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Biological Resources, including Endangered Species

The effects of a proposed project on wildlife and vegetation, including rare animal and plant species and their habitats, must be considered as part of the NEPA process. The primary legal mandates that protect fish and wildlife species include the Endangered Species Act of 1973 (16 USC § 1531), Migratory Bird Treaty Act (16 USC § 703), Magnuson-Stevens Fishery Conservation and Management Act, and the Marine Mammal Protection Act of 1972. In addition, Section 4(f) of the U.S. Department of Transportation Act provides protection for publicly-owned wildlife and waterfowl refuges that are significant resources functioning primarily for refuge purposes.

What is the Endangered Species Act?
The Endangered Species Act of 1973 (16 USC § 1531) protects “endangered” and “threatened” species and the critical habitat on which they depend. An "endangered" species is one that is "in danger of extinction" throughout all or a significant portion of its range. A "threatened" species is one that is "likely to become endangered" within the foreseeable future. The U.S. Fish and Wildlife Service (FWS) coordinates Endangered Species Act (ESA) activities for terrestrial and freshwater species, and the National Marine Fisheries Service (NMFS) coordinates ESA activities for marine and anadromous species. FWS and NMFS are jointly referred to as “the Services.”

Under ESA, the Services list plant and animal species that are endangered or threatened, and also designate the species’ “critical habitat.” The Services must base theirlisting decisions solely on the best scientific and commercial data available, and the Act expressly prohibits consideration of economic impacts during the listing process (although they may be considered during habitat designation). Section 7 of the ESA requiresconsult with the Services if they are proposing an "action" that may affect listed species or their designated habitat. Action is defined broadly to include funding, permitting and other regulatory actions. Section 7 applies to any local or state government project that requires a federal permit or receives federal funding.The consultation process is described in detail below. 

In addition to the procedural consultation requirement, ESA substantively prohibits any requires interagency cooperation to ensure that actions (i.e. funding or authorization) taken by Federal agencies do not jeopardize the existence of any listed species. Any federal action that would jeopardize a listed species or destroy or adversely modify its critical habitat, and Section 9 prohibits anyone from “taking” an individual of a listed species.

What is FTA's Endangered Species Coordination Process?
FTA, in consultation with the Services, must ensure that no federally funded mass transportation projects will jeopardize the continued existence of any listed species, or result in the destruction or adverse modification of critical habitat. During project scoping, FWS and NMFS should be contacted for information about listed species that may be present in the project area. The Services maintain comprehensive listings of endangered and threatened wildlife and plants are maintained on their websites.

Section 7 Process: FTA must consult with the appropriate Service when any activity permitted, funded or conducted by it may affect a listed species or designated critical habitat, or is likely to jeopardize proposed species or adversely modify proposed critical habitat. The Service conducts several types of consultations on federal agency activities, most commonly informal or formal consultations for listed species or designated critical habitats. Title 50: Part 402 (50 CFR Part 402) establishes requirements for the consultation process.

Informal Consultation: Informal consultation precedes formal consultation, and usually begins with a request to FWS or NMFS for information on endangered species in the project area. Discussions during this phase may include whether and which species may occur in the proposed action area and what effect the action may have on listed species or critical habitats. Informal consultation often concludes with the Service's written concurrence with the federal agency's determination that its action is not likely to adversely affect listed species or their critical habitat.

If listed or proposed species or critical habitats are identified as potentially being present within the project area and would likely be adversely affected by the proposed project, a biological assessment (as defined in the Section 7 regulations) (BA) must be prepared to identify probable locations of, and project effects on, listed species and habitat. Typically, the grant applicant and/or its consultant will prepare a draft BA for FTA review and approval. FTA will submit the final BA to the Services for their review.  If timing allows, the results of the BA should be included or summarized in the draft Environmental Impact Statement (EIS) or Environmental Assessment (EA). If the BA concludes that no listed or proposed species or critical habitat will be adversely affected and the Services concur in writing with that conclusion, the consultation process is terminated.

Formal Consultation: If the BA assessment concludes that the action is likely to cause adverse effects, FTA must initiate a formal consultation process. Section 7 specifies the information that must be included in the request for formal consultation. Again, the grant applicant and/or its consultant typically prepare the draft for FTA’s review and approval and submission to the Services. After reviewing the required information, the Services will issue a “biological opinion” (BO) on whether the action is or is not likely to jeopardize the continued existence of a listed species or result in the destruction or adverse modification of critical habitat.

