ESA Section 7 Consultation Handbook lists several other functions of formalconsultation including:

identifying the nature and extent of the effects of federal (agency) actions on listed speciesand critical habitat;

identifying reasonable and prudent alternatives, if any, when a proposed action is likely toresult in jeopardy or adverse modification;

providing an allowance for specified levels of "incidental take" otherwise prohibited underSection 9 of the Act;

providing mandatory reasonable and prudent measures to minimize the impacts of incidentaltake to listed species;

identifying ways the action agencies can help conserve listed species or critical habitat whenthey undertake an action; and

providing an administrative record of effects on species that can help establish the species'environmental baseline in future biological opinions.

Conference is a process of early interagency cooperation involving informal or formaldiscussions between a federal action agency and the Services regarding the likely impact of anaction on proposed species or proposed critical habitat. Conferences are:

required for proposed federal actions likely to jeopardize proposed species, or destroy oradversely modify proposed critical habitat;

designed to help federal agencies identify and resolve potential conflicts between an actionand species conservation early in a project's planning; and

designed to develop recommendations to minimize or avoid adverse effects to proposedspecies or proposed critical habitat.

Article 11 of the New York State Environmental Conservation Law

The Environmental Conservation Law (ECL) Article 11 Title 5, and its implementing regulationsin 6 NYCRR Part 182, protects endangered and threatened species of fish, shellfish, crustacea orwildlife by prohibiting the taking, importation, transportation, possession or sale of any suchspecies, or hides or other parts thereof, or the sale or possession with intent to sell any articlemade in whole or in part from the skin, hide or other parts of any such species, except underlicense or permit from the NYS Department of Environmental Conservation. The law alsodefines species of special concern as those at risk of becoming threatened. While such specieswarrant attention and consideration, they are afforded legal protection only insofar as otherwildlife are protected; they cannot be taken except as permitted by law or byregulation/permit/license.


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Article 9 of the New York State Environmental Conservation Law

The Environmental Conservation Law (ECL) Article 9 Title 15, and its implementing regulations

in 6 NYCRR Part 193, protects species of plants that are listed as endangered, threatened, rare, or

exploitably vulnerable by prohibiting any person from collecting or destroying any such species

without the consent of the landowner.

Other Related Regulations

The federal Magnuson-Stevens Fishery Conservation and Management Act Section 305(b)(2)

requires an Essential Fish Habitat (EFH) consultation with the National Marine Fisheries Service

for any action or proposed action authorized, funded, or undertaken by a federal agency that may

adversely affect EFH.

The federal Fish and Wildlife Coordination Act includes provisions that require consultation with

the Fish and Wildlife Service when waters will be impounded, diverted, or otherwise controlled

or modified by any agency under a federal permit or license. The Service may recommend that

the permit/license be granted, with or without additional permit conditions, or recommend denial

of the permit/license depending upon potential adverse impacts on fish and wildlife resources

associated with project construction or implementation.

The federal Migratory Bird Treaty Act implements the treaties that the U.S. has signed with a

number of countries protecting birds that migrate across international borders. It makes illegal

the taking, possessing or selling of protected species, which includes those species of migratory

birds that are native to the U.S. or its territories.

The federal Bald and Golden Eagle Protection Act provides for the protection of the bald eagle

and the golden eagle by prohibiting, except under certain specified conditions, the taking,

possession and commerce of such birds. Bald and golden eagles are afforded similar protection

under NYS Environmental Conservation Law Article 11 Title 5. The Bald and Golden Eagle

Protection Act and Migratory Bird Treaty Act continue to provide protection for the bald eagle

despite their removal from the federal list of endangered ad threatened species on 8/8/2007.

4.4.9.3.5 General Methodology Analysis and Evaluation

The state and federal review processes for endangered and threatened species are presented

separately in this guidance. However, the processes are typically carried out concurrently, and

the state and federal screening steps may be accomplished in a single effort.

It is important to note that all federally listed species are also state listed. Therefore, when

federally listed species are present completion of both processes, federal and state, is required.

Agency coordination for these species may be carried out concurrently, but differences between

the federal and state regulations prevent them from being combined into a single process.

2018 Update: Follow the procedures outlined in “Appendix H: Coordination Regarding

Waterbodies Supporting S1 OR S2 Mollusks” for projects requiring a Water Quality

Certification and located on S1/S2 waterbodies.




August 2011 TEM 4.4.9.3

State Endangered and Threatened Species

The following procedures ensure that NYSDOT activities meet the requirements set forth in ECLArticle 11 Title 5 and 6 NYCRR Part 182 for protection of endangered and threatened species ofanimals and their occupied habitat.

State listed plants are not afforded the same level of protection as state listed animals. Inaccordance with ECL Article 9 Title 15 and 6 NYCRR Part 193, protected plants may bedestroyed with permission of the landowner, thus agency coordination is not necessary.Regardless, when protected plants are identified during screening, a concerted effort should bemade to avoid and minimize impacts to them.

Unless stated otherwise, the following steps are to be undertaken by the Regional Endangeredand Threatened Species Contact, other qualified Department staff, or the project consultant.Correspondence with outside agencies (e.g., effect determination letter) is typically signed by theRegional Environmental Unit Supervisor or designee.

Step S1. State Species Screening (Project Scoping Stage)

S1.a. Identify the limits of the project action area. Apply the screening distances found in Table2 to the project action area boundary to determine the extent of the screening area. Whenevaluating multiple project alternatives, the action area should be identified separately foreach, although the screening may be conducted simultaneously. Continue to S1.b.


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Table 2. NYNHP Data Screening Distances (measured from project action area boundary)

General screening for NYNHP records of listed species and/or known habitat:

1.5 mi radius (projects within DOT Regions 1, 2, 3, 4, 5, 6, 7, 9)

0.5 mi radius (projects within DOT Regions 8, 10, 11)

Species-specific screening for NYNHP records of:

Indiana bat 2.5 mi radius (maternity colonies),

5 mi radius (documented mist net captures, if no known maternitycolonies)

40 mi radius (hibernacula)

bog turtle 1 mi radius

Blanding’s turtle 0.6 mi radius

timber rattlesnake 1.5 mi radius

tiger salamander variable (coordination with NYNHP/NYSDEC recommended)

aquatic species 2 mi downstream (if the action has a potential to affect water quality,level, or flow)

S1.b. Review the NY Natural Heritage Program database for known and potential occurrencesof rare species and rare/significant ecological communities in the screening area. Staffperforming this screening must first receive training in the use and interpretation ofNYNHP data. The Main Office Environmental Science Bureau may be contacted for acurrent list of trained individuals or to request training. NYSDOT consultants are noteligible to access Natural Heritage data through the Department’s data sharing agreement.Screenings conducted by consultants must either be accomplished through coordinationwith NYNHP or through the consulting firm’s own data sharing agreement.

If the NYNHP data indicates presence of a rare/significant ecological community, reviewthe NYNHP online conservation guides and other available published information todetermine whether or not the community may provide habitat for listed species. Note thatthe communities themselves are not directly regulated.

Review the New York State Breeding Bird Atlas, Amphibian & Reptile Atlas, and FloraAtlas to determine if any state listed species belonging to these taxa have beendocumented or may occur in the screening area.

If the screening yields no known/potential occurrences of listed species and norare/significant ecological communities that may provide habitat for listed species,then the State review is complete. Document the negative screening result in theInitial Project Proposal/Final Design Report or Project Scoping Report.


August 2011 TEM 4.4.9.3

If the screening yields known/potential occurrences of listed species orrare/significant ecological communities that may provide habitat for listed species,document this in the Initial Project Proposal/Final Design Report or Project ScopingReport. Continue to Step S2.

Step S2. Habitat Assessment (Preliminary Design: Phase I)

If the NYNHP database includes potential occurrences within the project action area, begin atS2.a, otherwise go to S2.b.

S2.a. Determine whether or not any potential occurrences can be discounted. A potentialoccurrence may be discounted if there is an absence of occupied habitat in that location.This determination is based on correspondence with NYSDEC and NYNHP as well asreview of available information including maps, aerial photos, reports, personal accounts,historic land use change, etc. Factors to consider may include, but are not limited to:habitat conversion or severe degradation subsequent to the last documented occurrence;imprecise location information; or recent appropriate surveys that failed to confirm thespecies.

S2.b. Conduct a habitat assessment for all state listed species having known occurrence withinthe project action area, and for any potential locations that could not be discounted in S2.a.Review available published information on habitat requirements of the species in question,as well as any additional desktop resources that may assist in making a determination ofhabitat suitability, such as topographic maps, county soil surveys, and aerial photography.

