Species covered

Species with a Likely to Adversely Affect (LAA) Determination

The PBO analyzes impacts to species and critical habitats and provides take coverage for 36 animal species, including eight amphibians (with separate take coverage for distinct population segments of the California tiger salamander and foothill yellow-legged frog), four fish, three reptiles, eight birds, three mammals, and 10 invertebrate species. For those species that may be adversely affected by the restoration activities, the cooperating agencies proactively set self-imposed incidental take limits. ​

See the Self-Imposed Annual Take Limits in Section 2.1.5.1. Of the PBO. The take limit for each covered animal species is based on an annual limit that cannot be exceeded in any year. The take limits have been set using different metrics, including by field office, by project, by population, by recovery unit, by pond, and by occupied pool. 

Amphibians

• arroyo (=arroyo southwestern) toad (Anaxyrus californicus)
• California red-legged frog (Rana draytonii)
• California tiger salamander – Central California DPS (Ambystoma californiense)
• California tiger salamander – Santa Barbara County DPS (Ambystoma californiense)
• Foothill yellow-legged frog – Central Coast DPS (Rana boylii)
• Foothill yellow-legged frog – North Feather DPS (Rana boylii)
• Foothill yellow-legged frog – South Coast DPS (Rana boylii)
• Foothill yellow-legged frog – Southern Sierra DPS (Rana boylii)
• mountain yellow-legged frog – northern California DPS (Rana muscosa)
• Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum)
• Sierra Nevada yellow-legged frog (Rana sierrae)
• Yosemite toad (Anaxyrus canorus)

Reptiles

• Alameda whipsnake (Masticophis lateralis euryxanthus)
• giant garter snake (Thamnophis gigas)
• San Francisco garter snake (Thamnophis sirtalis tetrataenia)

Birds

• California least tern (Sterna antillarum browni)
• California Ridgway’s rail (Rallus obsoletus)
• coastal California gnatcatcher (Polioptila californica)
• least Bell’s vireo (Vireo bellii pusillus)
• light-footed Ridgway’s rail (Rallus obsoletus levipes)
• marbled murrelet (Brachyramphus marmoratus)
• Northern spotted owl (Strix occidentalis caurina)
• western snowy plover – Pacific Coast population DPS (Charadrius nivosus ssp. nivosus)

Mammals

• riparian woodrat (Neotoma fuscipes riparia)
• riparian brush rabbit (Sylvilagus bachmani riparius)
• salt marsh harvest mouse (Reithrodontomys raviventris)
• San Bernardino Merriam’s kangaroo rat (Critical Habitat Only) (Dipodomys merriami parvus )

Invertebrates

• California freshwater shrimp (Syncaris pacifica)
• Conservancy fairy shrimp (Branchinecta conservatio)
• longhorn fairy shrimp (Branchinecta longiantenna)
• Mount Hermon June beetle (Polyphylla barbata)
• Riverside fairy shrimp (Streptocephalus woottoni)
• San Diego fairy shrimp (Branchinecta sandiegonensis)
• Smith’s blue butterfly (Euphilotes enoptes smithi)
• valley elderberry longhorn beetle (Desmocerus californicus dimorphus)
• vernal pool fairy shrimp (Branchinecta lynchi)
• vernal pool tadpole shrimp (Lepidurus packardi)

Fish

• Delta smelt (Hypomesus transpacificus)
• Lahontan cutthroat trout (Oncorhynchus clarkii henshawi)
• tidewater goby (Eucyclogobius newberryi)
• unarmored threespine stickleback (Gasterosteus aculeatus williamsoni)

Non-vernal pool Plant Species

• Ben Lomond spineflower (Chorizanthe pungens var. hartwegiana)
• California seablite (Suaeda californica)
• La Graciosa thistle (Cirsium loncholepis)
• marsh sandwort (Arenaria paludicola)
• salt marsh bird’s-beak (Cordylanthus maritimus ssp. maritimus)
• Ventura marsh milk-vetch (Astragalus pycnostachyus var. lanosissimus)

Vernal Pool Plant Species

• Butte County meadowfoam (Limnanthes floccosa ssp. californica)
• California orcutt grass (Orcuttia californica)
• Contra Costa goldfields (Lasthenia conjugens)
• few-flowered navarretia (Navarretia leucocephala ssp. pauciflora)
• fleshy owl’s-clover (Castilleja campestris ssp. succulenta)
• hairy orcutt grass (Orcuttia pilosa)
• Hoover’s spurge (Chamaesyce hooveri)
• Otay Mesa-mint (Pogogyne nudiuscula)
• Sacramento orcutt grass (Orcuttia viscida)
• San Diego ambrosia (Ambrosia pumila)
• San Diego button-celery (Eryngium aristulatum var. parishii)
• San Joaquin orcutt grass (Orcuttia inaequalis)
• slender orcutt grass (Orcuttia tenuis)
• spreading navarretia (Navarretia fossalis)
• thread-leaved brodiaea (Brodiaea filifolia)

