United States Department of the Interior FISH AND WILDLIFE SERVICE Idaho Fish and Wildlife Office - Spokane 11103 East Montgomery Drive Spokane Valley, Washington 99206

January 30, 2018 Erin Chipps Environmental Protections Specialist Western Federal Lands Highway Division 610 E. Fifth Street Vancouver, WA 98661

Subject: Idaho Panhandle National Forests Roads and Bridges Repair Project—Bonner County, Idaho—Biological Opinion In Reply Refer to: 01EIFW00-2018-F-0035

Dear Ms. Chipps:

Enclosed are the U.S. Fish and Wildlife Service’s (Service) Biological Opinion (Opinion) and concurrence with the Federal Highway Administration’s (FHWA) determinations of effect on species listed under the Endangered Species Act (Act) of 1973, as amended, for the proposed Idaho Panhandle National Forests (IPNF) Roads and Bridges Repair Project in Bonner County, Idaho. In a letter received by the Service on December 1, 2017, the FHWA requested formal consultation on the determination under section 7 of the Act that the proposed project is likely to adversely affect bull trout (Salvelinus confluentus). The FHWA determined that the proposed project is not likely to adversely affect Canada lynx (Lynx canadensis), and grizzly bear (Ursus arctos horribilis) and bull trout critical habitat, and requested our concurrence with these determinations. The enclosed Opinion and concurrence are based primarily on our review of the proposed action as described in your December 2017 Biological Assessment (Assessment) and additional emails, as well as the anticipated effects of the action on listed species, and were prepared in accordance with section 7 of the Act. Our Opinion concludes that the proposed project will not jeopardize the survival and recovery of bull trout. A complete record of this consultation is on file at this office. Clean Water Act Requirement Language: This Opinion is also intended to address section 7 consultation requirements for the issuance of any project-related permits required under section 404 of the Clean Water Act. Use of this letter and Biological Opinion to document that the U. S. Army Corps of Engineers (Corps) has fulfilled its responsibilities under section 7 of the Act is contingent upon the following conditions: 1. The action considered by the Corps in their 404 permitting process must be consistent with the proposed project as described in the Assessment such that no detectable difference in the effects of the action on listed species will occur. Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project 2. Any terms applied to the 404 permit must also be consistent with conservation measures and terms and conditions as described in the Assessment and addressed in this letter and Biological Opinion. Thank you for your continued interest in the conservation of threatened and endangered species. Please contact Megan Kosterman at (509) 893-8013 if you have questions concerning this Opinion.

Sincerely,

For Gregory M. Hughes State Supervisor

Enclosure

cc: IDFG (Siitari)

2

BIOLOGICAL OPINION FOR THE IDAHO PANHANDLE NATIONAL FORESTS ROADS AND BRIDGES REPAIR PROJECT 01EIFW00-2018-F-0035

U.S. FISH AND WILDLIFE SERVICE IDAHO FISH AND WILDLIFE OFFICE SPOKANE VALLEY, WASHINGTON

______For Gregory M. Hughes State Supervisor

Date ______

Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Table of Contents 1. BACKGROUND ...... 7 1.1 Introduction ...... 7 1.2 Consultation History ...... 7 1.3 Concurrences ...... 8 1.3.1 Bull Trout Critical Habitat ...... 8 1.3.2 Canada Lynx ...... 8 1.3.3 Grizzly Bear ...... 9 2. BIOLOGICAL OPINION ...... 10 2.1 Description of the Proposed Action ...... 10 2.1.1 Action Area ...... 10 2.1.2 Proposed Action ...... 12 2.2 Analytical Framework for the Jeopardy Determination ...... 17 2.2.1 Jeopardy Determination ...... 17 2.3 Status of the Species ...... 18 2.3.1 Listing Status ...... 18 2.3.2 Reasons for Listing and Emerging Threats ...... 19 2.3.3 Species Description ...... 20 2.3.4 Life History...... 21 2.3.5 Population Dynamics ...... 22 2.3.6 Status and Distribution ...... 25 2.3.7 Conservation Needs ...... 30 2.4 Environmental Baseline of the Action Area ...... 32 2.4.1 Status of Bull Trout in the Action Area ...... 32 2.4.2 Factors Affecting Bull Trout in the Action Area ...... 39 2.5 Effects of the Proposed Action ...... 40 2.6 Cumulative Effects ...... 45 2.7 Conclusion ...... 45 2.8 Incidental Take Statement ...... 46 2.8.1 Form and Amount or Extent of Take Anticipated ...... 47 2.8.2 Effect of the Take ...... 47 2.8.3 Reasonable and Prudent Measures ...... 48 2.8.4 Terms and Conditions ...... 48