On-site field investigation is typically necessary to verify the presence or absence ofsuitable habitat, although there may be cases where a review of desktop resources alonewould yield a reliable habitat assessment (e.g., species with a distinct range or habitattype). Several habitat assessment forms are available to assist in conducting the fieldinvestigation (see Appendix D). Further assistance may be obtained by contacting theNYSDEC Regional Wildlife Manager or NYNHP.

If the habitat assessment concludes that suitable habitat is not present within the projectaction area, then the State review is complete. Document the “no habitat” finding in theInitial Project Proposal/Final Design Report or Design Approval Document.

If the habitat assessment concludes that suitable habitat is present within the project actionarea, continue to Step S3.

Step S3. Take Determination (Preliminary Design: Phase I)

Complete an assessment of the proposed action, including all practicable avoidance measuresand alternatives, to determine whether or not it may result in the taking of state listed species.This assessment must consider the nature, severity and geographic extent of the action’s directand indirect effects.


August 2011 TEM 4.4.9.3

NYSDEC concurrence is not required when NYSDOT environmental staff concludes witha high degree of certainty that a taking will not occur, however staff is encouraged tocoordinate with NYSDEC in arriving at this conclusion. Staff will share their conclusionwith the NYSDEC Regional Permit Administrator and, when doing so, may request a letterof concurrence. If such a request is made, NYSDEC will respond within 30 days. Anincidental take permit from NYSDEC is not required when a taking will not occur,therefore the State review is complete. Document this outcome in the Initial ProjectProposal/Final Design Report or Design Approval Document.

If staff is unable to determine with sufficient confidence the likelihood that a taking willoccur, continue to S3.a.

If staff determines that a taking is likely to occur, an incidental take permit from NYSDECis required. Continue to Step S4.

S3.a. Staff submits to the NYSDEC Regional Permit Administrator a written request for adetermination of the likelihood that taking of state listed species will occur. Thissubmittal should note the species in question, and include supporting information such asa project description, project location map, GIS maps (topography, aerial photography,project action area boundary), and completed habitat assessment forms. Within 30 days ofreceipt of such a request, the NYSDEC must provide a written answer stating whether theproposed activity is likely to result in a taking, requesting additional information necessaryto make such a determination, or advising that an extension of the 30-day time period isrequired. NYSDEC will also provide guidance as to how a taking can be avoided.

If NYSDEC determines that a taking is not likely to result, an incidental take permitis not required and the State review is complete. Document this outcome in theInitial Project Proposal/Final Design Report or Design Approval Document.

If NYSDEC determines that a taking is likely to result, an incidental take permit isrequired. Continue to Step S4.

Step S4. Incidental Take Permit (Preliminary Design: Phase I)

Using the NYS Joint Application Form, prepare and submit an incidental take permit application,including an Endangered or Threatened Species Mitigation Plan and Implementation Agreementas described in 6 NYCRR Part 182.11. Further coordination with NYSDEC may be required torefine elements of the Mitigation Plan.

Upon issuance of an incidental take permit, the proposed activity may proceed inaccordance with the terms and conditions of the incidental take permit, the Endangered orThreatened Species Mitigation Plan, and the Implementation Agreement. Document thisoutcome in the Initial Project Proposal/Final Design Report or Design Approval Document.


August 2011 TEM 4.4.9.3

Federal Endangered and Threatened Species

Any project that is a federal action must comply with the Endangered Species Act Section 7

requirement for interagency coordination, as outlined in the Procedures for Federal Actions

below. These procedures also ensure that the action will not result in unauthorized taking of any

federally listed animal species, as required by ESA Section 9.

If a project is not a federal action, it is not subject to the requirements of Section 7. However,

Section 9 does apply and the project must not result in unauthorized taking of any federally listed

animal species. These procedures are outlined in the Procedures for Non-Federal Actions below.

Procedures for Federal Actions

Among federal actions, there is a procedural variation between those where the action rests with

FHWA (i.e., federal-aid highway projects) and those where the action rests with a different

federal agency, such as the Federal Railroad Administration or U.S. Army Corps of Engineers.

In accordance with 50 C.F.R. § 402.08, FHWA has designated NYSDOT as its non-federal

representative in the ESA process, thereby delegating some of the responsibility for informal

consultation and preparation of biological assessments/evaluations for projects in the federal-aid

highway program. This delegation is valid only when FHWA is the federal action agency.

Therefore, when projects involve a federal action agency other than FHWA, that agency is fully

responsible for consultation with the Services and NYSDOT’s role must be determined. The

following procedures are written from the perspective of federal-aid highway projects

(FHWA action), with variations for other federal action agencies noted where applicable.

In steps where no variation is noted, the terms “FHWA” and “federal action agency” are

interchangeable.

Unless stated otherwise, the following steps are to be undertaken by the Regional Endangered

and Threatened Species Contact, other qualified Department staff, or the project consultant.

Correspondence with outside agencies (e.g., effect determination letter) is typically signed by the

Regional Environmental Unit Supervisor or designee.

Step F1. Applicability of Process Agreements (Project Scoping Stage)

Review Subsection 4.4.9.3.6. Interagency Coordination and Agreements to determine the

applicability of existing agreements to the proposed activities.

If the FHWA No Effect Blanket Concurrence is applicable to all activities associated

with the proposed action, no further federal review is required. Document this

outcome in the Initial Project Proposal/Final Design Report, or in the Project

Scoping Report and Design Approval Document.

If the FHWA Process Agreement for Minor Tree Removal Projects is applicable to all

activities associated with the proposed action, Step F5.a of these procedures should

be modified accordingly. Document this in the Initial Project Proposal/Final Design

Report, or in the Project Scoping Report and Design Approval Document.

2017 Update: Follow the procedures outlined in “Appendix G:

FHWA ESA Section 7 Process” for FHWA actions.



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VARIATION: When FHWA is not the federal action agency, the No Effect BlanketConcurrence and Process Agreement for Minor Tree Removal Projects may not be used.

ugust 2011 TEM 4.4.9.3

tep F2. Federal Species Screening (Project Scoping Stage)

2.a. Identify the limits of the project action area. When evaluating multiple projectalternatives, the action area should be identified separately for each, although thescreening may be conducted simultaneously. Continue to F2.b.

2.b. Conduct a screening for federally listed species and proposed species by consulting withthe county-based lists accessible through the USFWS New York Field Office website (seeAppendix D). Review all counties that contain or intersect the project action area.Informal Consultation is thereby initiated. It is recommended that the county list be re-checked every 90 days until construction is complete in order to ensure that speciespresence/absence data is current.

Designated critical habitat for non-marine species is identified on the USFWS county-based lists where applicable. For marine species, NMFS must be contacted on a case-by-case basis to determine if designated critical habitat is present in the project action area.Currently, the only designated critical habitat in New York State is for the Great Lakesbreeding population of the piping plover in Oswego and Jefferson Counties.

If no federally listed species appears on the county-based list(s) and no designatedcritical habitat is present, no further federal review is required. Document thisoutcome in the Initial Project Proposal/Final Design Report, or in the ProjectScoping Report and Design Approval Document. Absence of federally listed speciesdoes not denote absence of state listed species. Therefore, the action remains subject tothe state endangered and threatened species review process.

If one or more federally listed species appears on the county-based list(s) and/orcritical habitat is present, continue to F2.c.

2.c. Review the NY Natural Heritage Program database for occurrences of federally listedspecies and rare/significant ecological communities in the screening area (see Table 2 inthe preceding section for screening distance). Individuals performing this screening mustfirst receive training in the use and interpretation of NYNHP data. NYSDOT regionalstaff may contact the Main Office Environmental Science Bureau for a current list oftrained individuals or to request training.

Review the New York State Breeding Bird Atlas, Amphibian & Reptile Atlas, and FloraAtlas to determine if any federally listed species belonging to these taxa have beendocumented or may occur in the screening area.

Note that absence of NYNHP element occurrences and/or atlas records does not obviatethe need for a habitat assessment. The purpose of this step is not to prove absence of

Begin the federal review process at Step F2.


August 2011 TEM 4.4.9.3

protected species, but rather to identify geographic areas that warrant special scrutinyduring the subsequent habitat assessment.

Document the screening results in the Initial Project Proposal/Final Design Report orProject Scoping Report. Continue to Step F3.