Species with a Not Likely to Adversely Affect (NLAA) Determination

Birds

• Southwestern willow flycatcher (Empidonax traillii extimus)
• Yellow-billed cuckoo – Western DPS (Coccyzus americanus)

Mammal

• San Bernardino Merriam’s kangaroo rat (Species only) (Dipodomys merriami parvus)

Plants

• Howell’s spineflower (Chorizanthe howellii)
• Palmate-bracted bird’s-beak (Cordylanthus palmatus)
• Pedate checker-mallow (Sidalcea pedate)
• Santa Ana River woolly-star (Eriastrum densifolium ssp. sanctorum)
• Slender-horned spineflower (Dodecahema leptoceras)
• Soft bird’s-beak (Cordylanthus mollis spp. Mollis)
• Sonoma alopecurus (Alopecurus aequalis var. sonomensis)
• Suisun thistle (Cirsium hydrophilum var.hydrophilum)

Activities covered

See Section 2.1.3. Eligible Project Types and Design Guidelines of the PBO, starting on page 25 (page 43 of the PDF) for the full description of eligible project types and design guidelines.

1. Improvements to stream crossings and fish passage – Projects to address upstream and downstream movement by fish and other species, and to improve functions of streams
2. Removal of small dams, tide gates, flood gates, and legacy structures – Projects to improve fish and wildlife migration, tidal and freshwater circulation and flow, and water quality
3. Bioengineered bank stabilization – Projects to reduce fine sediment input, enhance aquatic and riparian habitat, and improve water quality
4. Restoration and enhancement of off-channel and side-channel habitat – Projects to improve aquatic and riparian habitat for fish and wildlife
5. Water conservation projects for enhancement of fish and wildlife habitat – Projects such as off-stream storage tanks and ponds, and including necessary off-channel infrastructure, to reduce low-flow stream diversions
6. Floodplain restoration – Projects including levee, berm, and dike setback; breaching and removal; and hydraulic reconnection and revegetation to improve ecosystem function through hydrological connection between streams and floodplains
7. Removal of pilings and other in-water structures – Projects to improve water quality and aquatic habitat for fish and wildlife
8. Removal of nonnative terrestrial and aquatic invasive species and revegetation with native plants – Projects to improve aquatic and riparian habitat for fish and wildlife and improve other watershed functions
9. Establishment, restoration, and enhancement of tidal, subtidal, and freshwater wetlands – Projects to restore and improve ecological functions and services of tidal, subtidal, and freshwater wetlands, including actions to benefit vernal pools and managed wetlands
10. Establishment, restoration, and enhancement of stream and riparian habitat and upslope watershed sites – Projects to restore and improve ecological functions and services of streams and riparian areas

Exclusions

The following activities are not within the scope of the PBO, and will require separate authorization:

1. Use of gabion baskets
2. Use of cylindrical riprap (e.g., Aqualogs).
3. Construction of permanent dams or concrete-lined channels of any sort.
4. Use of chemically treated timbers used for grade or channel stabilization structures, bulkheads, or other instream structures.
5. Activities that substantially disrupt the movement of those species of aquatic life indigenous to the waterbody, including those species that normally migrate through the project areas.
6. Elimination of a riffle, pool, or riffle/pool complex that is not replaced/enhanced elsewhere by the project.
7. New water diversions that would cause listed aquatic species stranding (i.e., those without controls that provide functional separation of the species from the project supported by the new diversion), except to temporarily dewater a project site (some water conservation projects are allowed under the Proposed Restoration Effort [Section 2.1.3.5, Water Conservation Projects for Enhancement of Fish and Wildlife Habitat]) or for diversions associated with delivery or conveyance to and within managed wetlands as described in Section 2.1.3.9.
8. Installation of flashboard dams, head gates, or other mechanical structures that would cause listed aquatic species stranding are generally prohibited; however, there are exceptions for certain projects that require them to meet ecological goals (e.g., storage projects to reduce low flow stream diversions [Section 2.1.3.5, Water Conservation Projects for Enhancement of Fish and Wildlife Habitat], off-channel/side-channel, managed floodplain, and managed wetland habitat) and for the required replacement of legacy structures (Section 2.1.3.2 Removal of Small Dams, Tide gates, Flood gates, and Legacy Structures).
9. Creation or potential creation of a barrier to anadromous fish passage, as determined by the NMFS fish passage guidelines (including any associated maintenance activities, or lack thereof).
10. Use of excess riprap bank protection or hard armoring of banks, other than the minimum amount needed to achieve project goals, as determined by the Lead Action Agency in coordination with USFWS ES.
11. Installation of infiltration galleries.
12. Managed surrogate floodplain and managed returned flows that do not allow for volitional movement (ingress and egress) of fish to the main channel (up and/or downstream).
13. Projects that would result in a net loss of aquatic resource functions and/or services.
14. Projects that would result in a net loss of vernal pool habitat.
15. Projects that would result in a net loss of designated critical habitat function for any federally listed species. Loss of function is considered in the context of the physical and biological features as described in the respective critical habitat designation and includes abiotic and biotic resources and conditions necessary to support one or more life processes of the species.
16. Projects overlapping the current range of amphibians endemic to the Sierra Nevada (i.e., Sierra Nevada yellow legged frog, mountain yellow-legged frog (Northern California DPS), and Yosemite toad) that would extend the range of predatory fish (e.g., salmonids or centrarchids); because amphibians in the Sierra Nevada evolved mostly in the absence of predatory fish, the recovery of amphibians in the Sierra Nevada can be hindered by the presence of predatory fish.