5 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project

2.8.5 Reporting and Monitoring Requirement ...... 48 2.9 Conservation Recommendations ...... 48 2.10 Reinitiation Notice ...... 49 3. LITERATURE CITED ...... 50 3.1 Published Literature ...... 50 3.2 In Litteris References ...... 58 3.3 Personal Communications ...... 58

List of Tables

Table 1. Redd counts within the Lightning Creek drainage, Idaho from 1983 through 2017. Surveys are conducted annually by the Idaho Department of Fish and Game...... 37 Table 2. Tributary monitoring results by stream, abundance, and density estimates sampled in 2012 (IDFG 2013)...... 38

List of Figures

Figure 1. Map showing the locations of the Lightning Creek repairs. Red denotes the location of the repair actions (FHWA 2017, p. 5)...... 11 Figure 2. NatureServe status assessment tool scores for each of the six bull trout recovery units. The Klamath RU is considered the least robust and most vulnerable, and the Upper Snake RU the most robust and least vulnerable (from USFWS 2015a, Figure 2)...... 30 Figure 3. Map showing the three parts that comprise the Lake Pend Oreille (LPO) core area. The action area is located in LPO-B between Cabinet Gorge Dam and Albeni Falls Dam...... 33 Figure 4. Number of bull trout redds in the Lake Pend Oreille Core Area (tributaries to Lake Pend Oreille basin proper including Priest River)...... 35 Figure 5. Lightning Creek (red box) is a tributary to the Clark Fork River, which flows into Lake Pend Oreille in northern Idaho. Map source: Irving 1986, p. 6...... 36

6 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project 1. BACKGROUND

1.1 Introduction The U.S. Fish and Wildlife Service (Service) has prepared this Biological Opinion (Opinion) of the effects of the Idaho Panhandle National Forests (IPNF) Roads and Bridges Repair Project (Project) on bull trout (Salvelinus confluentus). In a letter received by the Service on December 1, 2017, the Federal Highway Administration (FHWA) requested formal consultation with the Service under section 7 of the Endangered Species Act (Act) of 1973, as amended, for its proposal to carry out the action. The FHWA determined that the proposed action is likely to adversely affect bull trout. As described in this Opinion, and based on the Biological Assessment (Assessment; FHWA 2017, entire) developed by the FHWA and other email information provided by the FHWA, the Service has concluded that the action, as proposed, is not likely to jeopardize the continued existence of bull trout. The FHWA has also determined that the action is not likely to adversely affect Canada lynx (Lynx canadensis), grizzly bear (Ursus arctos horribilis), and bull trout critical habitat, and requested our concurrence with these determinations. In this document, the Service is providing concurrence with these determinations.

1.2 Consultation History The following correspondence and meetings have taken place between the FHWA and the Service prior to issuance of this Opinion. September 8, 2017 The Service’s Idaho Fish and Wildlife Office – Boise received the request for consultation and Assessment. October 11, 2017 The Service’s Idaho Fish and Wildlife Office – Spokane received the request for consultation and Assessment. October 20, 2017 The Service contacted the FHWA by phone to inform them that the Service would be unable to concur with their “may affect, not likely to adversely affect” determination for bull trout because the project will occur in bull trout spawning and rearing habitat. December 1, 2017 The Service received a revised Assessment from the FHWA with more detailed project action descriptions, updated conservation measures, and a “may affect, likely to adversely affect” determination for bull trout (and maintained the “may affect, not likely to adversely affect” determination for designated bull trout critical habitat). January 16, 2018 The Service provided a draft Biological Opinion to the FHWA. January 18, 2018 The Service received an email from the FHWA indicating that they had reviewed the Opinion and have no issues with the contents of the Opinion.