Step F3. Habitat Assessment (Preliminary Design: Phase I)

Conduct a habitat assessment for all federally listed species that potentially exist within theproject action area. If any rare/significant ecological communities were identified in F2.c above,review the NY Natural Heritage Program conservation guides to determine whether or not thecommunity may provide habitat for federally listed species. Review available publishedinformation on habitat requirements of the species in question, as well as any additional desktopresources that may assist in making a determination of habitat suitability, such as topographicmaps, county soil surveys, and aerial photography.

On-site field investigation is typically necessary to verify the presence or absence of suitablehabitat, although there may be cases where a review of desktop resources alone would yield areliable habitat assessment (e.g., species with a distinct range or habitat type). Several habitatassessment forms are available to assist Department staff in conducting the field investigation(see Appendix D). Further assistance may be obtained by contacting the USFWS, NMFS,NYSDEC, or NYNHP.

Document the results of the habitat assessment in the Initial Project Proposal/Final DesignReport or Design Approval Document. Continue to Step F4.

Step F4. Effect Determination (Preliminary Design: Phase I)

Complete an assessment of the proposed action to determine whether or not it may affect listedspecies or critical habitat. This effect determination assessment must consider:

the nature of the action and any direct and indirect effects on listed species or critical habitat;

the geographic limits of these effects (i.e., the project action area);

the environmental baseline condition of the project action area, including potential forsuitable habitat to exist as determined in Step F3; and

measures than can be integrated into the project to avoid and minimize effects to listedspecies.

The two possible conclusions for this assessment are “No Effect” and “May Affect.”

If the effect determination assessment concludes that the proposed action will have noeffect on federally listed species or critical habitat, continue to F4.a.

If the effect determination assessment concludes that the proposed action may affectfederally listed species or critical habitat, continue to Step F5.


August 2011 TEM 4.4.9.3

F4.a. “No Effect” determination. Staff must submit a written request for concurrence with theNo Effect determination to the FHWA New York Division Office. This submittal shouldinclude a short discussion of the species in question, rationale for the No Effectdetermination, and all supporting information such as a project location map, GIS maps(topography, aerial photography, project action area boundary), and completed habitatassessment forms. The federal review is complete upon receipt of written concurrencefrom FHWA. Document the No Effect determination and FHWA concurrence in theInitial Project Proposal/Final Design Report or Design Approval Document.

If FHWA does not concur with the No Effect determination (i.e., believes that the actionmay affect listed species or critical habitat), the effect determination assessment (Step F4)must be restarted. Upon reexamination of the potential impacts, if staff maintains that theproposed action will have no effect on federally listed species or critical habitat, thenadditional supporting information must be provided to FHWA. Otherwise, it must beconcluded that the proposed action may affect federally listed species or criticalhabitat; notify FHWA of this decision and continue to Step F5.

Step F5. Biological Assessment / Biological Evaluation (Preliminary Design: Phase I)

A biological assessment (BA) or biological evaluation (BE) must be prepared to document thelikelihood and severity of all potential effects of the proposed action on listed species and/ordesignated critical habitat.

A biological assessment is a document prepared for the Section 7 process to determine if aproposed activity is likely to: (1) adversely affect listed species or designated critical habitat; (2)jeopardize the continued existence of species that are proposed for listing; or (3) adverselymodify proposed critical habitat.

Biological evaluations are differentiated from biological assessments in that they are used forprojects with low likelihood/severity of effects on listed species or designated critical habitat.While there is no difference between these documents in regard to the type of information theycontain, a BA includes more in-depth analysis than a BE, commensurate with the potentialimpacts.

Pursuant to Federal regulations (50 C.F.R. § 402.12), a biological assessment is required only forfederal actions that are major construction activities (requiring an environmental impactstatement) which may affect listed species or designated critical habitat. All other types ofactions require preparation of either a BA or BE.

The outcome of the BA/BE determines if formal consultation is necessary. This document istypically provided to FHWA in draft form. Upon review and acceptance of the effectdetermination, FHWA will finalize the BA/BE and forward it to the Services for concurrence.


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VARIATION: When FHWA is not the federal action agency (i.e., no federal highwayfunding), NYSDOT is not responsible for preparation of the draft BA/BE. However,NYSDOT may facilitate this task by providing the federal action agency with all pertinentinformation organized in a manner consistent with that of a BA/BE. Alternatively, thefederal action agency may designate NYSDOT as preparer of the biological assessment, in

ugust 2011 TEM 4.4.9.3

here are established regulatory timeframes for submittal and review of biological assessments:he ESA requires that biological assessments be submitted to the Services within 180 calendarays after receipt of a species list from the Services. When the USFWS county-based list isccessed through the NY Field Office website, the date of receipt appears in the page footer asInformation current as of: MM/DD/YYYY”. Federal regulations require that the Servicesrovide a written response within 30 calendar days stating whether or not they concur with theindings of the biological assessment. Note that federal regulations do not prescribe timeframesor biological evaluations, but it is reasonable to assume a comparable time period.

fter reviewing the final BA/BE, the Services may: 1) provide concurrence with the effectetermination as presented; 2) recommend project modification or conservation measures that, ifncorporated, would allow their concurrence with the effect determination; or 3) denyoncurrence with the effect determination.

n some circumstances, the Services may be unable to adequately assess the effects of a proposedction due to lack of information on listed species within the project action area, and will requesthat a study be conducted. Such a study may include biological sampling and/or habitat analysis.YSDOT has no legal obligation to conduct or pay for these studies, although it may be in theepartment’s interest to do so, particularly if the data gathered might suggest that formal

onsultation is not necessary.

he BA/BE should include results of investigations to determine the presence of listed orroposed species (e.g., habitat assessment, on-site inspections), and an analysis of the likelyffects of the action on the species or habitat based on biological studies, literature review, andhe judgment of species experts. Any known, unrelated future non-federal activities"cumulative effects") reasonably certain to occur within the action area that are likely to affecthe species should also be described in the BA, although the Department is not obligated toitigate for cumulative effects. A biological evaluation should follow the same guidelines as a

iological assessment and include all relevant information for justifying the effect determination.urther guidance in development of the BA/BE is available through coordination with theervices and FHWA, and on the Internet through the FHWA ESA Webtool and National BAemplate.

f the draft BA/BE concludes that the proposed action is not likely to adversely affectederally listed species or critical habitat (i.e., all of the reasonably expected effects will beeneficial, insignificant, or discountable), continue to F5.a.

f the draft BA/BE concludes that the proposed action is likely to adversely affect federallyisted species or critical habitat, continue to F5.b.

which case the procedure is the same as that used for federal-aid projects.


August 2011 TEM 4.4.9.3

F5.a. “May Affect, Not Likely to Adversely Affect” determination. Staff must submit a writtenrequest for concurrence with the “May Affect, Not Likely to Adversely Affect”determination to the FHWA New York Division Office. Include the draft BA/BE in thissubmittal. Upon review and acceptance of the effect determination, FHWA will finalizethe BA/BE and forward it to the Services. The Services will then review the BA/BE andnotify FHWA of their concurrence or non-concurrence within 30-calendar days. In caseswhere the Services’ concurrence is contingent on implementation of project modificationor conservation measures, such measures must be developed and agreed upon by allagencies. The federal review is complete upon receipt of written concurrence fromthe Services. Document the May Affect, Not Likely to Adversely Affectdetermination, federal concurrence, and any applicable projectmodifications/conservation measures in the Initial Project Proposal/Final DesignReport or Design Approval Document.

If the Services do not concur with the effect determination as presented and impactscannot be sufficiently reduced through project modification and conservation measures,then the effect determination shall be “May Affect, Likely to Adversely Affect” andFHWA/NYSDOT will enter into Formal Section 7 Consultation. Continue to Step F6.

F5.b. “May Affect, Likely to Adversely Affect” determination. Staff must forward the “MayAffect, Likely to Adversely Affect” determination and draft BA/BE to the FHWA NewYork Division. Upon review and acceptance of the effect determination, FHWA willfinalize the BA/BE and forward it to the Services to initiate Formal Section 7Consultation. Continue to Step F6.

Step F6. Formal Consultation (Preliminary Design: Phase I)

The process of formal consultation begins when FHWA sends an initiation package, includingthe BA/BE, to the Services. Within 30 calendar days of its receipt, the Services will notifyFHWA as to whether the package is complete or incomplete. Notification of an incompletepackage will be accompanied by a request for further information that is necessary to make thepackage complete. The Services then prepare a draft biological opinion (BO), including anyreasonable and prudent alternatives that would avoid the likelihood of jeopardy to the species ordestruction or adverse modification of designated critical habitat. Upon completion of the draftBO, the Services will provide NYSDOT and FHWA with an opportunity for comment. Allcomments must be submitted through the federal action agency. The ESA and Section 7regulations require that formal consultation be concluded within 90 calendar days after receipt ofa complete initiation package and that the final BO be issued within 45 calendar days afterconsultation ends, unless an extension is agreed upon by both the Service and the federal actionagency.