Application Tips and Resources

Administrative Process Details

See the Administrative Process flowchart and Section 2.1.2. Administration of the PBO (starting on page 18, page 36 of the PDF) for more details about the application and post-construction reporting process.

The Federal Action Agencies will coordinate to evaluate project eligibility and to determine the role of Lead Action Agency for the proposed restoration project. The Lead Action Agency will vary depending on a project’s permitting and funding.

• If the USFWS provides funding through one of its programs, such as the USFWS FAC, Refuge, Coastal, Central Valley Joint Venture, or Partners programs, USFWS will likely be the Lead Action Agency.
• If a project is in a USFWS Refuge, USFWS will be the Lead Action Agency.
• If NOAA RC provides funding through one of its programs such as the Community-Based Restoration Program or NOAA’s DARRP, then NOAA RC will likely be the Lead Action Agency.
• USACE may serve as the Lead Action Agency if the project requires Clean Water Act Section 404 and/or Rivers and Harbors Act Section 10 and/or 408 authorization.

The Section 7(a)(2) Review Form is used to document metrics needed to calculate estimated incidental take so that the USFWS Field Office can identify the incidental take expected from the project and enter that estimate into a USFWS-maintained internal tracking tool. ​

The goal is that within 30 calendar days (and in no more than 60 days) of receiving a complete Review Form, the Lead Agency will:

1. review the Form for completeness;
2. if the Form is complete, submit the Form to the USFWS Field Office to request concurrence of coverage under the PBO, and
3. notify the Project Proponent if their Form is complete or incomplete. Response times will depend on the nature of the project and the amount of coordination that has occurred prior to submitting the Review Form.​

Project Proponents are responsible for conducting all applicable project monitoring and reporting requirements prior to, during, and after project construction (e.g., revegetation monitoring, species rescue, and relocation reporting), and submitting the Post-construction Report Form to the Field Office and lead agency by December 1.

If there is ongoing revegetation or species monitoring beyond the report due date, a report will be provided annually on December 1 until success criteria have been met or monitoring has ceased.

In addition, the Field Office should be notified of all injury or mortality of listed species within 48 hours. The Post-construction Report Form will be used to document actual incidental take from the project.​

Late Arriving Action Agency Process

In addition to the Action Agencies identified above and the multiple programs associated with these Action Agencies, this PBO may also provide section 7(a)(2) consultation coverage for federal agencies that are not a part of this programmatic consultation but later request to use the PBO for restoration actions they fund, oversee, or carry out. Such federal agencies are referred to as a “Late Arriving Action Agency.”

The Late Arriving Action Agency can choose to use the PBO or not. If they choose to use the PBO, they would need to ensure any restoration actions they propose to be covered by this PBO meet all the requirements of the PBO and coordinate with the USFWS to determine which of the following options are available:

1. If the USFWS Field Office concludes that no additional analysis, protection measures, or terms and conditions are necessary or appropriate, the USFWS Field Office could include the federal agency as a Late-Arriving Action Agency via formal correspondence indicating their participation in the Effort and potential to use the ESA Section 7(a)(2) Review Form process to potentially be covered by this PBO.
2. The USFWS Field Office could require the Late-Arriving Action Agency to initiate a new separate consultation with the USFWS Field Office, with some efficiencies potentially available by incorporating the PBO by reference in the new consultation, along with information specific to the Late-Arriving Action Agency and any new protection measures and terms and conditions.
3. The USFWS Field Office could recommend the use of other existing programmatic biological opinions or a combination of such biological opinions, if available and appropriate.
4. If additional analysis, incidental take, or terms and conditions are necessary or appropriate, the USFWS Field Office could reinitiate consultation to revise the PBO to accommodate the Late Arriving Action Agency. However, due to workload constraints, this option would not be the most efficient path.