7 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project 1.3 Concurrences

1.3.1 Bull Trout Critical Habitat The FHWA has requested the Service’s concurrence with their determination that Project implementation may affect, but is not likely to adversely affect bull trout critical habitat. This section of Lightning Creek is designated spawning and rearing habitat (SR) critical habitat for bull trout. Project implementation has the potential to affect bull trout critical habitat through the introduction of sediment and short-term modification to physical or biological features. Project implementation will result in the introduction of sediment into Lightning Creek. However, as described in the Assessment (FHWA 2017, pp. 12-13), the Project includes implementation of BMPs and conservation measures specifically designed to minimize sediment effects, including dewatering the repair area and conducting repairs below the ordinary high water mark in an isolated, “dry” area; re-watering the dewatered area in a controlled manner to control sediment release; turbidity monitoring with response measures protective of bull trout; and limiting in-water work to periods of low river stages. Therefore, effects to bull trout critical habitat from sedimentation are expected to be temporary and insignificant. Additionally, dewatering portions of designated bull trout critical habitat will have direct effects to critical habitat in the form of temporary total loss of physical or biological features in the dewatered areas. However, this Project will not affect the ability of Lightning Creek to support its biological function as SR habitat, as fish passage will be available at all times. Further, the Project includes BMPs specifically designed to minimize effects to bull trout critical habitat (e.g., limiting in-water work to periods of low river stages, re-introducing water into dewatered areas in a controlled manner). Therefore, the short-term effects to a small portion of bull trout critical habitat from dewatering portions of Lightning Creek during Project implementation are expected to be insignificant. We have reviewed the information provided and concur with your finding that implementation of the proposed Project may affect, but is not likely to adversely affect bull trout critical habitat. Concurrence by the Service is contingent upon implementation of the Project and conservation measures as described in the Assessment, and in this Opinion.

1.3.2 Canada Lynx Project activities will occur within the Lightning and Trestle Lynx Analysis Units (LAUs), which is within an occupied, secondary area (USFWS 2005d, p. 6; USFWS 2006, p. 3). Service concurrence that the Project is not likely to adversely affect Canada lynx is based on the following rationales. 1. Lynx may occur within Project area; however, there have been no confirmed sightings of lynx in the Lightning and Trestle LAUs. 2. No mapped suitable habitat nor designated critical habitat for Canada lynx occurs within the Action Area, which is located below the typical elevational range for Canada lynx (4000 to 7000 feet). The Action Area may contain dispersal habitat for Canada lynx, providing genetic connectivity and linking higher quality habitats; however, the Action Area is not likely to be

8 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project occupied by Canada lynx for foraging and denning. 3. The LAUs currently meet all standards required by the Northern Rockies Lynx Management Direction (NRLMD). As described in the BA, Project activities will comply with all standards and guidelines of the NRLMD. No primary or secondary habitat occurs in the action area (FHWA 2017, p. 17). 4. Project activities will not result in any permanent increase in travel routes within the LAUs.

Because of the low likelihood that lynx will be in the projects area, low magnitude of disturbance by Project activities to lynx or their suitable habitat, and due to the use of minimization measures described in the BA (pp. 12-13), the potential impacts to lynx are expected to be insignificant or discountable. We have reviewed the information provided and concur with your finding that implementation of the proposed Project may affect, but is not likely to adversely affect Canada lynx. Concurrence by the Service is contingent upon implementation of the Project and conservation measures as described in the Assessment, and in this Opinion.

1.3.3 Grizzly Bear Project activities will occur within the Cabinet-Yaak Grizzly Bear Recovery Zone, more specifically in the North Lightning bear management unit (BMU). Service concurrence that the Project is not likely to adversely affect Grizzly bear is based on the following rationales. 1. Grizzly bears may be present in the area during Project implementation; however, Project activities will be short in duration and there will be ample adjacent displacement habitat available. 2. The Project does not occur near sensitive grizzly bear denning habitat. 3. Project activities will not result in an increase in open or total roads. 4. Project activities will not retard or reduce huckleberry production or hiding cover, and alternative hiding cover will remain to facilitate grizzly movement. 5. All employees, contractors, and/or subcontractors will be required to adhere to the IPNF Food Storage Order (Chipps, pers. comm. 2018). Because Project activities will not occur near sensitive grizzly bear denning habitat, there will be no net increase in linear miles of total or open roads, and because ample adjacent displacement habitat will be available during Project implementation, the effects to grizzly bears will be insignificant. We have reviewed the information provided and concur with your finding that implementation of the proposed Project may affect, but is not likely to adversely affect grizzly bear. Concurrence by the Service is contingent upon implementation of the Project and conservation measures as described in the Assessment, and in this Opinion. Conclusion This concludes the informal consultation pursuant to section 7(a)(2) of the Act. This project should be re-analyzed if new information reveals that effects of the action may affect listed species or critical habitat in a manner or to an extent not considered in this informal consultation; if the project is subsequently modified in a manner that causes an effect to the listed species or