The formal consultation process must result in a biological opinion reaching a finding of eitherjeopardy or no jeopardy to listed species (or adverse or no adverse modification of criticalhabitat). In addition, the Services must prepare an incidental take statement when either: 1) theBO results in a no jeopardy/no adverse modification finding, or 2) the BO results in a


August 2011 TEM 4.4.9.3

jeopardy/adverse modification finding, but reasonable and prudent alternatives are identified thatwould eliminate the likelihood of jeopardy to the species or adverse modification of designatedcritical habitat.

The incidental take statement outlines the amount of incidental take anticipated from theproposed action, and identifies reasonable and prudent measures to minimize take. It exemptsthe action agency and permittee from the ESA Section 9 prohibitions if they comply with thereasonable and prudent measures and the implementing terms and conditions. Terms andconditions of the incidental take statement include provisions for monitoring and reporting theamount and extent of take.

In some circumstances, the Services may be unable to adequately assess the effects of a proposedaction due to lack of information on listed species within the project action area, and will requestthat a study be conducted. Such a study may include biological sampling and/or habitat analysis.NYSDOT has no legal obligation to conduct or pay for such a study. However, if theDepartment elects not to conduct a study, the Services will develop the biological opinion basedon the limited available information, giving the benefit of the doubt to the species. This couldhave major consequences, depending on the significance of the missing data to the effectdetermination.

If the Services’ biological opinion concludes that the proposed action is not likely tojeopardize the continued existence of a listed species or result in adverse modification ofcritical habitat, then the project may proceed in accordance with the terms and conditionsof the incidental take statement and its associated reasonable and prudent measures.Document this outcome in the Initial Project Proposal/Final Design Report or DesignApproval Document.

If the Services’ biological opinion concludes that the proposed action is not likely tojeopardize the continued existence of a listed species or result in adverse modification ofcritical habitat, contingent upon implementation of reasonable and prudent alternatives ormeasures, then FHWA, upon reaching agreement with NYSDOT, will send a letter to theServices stating its decision to either: 1) progress the action under one of the reasonableand prudent alternatives, or in accordance with the terms and conditions of the incidentaltake statement and its associated reasonable and prudent measures, or 2) decline toimplement the reasonable and prudent alternatives or measures. In the former case, Section7 formal consultation is concluded and the project may proceed. In the latter case, the Serviceswill respond in writing stating that any taking of listed species as a result of the action isprohibited under Section 9. In either situation the proposed action must not exceed the Services’stated limitations on take.

If the Services’ biological opinion concludes that the proposed action is likely to jeopardizethe continued existence of a listed species or result in adverse modification of criticalhabitat and these impacts can not be avoided or sufficiently minimized through reasonableand prudent alternatives/measures, then FHWA, upon reaching agreement with NYSDOT,will send a letter to the Services stating its decision to either: 1) not progress the action, or2) pursue an exemption. The exemption process is long and involved. It is initiated by filing


August 2011 TEM 4.4.9.3

an application for exemption within 90 days of completion of consultation. Exemptions must beapproved by a 7-member committee including the secretaries of Agriculture, Army, and Interior;Administrators of the Environmental Protection Agency and the National Oceanic andAtmospheric Administration; the Chair of the Council of Economic Advisors; and a presidentialappointee from each affected State.

Step F7. Reinitiation (Final Design through Construction)

If any of the following occurs after consultation with the Services has been completed, FHWANew York Division must be notified immediately and consultation with the Services must bereinitiated:

The amount or extent of authorized incidental take is exceeded.

New information reveals effects of the action that may affect listed species or critical habitat ina manner or to an extent not previously considered.

The action is modified in a manner causing effects to listed species or critical habitat notpreviously considered.

A new species is listed or critical habitat designated that may be affected by the action.

It is also possible that changes to the scope of a project will result in significantly less take thanwas originally anticipated. Reinitiation of consultation may be considered for the purpose ofrenegotiating reasonable and prudent measures. The decision to request reinitiation must weighthe potential cost savings against the time required to repeat the formal consultation process.

Procedures for Non-Federal Actions

If a project is not a federal action, it is not subject to the interagency consultation requirements ofSection 7 of the Endangered Species Act. However, Section 9 applies to all actions whetherfederal or non-federal, public or private, and requires that a permit be obtained before a projectwill be allowed to result in the taking of any federally listed animal species.

The following procedures ensure that any non-federal action undertaken by NYSDOT complieswith the ESA Section 9 prohibition of take. Unless stated otherwise, these procedures are to beundertaken by the Regional Endangered and Threatened Species Contact, other qualifiedDepartment staff, or the project consultant. Correspondence with outside agencies (e.g., effectdetermination letter) is typically signed by the Regional Environmental Unit Supervisor ordesignee.

Step NF1. Screening, Habitat Assessment, and Effect Determination (Project Scoping –Preliminary Design: Phase I)

Complete a species screening, habitat assessment, and effect determination assessment asoutlined in the Procedures for Federal Actions above to determine if listed species are potentiallypresent within the project action area and may be affected.


August 2011 TEM 4.4.9.3

If federally listed species are not potentially present within the project action area, thefederal review is complete. Document this outcome in the Initial Project Proposal/FinalDesign Report, or in the Project Scoping Report and Design Approval Document.

If federally listed species are potentially present within the project action area, but will notbe affected by the proposed action, the federal review is complete. Document this outcomein the Initial Project Proposal/Final Design Report, or in the Project Scoping Report andDesign Approval Document.

If federally listed species are potentially present within the project action area and may beaffected by the proposed action, continue to Step NF2.

Step NF2. Incidental Take (Preliminary Design: Phase I)

An evaluation must be conducted to determine if the action will result in incidental take. Staffsubmits the following information to the Services with a request for determination of whether ornot incidental take is likely to occur (note: the request should clearly state that the proposedproject is not a federal action):

Detailed description of the proposed project, including approximate construction scheduleand project activities that may potentially affect listed species.

Description of the natural characteristics of the property and surrounding area (e.g., forestedareas, freshwater wetlands, open waters, and soils). Include a description of surroundingland use (residential, agricultural, or commercial).

Description of the area to be impacted by the proposed project, including trees to beremoved.

Location of the project and extent of any project-related activities or discharges clearlyindicated on a copy of a USGS 7.5 Minute Topographic Quadrangle (Quad) with the name ofthe Quad(s) and latitude/longitude clearly labeled.

Description of conservation measures to avoid or minimize impacts to listed species.

The Services’ role in review of non-federal actions is to provide technical assistance to projectproponents. There are no regulatory procedures or timeframes for this review. However, if it isdetermined that the action is likely to result in incidental take, issuance of an incidental takepermit is subject to the procedures and timeframes discussed in Step NF3.

If the Services determine that an incidental taking is not likely to occur, then a letterstating such will be sent to NYSDOT, concluding the federal review. Document thisoutcome in the Initial Project Proposal/Final Design Report or Design Approval Document.

If the Services determine that an incidental taking is likely to occur, but can be avoided orsufficiently minimized through project modification or conservation measures, then suchmeasures should be developed cooperatively by the Services and NYSDOT. The projectmay proceed in accordance with recommended project modifications and conservation


August 2011 TEM 4.4.9.3

measures. Document this outcome in the Initial Project Proposal/Final Design Report orDesign Approval Document.

If it is determined that an incidental taking is likely to occur and can not be avoided orsufficiently minimized, then the Services will notify NYSDOT that an incidental takepermit is required for the action. Continue to Step NF3.

Step NF3. Incidental Take Permit (Preliminary Design: Phases I-II)

ESA Section 10(a)(1)(B) requires that an incidental take permit be issued before commencingany proposed action that is likely to result in the taking of a federally listed animal species.Contact the Services for assistance in developing complete and adequate application materials.Additional guidance is available in the Section 10 Habitat Conservation Planning Handbook.

This permit differs from incidental take statements developed through formal consultation. Itrequires development of a habitat conservation plan (HCP) to offset any harmful effects theproposed activity may have on the species. The HCP must specify the impacts which will likelyresult from the taking, steps to be taken to minimize or otherwise mitigate such impacts,alternative actions considered, and other measures determined by the Services. Notice of theHCP must be published in the Federal Register and is subject to a 30-day public commentperiod. Upon review of the HCP and public comments, the Services will proceed with issuanceof an incidental take permit for the proposed action. Staff should inquire with the Services at theend of the public comment period to gauge the amount of time required for permit issuance.