If the opinion states that the action is not likely to jeopardize a listed species or destroy/adversely modify critical habitat, the issuance of the opinion ends the consultation process. Where appropriate, the biological opinion may provide an exemption for the  of listed species and specify the extent of “incidental take” allowed, identify the Reasonable and Prudent Measures (RPMs) necessary to minimize impacts from the Federal action, and include Terms and Conditions with which the project must comply. If a jeopardy biological opinion is issued, it must include reasonable and prudent alternatives (RPAs) to the proposed action that will not jeopardize the species. The biological opinion should be included in the final EIS or EA.

FTA strongly prefers not to publish an EA or Final EIS until the biological opinion is complete. The opinion must be complete before FTA can issue a ROD or FONSI. When a jeopardy opinion is involved, the formal consultation process ends when FTA submits its final decision on the project to the Service. Informal consultation may and should continue during project design. Re-initiation of consultation may be required if there are significant changes to the project design, its anticipated effects, or the status of affected species, or if new species are listed.

Online Certification: For some areas of the U.S. an online tool is available to expedite Section 7 consultations. This tool expedites consultation requests by offering an online certification for projects that are located on specified USGS topographic maps. If the project falls within a quad that has been determined to not contain threaten or endangered species, an online certification letter is instantly provided, which concludes the Section 7 consultation.

There are also certain activities that automatically receive a letter because the U. S. Fish and Wildlife Service has determined that these activities do not jeopardize listed species or destroy or adversely modify critical habitat. The use of these tools should be applied to a greater extent throughout the environmental permitting and review process to help improve the efficiency of Federal actions without undermining environmental protection.

How are migratory birds protected?
The Migratory Bird Treaty Act of 1918 (MBTA (16 USC § 703-1)) prevents the “taking” (as defined in 50 CFR Part 10.12) of birds listed as "migratory birds," including all common songbirds, waterfowl, shorebirds, raptors, owls, crows, native doves and pigeons, swifts, and swallows. The responsibilities of Federal agencies to protect migratory birds are set forth in . US Fish and Wildlife Service (FWS) is the lead agency for migratory birds. Federal-aid transit projects that are likely to result in take of birds protected under the MBTA may require take permitsfrom FWS. Unlike ESA, there is not a clear regulatory process to define consultation.

How are fish species and marine mammals protected?
The Magnuson-Stevens Fishery Conservation and Management Act (Public Law 94-265, as amended through January 12, 2007) conserves and manages the nation’s fishery resources through fishery management plans (FMPs). The Magnuson-Stevens Act (MSA) mandates that the National Oceanic and Atmospheric Administration's National Marine Fisheries Service (NOAA Fisheries) coordinate with and provide information to federal agencies to further the conservation and enhancement of an essential fish habitat (EFH). Federal agencies must consult with NOAA Fisheries on any action that might adversely affect EFH. NOAA Fisheries must provide conservation recommendations (mitigation) when it finds that a federal or state action would adversely affect EFH. When a project may affect listed fish species, FTA commonly consults with NOAA-Fisheries on MSA issues at the same time that it consults under Section 7 of ESA.  Note, however, that MSA applies to many non-listed fish.

The Marine Mammal Protection Act (MMPA) of 1972(16 USC Parts 1361 through 1407) protects all marine mammals, whether listed or not. The MMPA generally prohibits "taking" of marine mammals in U.S. waters by any person and by U.S. citizens in international waters. “Take” under this act is even more broadly defined than under ESA. If a proposed project could result in a “take” of these mammals, NOAA Fisheries may authorize an incidental take for ESA and non-ESA protected marine mammals. The NOAA Fisheries webpage includes more information regarding marine mammal permits and authorizations Note that compliance with ESA does not satisfy MMPA for listed marine mammals. Note, too, that the process for securing NOAA-Fisheries’ authorization for a take under MMPA can be very time-consuming and require a federal rulemaking.

Additional Resources:

  • Endangered Species Bulletin
    • Used by the U.S. Fish and Wildlife Service to disseminate information on rulemakings (listings, reclassifications, and de-listings), recovery plans and activities, regulatory changes, interagency consultations, changes in species' status, research developments, new ecological threats, and a variety of other issues related to the endangered species program.
  • U.S. Fish and Wildlife Service Endangered Species Program 
  • Marine Mammal Protection website and regulations, 50 CFR Part 216
    • These regulations restricts the taking, possession, transportation, selling, offering for sale, and importing of marine mammals.
  • Executive Order 13186 – Responsibilities of Federal Agencies to Protect Migratory Birds, January 10, 2001
Updated: Wednesday, March 16, 2016
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