9 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project critical habitat that was not considered in this consultation; and/or if a new species is listed or critical habitat is designated that may be affected by this project. Effects to Canada lynx, grizzly bear, and designated bull trout critical habitat will not be analyzed further in this Biological Opinion.

2. BIOLOGICAL OPINION

2.1 Description of the Proposed Action This section describes the proposed Federal action, including any measures that may avoid, minimize, or mitigate adverse effects to listed species or critical habitat, and the extent of the geographic area affected by the action (i.e., the action area). The term “action” is defined in the implementing regulations for section 7 as “all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies in the United States or upon the high seas.”

2.1.1 Action Area The action area is defined as all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action (50 CFR 402.02). In delineating the action area, we evaluated the farthest-reaching physical, chemical, and biotic effects of the action on the environment. The project is located near the city of Clark Fork in Bonner County, Idaho. The project occurs on the Idaho Panhandle National Forest (IPNF) on Forest Development Road (FDR) 419 between mileposts 9 and 14.3 (Figure 1). The extent of the action area is based on direct and indirect impacts within the Project footprint, as well as construction-related noise extending outside the footprint, potentially affecting threatened and endangered wildlife species; therefore, the action area includes areas within 1,320 feet from construction due to potential noise impacts on wildlife species, and 600-feet downstream of work below ordinary high water due to potential impacts related to increased suspended sediment downstream.

10 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project

Figure 1. Map showing the locations of the Lightning Creek repairs. Red denotes the location of the repair actions (FHWA 2017, p. 5).

11 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project 2.1.2 Proposed Action The following is excerpted from the Assessment and additional information received from the FHWA by email, and outlines the actions that will be implemented as part of the Project. For the full Project description, refer to the “Proposed Action” section of the Assessment (FHWA 2017, pp. 7-12). A total of 0.67 miles of existing gravel roads would be rehabilitated to pre-existing condition by repairing bridges and culverts, reconstructing roads, resurfacing roads, and, in some areas, rerouting roads. Road resurfacing activities generally include removing soil, rock, and sediment on the road surface, replacing drainage structures, regrading, regravelling, installing riprap, and removing vegetation, as needed. Construction will occur between May 17, 2018 through October 19, 2018. The majority of the in-water work will occur within the Service’s recommended in-water work window (July 15 through August 31). All diversion berms and fish handling completed by the end of the in-water work window (August 31), and all in-water work will be completed by September 15. The following descriptions of equipment, diversion berm, and fish handling will apply to each of the specific areas described below:  Equipment - Equipment used at this site will include hydraulic excavators, dump trucks, bulldozers, motor graders, backhoe loaders, and rollers.  Diversion Berm - To separate the wetted work area from the active channel, a temporary stream diversion berm will be installed. This consists of a combination of concrete barrier, visqueen sheeting, and sand bags. The concrete barrier will be placed using machinery staged atop the adjacent stream bank. The visqueen sheeting and sand bags will be manually placed. Sand will be clean and imported from outside the action area. After use, sand will be placed in an approved upland location. The temporary stream diversion berm will be installed beginning upstream and working downstream to provide opportunity for fish to naturally escape. Approximately half of the channel will be separated; the remaining approximate half of the channel will remain open and flowing and available for fish passage. The temporary stream diversion berm will be removed in such a manner as to return water to the river slowly at first to minimize the amount of sediment pulsed out.  Fish Handling - Trapped fish will be captured and relocated upstream of the work area by Idaho Transportation Department approved personnel following National Marine Fisheries Service (NMFS) protocols, such as using a plastic-lined dip net to minimize gill and scale injury. Fish salvage may include electrofishing, in which case NMFS Backpack Electrofishing Guidelines (NMFS 2000) will be followed. The person leading the electrofishing effort will have a valid Scientific Collecting Permit from the Idaho Department of Fish and Game (IDFG). FDR 419 MP 12.1 (Lightning Creek) The work for this site includes shifting the road east, away from the river, and installing a 150- foot (ft) long riprap revetment to protect against future damage. Deflective structures, including root wads and large boulder clusters, will be installed to reduce velocities and deflect flow away from the revetment toe.