The ESA does not dictate time frames for permit processing, however the Section 10 HabitatConservation Planning Handbook establishes the following targets, depending on the type ofNEPA action associated with the permit application: HCP with EIS – less than 10 months; HCPwith EA – 3 to 5 months; Low-effect HCP (Categorical Exclusion) – less than 3 months. Thesetargets may also be applied to the equivalent SEQR types.

Once an incidental take permit is issued, the project may proceed in accordance with theHCP and its terms and conditions. Document this outcome in the Initial ProjectProposal/Final Design Report or Design Approval Document.

4.4.9.3.6 Interagency Coordination and Agreements

FHWA NY Division No Effect Blanket Concurrence for select element-specific activities [NOTYET FINAL - link to be added]

FHWA NY Division Process Agreement for “May Affect, Not Likely to Adversely Affect”determinations for Minor Tree Removal Projects within counties with known Indiana bat habitat[NOT YET FINAL - link to be added]


August 2011 TEM 4.4.9.3

4.4.9.3.7 Project Development and Construction Guidance

The presence of endangered or threatened species has the potential to impact project design andconstruction practices. It is imperative that any potential issues be identified as early as possibleto avoid late scope changes and project delays.

Project Scoping Stage

The scoping document should reflect, in general terms, the screening outcomes for state andfederally listed species and indicate whether or not further investigation and agency coordinationwill be subsequently required in preliminary design.

Preliminary Design (Phases I-IV)

The Design Approval Document should document the results of the species screening conductedduring project scoping, as well as any subsequent resource agency review/coordination, ifapplicable. If the screening found that listed species are potentially present, then the DesignApproval Document should include:

Identification and listing status (state and federal) of the species involved.

Summary of the habitat assessment.

Measures to avoid and/or minimize impacts, including those considered prior to agencycoordination.

Effect determination with supporting rationale.

Letters of concurrence from FHWA, USFWS, NMFS and/or NYSDEC as necessary.

Discussion of special conditions required by the regulating agencies and NYSDOTcommitments, including scope modifications and special construction considerations.

Endangered and threatened species process documents must be redacted to obscure preciselocations of sensitive species when attached to publicly available documents.

Due to potential design implications, agency coordination regarding endangered and threatenedspecies should be completed before the beginning of final design.

Final Design (Phases V & VI)

Prior consultation with the Services and/or NYSDEC may identify special construction methods,timing, or work limits to ensure that impacts to listed species are avoided and/or minimized tothe extent required. These must be stated in the Design Approval Document and constructiontransmittal package, and clearly articulated to contractors and site inspectors using special noteson project plans and/or special specifications.


August 2011 TEM 4.4.9.3

Construction Considerations

Contract documents may reflect specific commitments made during agency coordination withregard to protection of endangered/threatened species. Any deviation from the contractdocuments should be coordinated with appropriate regional environmental staff.

Construction staff should be familiar with thresholds for reinitiation of Section 7 consultation(see Step F7) so that these can be monitored throughout the construction phase. If a reinitiationthreshold is exceeded, regional environmental staff should be contacted immediately.

It is recommended that the USFWS county list be re-checked every 90 days until construction iscomplete in order to ensure that species data is current.


August 2011 TEM 4.4.9.3

4.4.9.3.8 Operations Guidance

Many types of activities associated with operation and maintenance of the State highway systemmay potentially affect endangered or threatened species. Such activities include, but are notlimited to: vegetation management (tree/brush cutting, mowing, herbicide application), drainagesystem maintenance, bridge/culvert repair, and placement/replacement of hydraulic scourprotection.

The regional Maintenance Environmental Coordinator or other qualified staff should review allsuch activities to assess their potential effects on protected species. Follow the procedures statedabove to ensure compliance with state (Subsection 4.4.9.3.5.1) and federal (Subsection4.4.9.3.5.2) endangered species regulations.

Emergency Procedures

State listed species

Incidental take permits issued pursuant to 6 NYCRR Part 182 are administered in accordancewith the Uniform Procedures Act, including its emergency provisions.

In the event of an emergency that requires a prompt response to conditions that immediatelythreaten life, health, property, general welfare or natural resources, the Uniform Procedures Act(UPA) regulations (6NYCRR Part 621.12) provide for expedited project review and issuance ofan Emergency Authorization.

Prior to commencing any action or project staff must notify the NYSDEC Regional PermitAdministrator and provide:

a description of the proposed action;

a location map and plan of the proposed action;

reasons why the situation is an emergency based on the immediate protection of life, health,general welfare, property or natural resources;

actions to be taken to minimize environmental impacts; and

any additional information requested by NYSDEC.

If prior notice is not possible, immediate action may be undertaken, but notice must be providedto the NYSDEC Regional Permit Administrator and NYSDEC Regional EnvironmentalConservation Officer within 24 hours of taking action. The notification must provide NYSDECa basis on which to issue an Emergency Authorization.

Federally listed species

In the event of an emergency, the Endangered Species Act and federal regulations provide for 1)Presidential authority to grant an exemption to Section 7 requirements, and 2) expedited Section7 review and after-the fact formal consultation (16 U.S.C. 1536 (p), 50 C.F.R. § 402.05). These


August 2011 TEM 4.4.9.3

emergency procedures are applicable to any federal action that must be taken to preventimminent loss of human life or property.

It may not be known at the time of the emergency whether the response activity will laterbecome a federal action through federal reimbursement. The Regional Environmental UnitSupervisor should work with others (e.g., Regional Program Planning Manager) to determine thebest course of action based on potential funding.

Step E1. Initial Review/Informal Consultation

Contact the Services through a telephone call, email and/or facsimile. Explain the nature of theemergency and the necessary response action. The Services will offer recommendations tominimize the effects of the emergency response action on listed species or their critical habitat(informal consultation). As soon as possible thereafter, the Services will provide follow-upcorrespondence to document the initial consultation and commitments made by NYSDOT.

If this initial review indicates that either 1) the action will not result in jeopardy or adversemodification, or 2) the action may result in jeopardy or adverse modification, but means ofreducing or avoiding this effect are available, then no further federal review is required.Proceed with the emergency response action.

If the action may result in jeopardy or adverse modification, and no means of reducing oravoiding this effect are apparent, NYSDOT will be so advised, and the Services willdocument their conclusion. Proceed with the emergency response action. As soon aspracticable after the emergency is under control, continue to Step E2.

Step E2. Formal Consultation

As soon as practicable after the emergency is under control, the federal action agency mustinitiate formal consultation. Procedurally, formal consultation after-the-fact is no different fromtypical formal consultation, except that additional information must be provided regarding thenature of the emergency action, justification for the expedited consultation, and the impacts toendangered or threatened species and their habitats. The Service will evaluate such informationand issue a biological opinion, including the information and recommendations given during theemergency consultation, to document impacts to the species or habitat.

NYSDOT-Issued Permits

Work being conducted by other entities under a NYSDOT-issued permit such as a HighwayWork Permit or Use and Occupancy Permit may potentially affect protected species. Inreviewing permit applications, NYSDOT must comply with the State Environmental QualityReview Act (SEQRA) and consider the potential impacts to environmental resources. WhileNYSDOT is not responsible for conducting the endangered species review, it is the Department’sresponsibility to ensure that the permittee has sufficiently addressed endangered species.


August 2011 TEM 4.4.9.3

Location-Specific Considerations

Special mowing restrictions apply in the Capital District for protection of the Karner bluebutterfly, a federally and state listed endangered species. In portions of Albany, Saratoga, andWarren Counties, some areas of the right of way contain blue lupine, a plant that serves as thehost and exclusive food source for eggs and caterpillars of the Karner blue butterfly. Mowingblue lupine plants before September 1st violates state and federal law. Consult the regionalMaintenance Environmental Coordinator to identify areas with blue lupine so that mowingactivities can be scheduled accordingly.

Certain stormwater recharge basins on Long Island are inhabited by eastern tiger salamanders, astate listed endangered species. Consult the regional Maintenance Environmental Coordinator todetermine which recharge basins have restrictions on maintenance activities.

When a transportation project will take place within or adjacent to nature preserves, wildlifemanagement areas, refuges, etc., Department staff should coordinate with the responsible entityto ensure that the activities are planned and conducted in a manner sensitive to existingmanagement objectives.