12 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project The revetment construction includes excavating the channel bottom approximately 6 feet and filling with Class 6 riprap. This will provide a scour resistant toe and solid base to build up the revetment. The excavated streambed material will be conserved at an upland location. Class 6 riprap at a thickness of 6 feet will be used to build up the bank at a slope of 1.5H:1V height:depth ratio. The riprap revetment will be constructed to approximately 4 feet below finished grade of the road. Logs (18-24 inches (in.) in diameter) with root wads will be embedded in the riprap, only exposing the root wads, to slow and deflect the flow. Boulders will be placed around root wads to further protect the revetment. Unclassified borrow will be used to bring the roadway up to grade, and 4 inches of compacted aggregate will be used to construct a 20-foot wide roadway. The gravel substrate streambed will be restored by placing the conserved streambed material over the completed toe. Excavated material will be utilized within the existing project footprint as much as possible, and excess material that is not used within the project levee footprint will be taken to an approved disposal site. Upon completion of all construction activities, disturbed areas will be re-seeded with native grasses. In-water work is expected to last approximately 10 days at this site. FDR 419 MP 12.8 (Mink Creek) The work for this site includes cleaning and resetting the existing 48- x 32- x 48-inch concrete box culvert to approximately 1 foot below the original elevation and grade and reconstructing 45 feet of roadway that was washed out. The roadway will be reconstructed with a minimum of 24 inches of Class 2 riprap with 4 inches of compacted aggregate surfacing for a total travel way width of 20 feet. Approximately 3.5 feet of Class 5 riprap will be placed on the upstream and downstream embankment face at a slope of 2H:1V to protect the roadway from future flood events. Material deposited 50 feet upstream and downstream during the flood event will be removed. The deposited material will be used to create deflection berms on each side of the creek to direct future flood flows toward the armored roadway crossing. In-water work is expected to last approximately 4 days at this site. FDR 489 MP 0.1 (Lightning Creek) Flood water caused the west abutment at this site to fail. The superstructure and east abutment were not significantly impacted by the event, so they can be salvaged and reused. The work for this site includes hydraulically jacking the superstructure up to the original design elevation at the west abutment, removing the existing timber abutment and replacing it with a cast-in-place concrete foundation, abutment, and wingwalls to support the existing steel beams and timber decking. Class 6 riprap will be placed 5 feet thick to protect the new abutment. The riprap will be placed at a slope of 1.75H:1V. The west approach will be reconstructed with 4 inches of aggregate surfacing for a top width of 14 feet. The damaged guardrail will also be replaced, if needed. Upon completion of all construction activities, disturbed areas will be re-seeded with native grasses.