August 2011 TEM 4.4.9.3

4.4.9.3.9 Flow Charts

The following flow charts illustrate the typical review processes to be followed for:

1) state listed species (as discussed in subsection 4.4.9.3.5.1)2) federally listed species, where the project is a federal action and FHWA is the Federal

Action Agency (as discussed in subsection 4.4.9.3.5.2)3) federally listed species, where the project is a federal action and an agency other than

FHWA is the Federal Action Agency (as discussed in subsection 4.4.9.3.5.2)

The flow charts omit some procedural details found within the text of this document. Therefore,the reader is cautioned against using them as stand-alone guidance.

State Endangered and Threatened Species ProcessTa

ke D

eter

min

atio

nH

abita

t Ass

essm

ent

Inci

dent

al T

ake

Per

mit

Sta

te S

peci

es S

cree

ning

Document negative

screening in Design

Approval Document

END STATE

PROCESS

Conduct a habitat assessment of the project action area for all known

occurrences identified during screening3

Determine whether potential occurrences can be discounted4

Complete appropriate habitat assessment forms, if available, to

document findings

Issuitable

habitat presentwithin the project

action area?

Document this outcome in

Design Approval

Document

YES

YES

NO

NYSDOT prepares and submits an incidental take

permit application, including an endangered

or threatened species mitigation plan

Arethere records

of known or potential occurrence of state

listed species?

NO

If necessary, NYSDOT and

NYSDEC further refine minimization/mitigation measures

NYSDEC issues incidental take permit

Document“no habitat” finding in Design

Approval Document

NO

Review state atlases1 and

NYNHP database for occurrence of listed species or rare/significant communities in screening area2

Is arare/significant

community presentthat may providehabitat for listed

species?3

If necessary, consult with

NYSDEC and NYNHP to identify

suitable habitat

Istake likelyto result?

Document this

outcome in Design

Approval Document

NYSDOT reviews

proposed action,

including all practicable avoidance

measures, to determine

whether or not take is likely to

result

Incidental take

permit is NOT

required

MAYBE

30DAYS(unless

extended)

HasNYSDEC

found that takeis likely to

result?

NYSDOT sends site/project info

(screening, habitat, proposed action) to

NYSDEC with request for

determination of likelihood of take

YES YES

NO

NO

YES

1. New York State Breeding Bird Atlas, New York State Amphibian & Reptile Atlas, and New York Flora Atlas2. Refer to TEM 4.4.9.3 Endangered and Threatened Species for screening distances.3. Refer to NYNHP Conservation Guides and other available published information.4. Occurrence may be discounted if there is an absence of “occupied habitat” as defined in 6 NYCRR Part 182. This determination is based on correspondence with NYSDEC / NYNHP and review of available information including maps, aerial photos, reports, personal accounts, historic land use change, etc.

Final, 8/15/11

NYSDOT sends notification to NYSDEC. Correspondence may include a request for

NYSDEC concurrence, if desired.

Federal Section 7 Endangered and Threatened Species Process – FHWA as Federal Action Agency1

Hab

itat A

sses

smen

tE

ffect

Det

erm

inat

ion

Ass

essm

ent

Nat

ural

Her

itage

Scr

eeni

ngFe

dera

l Spe

cies

Scr

eeni

ngFo

rmal

Con

sulta

tion

Bio

logi

cal A

sses

smen

t (B

A) /

B

iolo

gica

l Eva

luat

ion

(BE

)

Review USFWS-NYFO website for county-level

screening of federal sp.

Contact NMFS to determine presence of Desig- nated Critical Habitat (marine species only)

Arefederally

listed speciesor Designated Critical Habitat indicated for

the projectcounty?

Conduct a habitat assessment of the project action area for all federally

listed species identified during screening4

Complete appropriate habitat assessment forms, if available, to document

findings

Issuitable habitat

present within project action area?

For each listed species with

habitat present, complete Effect Determination Assessment

Mightthe species or

habitat be affected?(direct, indirect,

cumulativeeffect)

HasFHWA provided

concurrence with the NE determination?

(30 days)

Document“No Effect”

determination in Design Approval

Document

Draft BA/BE with enough

information to support a

“May Affect” determination

HaveServices providedconcurrence withMA-NLAA deter-

mination?

Document“May Affect, Not

Likely to Adversely Affect” determination in Design Approval

Document

HaveServices

determined that jeopardy/adverse mod.

is likely andunavoidable?

Services prepare Biological Opinion

(BO) and Incidental Take Statement

NYSDOT provides Draft BA/BE with MA-LAA

determination to FHWA

FHWA finalizes BA/BE, prepares initiation

package

YES

YES

YES

YES

NO

NO YES

NO

NO YES

NO

NO

Consider project modification

Document“May Affect, Likely

to Adversely Affect”


Document

PROJECT CAN NOT PROCEED

Is thespecies likely to be adversely affected?

NYSDOT sendsNE determination and supporting

info to FHWA for concurrence

NYSDOT provides Draft BA/BE with MA-NLAA

determination to FHWA

FHWA finalizes BA/BE, forwards to Services5 for

concurrence

(FHWA Web BA tool is recommended)

FHWA initiates Formal

Consultation with Services

(135 days)

Info

rmal

Con

sulta

tion

YES

NO

Document in Design

Approval Document

END FEDERAL PROCESS

Review state atlases2

and NYNHP databasefor occurrence of listed

species or rare/significant communities in the screening area3

NYSDOT/FHWA may initiate the Exemption process

Doesthe project

consist solely ofactivities subject to FHWA

“No Effect” BlanketConcurrence?

NO

YES

final, 8/15/111. FHWA is the Federal Action Agency when federal funding is used. If no federal aid exists, the Federal Action Agency is that agency with the primary responsibility for the action (e.g., permit issuance).

2. New York State Breeding Bird Atlas, New York State Amphibian & Reptile Atlas, and New York Flora Atlas.3. Refer to TEM 4.4.9.3 Endangered and Threatened Species for screening distances.4. Refer to NYNHP Conservation Guides and other available published information.5. “Services” refers to USFWS and/or NMFS as appropriate given the species in question.NOTE: This flow chart is intended to illustrate the general process. Refer to TEM 4.4.9.3 Endangered and Threatened Species for detailed procedures.

Federal Section 7 Endangered and Threatened Species Process – Federal Action Agency Other Than FHWA1

Hab

itat A

sses

smen

tE

ffect

Det

erm

inat

ion

Ass

essm

ent

Nat

ural

Her

itage

Scr

eeni

ngFe

dera

l Spe

cies

Scr

eeni

ngFo

rmal

Con

sulta

tion

Bio

logi

cal A

sses

smen

t (B

A) /

Bio

logi

cal

Eva

luat

ion

(BE

)

Document in Design

Approval Document

END FEDERAL PROCESS

Issuitable habitat

present within project action area?

For each listed species with

habitat present, complete Effect Determination Assessment

Mightthe species or

habitat be affected?(direct, indirect,

cumulativeeffect)

Document“No Effect”


Document

Document“May Affect, Not

Likely to Adversely Affect” determination in Design Approval

Document

HaveServices

determined that jeopardy/adverse mod.

is likely andunavoidable?

Services prepare Biological Opinion

(BO) and Incidental Take Statement

YES

YES

YES

NO

NO

NO YES

NO

YES (MA-LAA)

NO

YES (MA-NLAA)

Document“May Affect, Likely

to Adversely Affect”


Document

PROJECT CAN NOT PROCEED

NYSDOT sendsNE determination and supportinginfo to action agency for

concurrence

Action Agency begins Formal

Consultation with Services

(135 days)

Info

rmal

Con

sulta

tion

YES

Hasthe Action

Agency providedconcurrence with

the NE deter-mination?

Action Agency provides written authorization to proceed (stating

necessary project modification/conservation

measures, when applicable)

Services provide concurrence

with MA-NLAA determination

(cc: NYSDOT)

NYSDOT provides Action Agency with

“May Affect” determination and

supporting info

(FHWA Web BA tool is recommended)

Action Agency prepares final BA/BE

with MA-NLAA or MA-LAA

determination and begins coordination

with Services5

Action Agency provides written authorization to proceed (in accordance

with reasonable and prudent alternatives/

measures, when applicable)

Services, Action Agency and

NYSDOT jointly develop

appropriate project modification/conservation

measures

Review state atlases2

and NYNHP databasefor occurrence of listed

species or rare/significant communities in the screening area3

Conduct a habitat assessment of the project action area for all federally

listed species identified during screening4

Complete appropriate habitat assessment forms, if available, to document

findings

DidServices concur?

NYSDOT/Action Agency may initiate the Exemption

process

Review USFWS-NYFO website for county-level

screening of federal sp.

Contact NMFS to determine presence of Desig- nated Critical Habitat (marine species only)

Arefederally

listed speciesor Designated Critical Habitat indicated for

the projectcounty?

NO

final, 8/15/111. FHWA is the Federal Action Agency when federal funding is used. If no federal aid exists, the Federal Action Agency is that agency with the primary responsibility for the action (e.g., permit issuance).

2. New York State Breeding Bird Atlas, New York State Amphibian & Reptile Atlas, and New York Flora Atlas.3. Refer to TEM 4.4.9.3 Endangered and Threatened Species for screening distances.4. Refer to NYNHP Conservation Guides and other available published information.5. “Services” refers to USFWS and/or NMFS as appropriate given the species in question.NOTE: This flow chart is intended to illustrate the general process. Refer to TEM 4.4.9.3 Endangered and Threatened Species for detailed procedures.


August 2011 TEM 4.4.9.3

4.4.9.3.10 Local Projects Guidance

Sponsors of locally-administered federal aid projects must follow the procedures stated above toensure compliance with state (State Endangered and Threatened Species Subsection) and federal(Federal Endangered and Threatened Species Subsection) endangered species regulations. Forsuch projects, FHWA is always the federal action agency.

The project sponsor or its consultant is responsible for the species screening and habitatassessment. For the purpose of federal coordination, the results of these analyses are to be sentto FHWA through the Regional Local Projects Liaison. FHWA will then make an effectdetermination and, if necessary, request the Services’ concurrence. The Services will notofficially concur with an effect determination made directly by the local project sponsor unlessthat sponsor has been designated by FHWA as its non-federal representative. Currently, nomunicipalities in NYS bear this designation.

Regional environmental staff may provide local sponsors with support and/or quality assuranceupon request. Further assistance regarding technical/biological questions may be obtained fromUSFWS, NMFS, NYSDEC or NYNHP.

4.4.9.3.11 Appendices

A. Legal Citation

The following state and federal laws and regulations are used as a source for the proceduresoutlined in this section:

Federal Laws/Statutes

Endangered Species Act, 87 Stat. 884, as amended; 16 U.S.C. 1531-1544

Federal Regulations

50 C.F.R. Parts 17 and 402

New York State Laws/Statutes

Environmental Conservation Law, Article 9, Title 15

Environmental Conservation Law, Article 11, Title 5

New York State Regulations

6 NYCRR Part 182

6 NYCRR Part 193

http://www.law.cornell.edu/uscode/16/usc_sup_01_16_10_35.html

http://ecfr.gpoaccess.gov/cgi/t/text/text-idx?sid=7ce6afd46b65b05865c32822d454c15a&c=ecfr&tpl=/ecfrbrowse/Title50/50tab_02.tpl

http://public.leginfo.state.ny.us/LAWSSEAF.cgi?QUERYTYPE=LAWS+&QUERYDATA=@SLENV0A9T15+&LIST=LAW+&BROWSER=EXPLORER+&TOKEN=34506398+&TARGET=VIEW

http://public.leginfo.state.ny.us/LAWSSEAF.cgi?QUERYTYPE=LAWS+&QUERYDATA=@SLENV0A11T5+&LIST=LAW+&BROWSER=EXPLORER+&TOKEN=34506398+&TARGET=VIEW

http://www.dec.ny.gov/regs/3932.html



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B. Scope of Services

Base Scope of Services Section 5050 – General Ecology and Endangered Species:https://www.dot.ny.gov/portal/page/portal/divisions/engineering/design/consultant-management/base-scope

C. Definitions

Action Area: the area directly or indirectly affected by the proposed action. This area willusually be larger than the project footprint. Direct and indirect effects may be eithertemporary or permanent in nature and include, but are not limited to: earthmoving; vegetativecommunity alteration; hydrologic alteration; lighting; noise; and water quality.

Beneficial Effects: contemporaneous positive effects without any adverse effects to thespecies.

Biological Assessment: a document prepared for the Section 7 process to determine if aproposed major construction activity under the authority of a federal action agency is likelyto: (1) adversely affect listed species or designated critical habitat; (2) jeopardize thecontinued existence of species that are proposed for listing; or (3) adversely modify proposedcritical habitat.

Biological Evaluation: a document that is essentially equivalent to a biological assessment,but is prepared for a project that is not considered a major construction activity.

Biological Opinion: a document stating the opinion of USFWS or NMFS on whether or nota federal action is likely to jeopardize the continued existence of listed species or result in thedestruction or adverse modification of critical habitat.

Candidate Species: plants and animals for which the U.S. Fish and Wildlife Service hassufficient information on their biological status and threats to propose them as endangered orthreatened under the Endangered Species Act, but for which development of a proposedlisting regulation is precluded by other higher priority listing activities. Candidate speciesare not provided protection under the ESA.

Critical Habitat: specific geographic areas, whether occupied by a listed species or not, thatare essential for its conservation and that have been formally designated by rule published inthe Federal Register.

Direct Effects: the direct or immediate effects of an action on a species or its habitat,whether beneficial or adverse, occurring at or very close to the time of the action itself.Examples include direct habitat loss and construction-related disturbances such as: noise,light, degraded air quality/water quality, ground disturbance, vegetation disturbance, andhydrologic alteration.

Discountable Effects: those effects of an action that are extremely unlikely to occur.

http://www.dot.ny.gov/portal/page/portal/divisions/engineering/design/consultant-management/base-scope

http://www.dot.ny.gov/portal/page/portal/divisions/engineering/design/consultant-management/base-scope


August 2011 TEM 4.4.9.3

Emergency: as defined by 50 C.F.R. § 402.05(a), situations involving acts of God, disasters,casualties, national defense or security emergencies, etc. Predictable events usually do notqualify as emergencies under the Section 7 regulations unless there is a significantunexpected human health risk.

Endangered Species (State): as defined by 6 NYCRR § 182.2(g) and 193.3(b), any speciesof fish, shellfish, crustacea, wildlife or plant that are native species in imminent danger ofextirpation or extinction in New York or are federally listed as endangered.

Endangered Species (Federal): any species which is in danger of extinction throughout allor a significant portion of its range and is listed as endangered in 50 C.F.R. §§ 17.11-17.12.

Endangered Species Act: the Endangered Species Act of 1973, a federal statute.

Federal Action: any action that is carried out, permitted, licensed, funded, or otherwiseauthorized by a federal agency.

Incidental Take: taking of listed fish or wildlife species that results from, but is not thepurpose of, carrying out an otherwise lawful activity conducted by a federal agency orapplicant.

Indirect Effects: those effects of an action that occur later in time after the action iscompleted. Examples include long-term changes to ecological systems such as: alteredpredator/prey relationships and increased potential for animal-vehicle collision; habitatalteration and fragmentation; and anticipated changes in human activities, including changesin land use.

Insignificant Effects: effects of an action that, due to the limited size of the impact, shouldnever reach the scale where a taking occurs. They can not be meaningfully measured,detected, or evaluated.

Known Occurrences: locations of rare plants and animals where the plant or animal hasbeen documented since 1980 and where the precise location is known.

Listed Species: any species of fish, shellfish, crustacea, wildlife or plant that has beendetermined to be endangered or threatened and is listed in 50 C.F.R. §§ 17.11-17.12 or 6NYCRR § 182.6.

Major Construction Activity: a construction project (or other undertaking having similarphysical impacts) which is a major federal action significantly affecting the quality of thehuman environment as referred to in the National Environmental Policy Act [NEPA, 42U.S.C. 4332(2)(C)], thus triggering the need for an Environmental Impact Statement.

Native Species: as defined by 6 NYCRR § 182.2(d), any species which spends some portionof its life cycle within New York State, has occurred in New York State on a regular basis for


August 2011 TEM 4.4.9.3

many years, and was not intentionally or accidentally released in New York or formerly metthe conditions of this definition.

Occupied Habitat: as defined by 6 NYCRR § 182.2(o), means a geographic area in NewYork within which a species listed as endangered or threatened in this Part has beendetermined by the NYSDEC to exhibit one or more essential behaviors. Once identified asoccupied habitat, the NYSDEC will continue to consider that area as occupied habitat untilthe area is no longer suitable habitat for that species or monitoring has indicated thatreoccupation by that species is unlikely.

Potential Occurrences: locations of rare plants and animals where the last documentation isbefore 1980, and/or where the precise location is not known (e.g., known only to the level oftown or NYS Breeding Bird Atlas survey block). These records indicate species that mayoccur at a specific site, if habitat and site conditions are favorable.

Proposed Species: as defined in 50 C.F.R. § 402.02, any species of fish, wildlife or plantthat is proposed in the Federal Register to be listed in 50 C.F.R. §§ 17.11-17.12.

Protected Plants: as defined by 6 NYCRR § 193.3, any plant species listed by NYSDEC asendangered, threatened, rare or exploitably vulnerable, including all plant species listed asendangered or threatened by USFWS in 50 C.F.R. § 17.12.

Reasonable and Prudent Alternatives: as defined in 50 C.F.R. § 402.02, recommendedalternative actions identified during formal consultation that can be implemented in a mannerconsistent with the intended purpose of the action, that can be implemented consistent withthe scope of the Federal action agency's legal authority and jurisdiction, that areeconomically and technologically feasible, and that the Director [of the Service] believeswould avoid the likelihood of jeopardizing the continued existence of listed species or thedestruction or adverse modification of designated critical habitat.

Reasonable and Prudent Measures: as defined in 50 C.F.R. § 402.02, actions that theDirector [of the USFWS or NMFS] believes necessary or appropriate to minimize theimpacts, i.e., amount or extent, of incidental take.

Screening Area: the area surrounding and including the project action area in whichscreening for records of occurrence of protected species is focused.

Species of Special Concern: as defined by 6 NYCRR § 182.2(i), species of fish and wildlifefound by NYSDEC to be at risk of becoming threatened in New York and are listed in 6NYCRR § 182.6(c). Species of special concern do not qualify as either endangered orthreatened and are not subject to the provisions of 6 NYCRR Part 182.

Take: as defined by Section 3(19) of the Federal Endangered Species Act, to harass, harm,pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any suchconduct. This includes direct injury, significant habitat modification or degradation that


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results in death or injury, and significant impairment of behavioral patterns such as breeding,feeding, or sheltering.

Threatened Species (State): as defined by 6 NYCRR § 182.2(h) and 193.3(c), any fish,shellfish, crustacea, wildlife or plant species that are native species likely to become anendangered species within the foreseeable future in New York or are federally listed asthreatened.

Threatened Species (Federal): any species which is likely to become an endangered specieswithin the foreseeable future throughout all or a significant portion of its range and is listedas threatened in 50 C.F.R. §§ 17.11-17.12.

D. References/Technical Documents

NYSDEC List of Endangered, Threatened and Special Concern Fish & Wildlife Species:http://www.dec.ny.gov/animals/7494.html

NYSDEC List of Protected Native Plants:http://www.dec.ny.gov/regs/15522.html

NYS Joint Application Form:http://www.dec.ny.gov/permits/6222.html

NYSDOT habitat assessment forms:http://www.dot.ny.gov/divisions/engineering/environmental-analysis/water-ecology/wildlife

NatureServe Explorer:http://www.natureserve.org/explorer/

New York Natural Heritage Program website:http://www.dec.ny.gov/animals/29338.html

New York Natural Heritage Program Conservation Guides:http://www.acris.nynhp.org/

New York Flora Atlas website:http://www.newyork.plantatlas.usf.edu/

New York State Amphibian & Reptile Atlas Project (Herpetile Atlas) website:http://www.dec.ny.gov/animals/7140.html

New York State Breeding Bird Atlas website:http://www.dec.ny.gov/animals/7312.html

FHWA ESA Webtool and National BA Template:http://www.environment.fhwa.dot.gov/esawebtool

http://www.dec.ny.gov/animals/7494.html


http://www.dec.ny.gov/permits/6222.html

http://www.dot.ny.gov/divisions/engineering/environmental-analysis/water-ecology/wildlife

http://www.natureserve.org/explorer/


http://www.acris.nynhp.org/

http://www.newyork.plantatlas.usf.edu/



http://www.environment.fhwa.dot.gov/esawebtool


August 2011 TEM 4.4.9.3

FHWA Joint Agency Agreement on the ESA Formal Consultation Process:http://nepa.fhwa.dot.gov/ReNepa/ReNepa.nsf/All+Documents/79681451970F2A5A85256FB1004F9C17/$FILE/JOINT AGENCY AGREEMENT ON ESA FORMALCONSULTATION PROCESS FINAL.pdf

FHWA Guidance Memorandum on Management of the Endangered Species Act (ESA)Environmental Analysis and Consultation Process:http://www.fhwa.dot.gov/environment/esaguide.htm

USFWS Endangered Species Program website:http://www.fws.gov/endangered/

USFWS New York Field Office, County Lists of Endangered, Threatened and CandidateSpecies:http://www.fws.gov/northeast/nyfo/es/CountyLists/CountySelect.htm

USFWS New York Field Office, Section 7 Consultation website:http://www.fws.gov/northeast/nyfo/es/section7.htm

USFWS/NMFS ESA Section 7 Consultation Handbook:http://www.fws.gov/endangered/consultations/s7hndbk/s7hndbk.htm

USFWS/NMFS ESA Section 10 Habitat Conservation Planning Handbook:http://www.fws.gov/endangered/esa-library/index.html#hcp

USFWS Information, Planning and Consultation System (IPaC):http://ecos.fws.gov/ipac/

USFWS Threatened and Endangered Species database System (TESS):http://ecos.fws.gov/tess_public/

E. Contacts

NYSDOT Environmental Science BureauProgram Area ContactBrandon Greco50 Wolf Road, POD 4-1, Albany, NY 12232(518) 485-7753(518) 457-6887 (fax)[email protected]

http://nepa.fhwa.dot.gov/ReNepa/ReNepa.nsf/All+Documents/79681451970F2A5A85256FB1004F9C17/$FILE/JOINT AGENCY AGREEMENT ON ESA FORMAL CONSULTATION PROCESS FINAL.pdf



http://www.fhwa.dot.gov/environment/esaguide.htm

http://www.fws.gov/endangered/

http://www.fws.gov/northeast/nyfo/es/CountyLists/CountySelect.htm

http://www.fws.gov/northeast/nyfo/es/section7.htm

http://www.fws.gov/endangered/consultations/s7hndbk/s7hndbk.htm

http://www.fws.gov/endangered/esa-library/index.html#hcp

http://ecos.fws.gov/ipac/

http://ecos.fws.gov/tess_public/

mailto:[email protected]


August 2011 TEM 4.4.9.3

New York State Department of Environmental Conservation (NYSDEC)

NYSDEC Regional Wildlife Manager (first point of contact):http://www.dec.ny.gov/about/50230.html

-or-

NYSDEC Central OfficeEndangered Species UnitWildlife Diversity Group625 Broadway, Albany, NY 12233(518) 402-8859(518) 402-8925 (fax)

U.S. Fish and Wildlife Service (USFWS)

For projects in New York City and Long Island:Long Island Field Office3 Old Barto Road, Brookhaven, NY 11719(631) 776-1401(631) 776-1405 (fax)

For projects outside of New York City and Long Island:New York Field Office3817 Luker Road, Cortland, NY 13045(607) 753-9334(607) 753-9699 (fax)

National Marine Fisheries Service (NMFS)

For ESA Section 7 consultation:Northeast Regional Office55 Great Republic Drive, Gloucester, MA 01930Julie Crocker ([email protected])(978) 282-8480(978) 281-9333 (fax)

For questions regarding the presence of listed species or critical habitat:Northeast Fisheries Science Center212 Rogers Avenue, Milford, CT 06460-6499Diane Rusanowsky ([email protected])(203) 882-6568(203) 882-6570 or -6517 (fax)

http://www.dec.ny.gov/about/50230.html




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Federal Highway Administration (FHWA)

New York Division Office

Planning and Program Development

Leo W. O'Brien Federal Building, Suite 719

Clinton Avenue & North Pearl Street, Albany, NY 12207

(518) 431-4125

(518) 431-4121 (fax)

F. Sample Statements

To be developed.

G. FHWA ESA Section 7 Process

(Issued via EB 17-024)

H. Coordination Regarding Waterbodies Supporting S1 or S2 Mollusks

(Issued via EB 18-010)


https://www.dot.ny.gov/portal/pls/portal/mexis_app.pa_ei_eb_admin_app.show_pdf?id=12436


https://www.dot.ny.gov/portal/pls/portal/MEXIS_APP.EI_EB_DOC_DETAILS.show?p_arg_names=doc_id&p_arg_values=12762