13 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project In-water work is expected to last approximately 5 weeks at this site. FDR 419 MP 12.85 (Lightning Creek) The work for this site includes reconstructing the damaged roadway and installing a 50-foot long riprap revetment to protect against future damage. Deflective structures including root wads and large boulder clusters will be installed to reduce velocities and deflect flow away from the revetment toe. The revetment construction includes excavating the channel bottom approximately 6 feet and filling with Class 6 riprap. This will provide a scour resistant toe and solid base to build up the revetment. The excavated streambed material would be conserved at an upland location. Class 6 riprap at a thickness of 6 feet will be used to build up the bank at a slope of 1.5H:1V. The riprap revetment will be constructed to approximately 4 feet below finished grade of the road. Logs (18-24 inches in diameter) with root wads will be embedded in the riprap, only exposing the root wads, to slow and deflect the flow. Boulders will be placed around root wads to further protect the revetment. Unclassified borrow will be used to bring the roadway up to grade, and 4 inches of compacted aggregate will be used to construct a 20-foot wide roadway. The gravel substrate streambed will be restored by placing the conserved streambed material over the completed toe. Excavated material will be utilized within the existing project footprint as much as possible, and excess material that is not used within the project levee footprint will be taken to an approved disposal site. Upon completion of all construction activities, areas will be re-seeded with native grasses. In-water work is expected to last approximately 1 week at this site. FDR 419 MP 13.5 (Lightning Creek) The work for this site includes reconstructing the damaged roadway and installing a 285-foot long riprap revetment to protect against future damage. Deflective structures including root wads and large boulder clusters will be installed to reduce velocities and deflect flow away from the revetment toe. The revetment construction includes excavating the channel bottom approximately 6 feet and filling with Class 6 riprap. This will provide a scour resistant toe and solid base to build up the revetment. The excavated streambed material would be conserved at an upland location. Class 6 riprap at a thickness of 6 feet will be used to build up the bank at a slope of 1.5H:1V. The riprap revetment will be constructed to approximately 4 feet below finished grade of the road. Logs (18-24 inches in diameter) with root wads will be embedded in the riprap, only exposing the root wads, to slow and deflect the flow. Boulders will be placed around root wads to further protect the revetment. Unclassified borrow will be used to bring the roadway up to grade, and 4 inches of compacted aggregate will be used to construct a 20-foot wide roadway. The gravel substrate streambed will be restored by placing the conserved streambed material over the completed toe. Excavated material will be utilized within the existing project footprint as much as possible, and excess material that is not used within the project levee footprint will be taken to an approved disposal site. Upon completion of all construction activities, disturbed areas will be re-seeded with native grasses.

14 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project In-water work is expected to last approximately 17 days at this site. FDR 419 MP 14.3 (Rattle Creek) Flood water caused log jams and washed out the south abutment and about 150 feet of roadway. The superstructure was not significantly impacted by the event, so it can be salvaged and reused. The work for this site includes reconstructing both timber abutments to accommodate a 5-foot increase in height, removing and resetting the existing 50-foot long superstructure, and repairing approximately 150 feet of the approach road. Class 6 riprap will be placed 5 feet thick to protect the new abutments. The riprap will be placed at a slope of 1.75H:1V. The road approaches will be reconstructed with 4 inches of aggregate surfacing for a top width of 14 feet. Damaged guardrail will also be replaced as needed. Deposited material and debris will be removed, the stream channel will be reestablished to approximately 300 feet upstream, and rock groins will be installed using the excavated channel material to prevent the main channel from migrating away from the new bridge. The groins will be placed well outside of the ordinary high watermark, against the south edge of the floodplain, where the 2016 flood waters created a low point in the floodplain. Upon completion of all construction activities, disturbed areas will be re-seeded with native grasses. In-water work is expected to last approximately 6 weeks at this site. Conservation Measures The Proposed Action includes a number of conservation measures or construction techniques that will be employed to minimize effects to listed species and designated critical habitat. These include general measures to be applied to all phases of the Project (FHWA 2017, pp. 12-13).  Minimize construction noise by avoiding blasting and other loud equipment to the extent possible.  Store trash in bear-proof garbage containers and remove trash from the project site daily. All employees will follow the IPNF Food Storage Order.  Minimize vegetation clearing to the extent possible.  Revegetate disturbed areas with native ground cover.  Locate temporary construction areas, such as staging areas, within already- disturbed/developed areas to the extent possible.  Divert stream flow around the work area and maintain downstream flow during construction.  Only clean material will be placed. There will be no end dumping of material into the river. Riprap will be individually placed.  Flows will be partially diverted around the work site through a combination of pumping and/or pre-approved, alternative methods and returned to the channel below the project area. Water will be slowly released back into the channel to minimize sediment movement in the channel.

15 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project  Turbidity monitoring will occur downstream of the project during all in-stream work activities. On-site turbidity measurements will be taken approximately 600 feet downstream from the activity. If turbidity were to exceed state standards (50 NTUs (Nephelometric Turbidity Units) above background), activities will be paused or additional mitigation measures will be employed to bring the turbidity back in compliance.  A silt fence will be installed along the toe of the existing road prism to capture larger pieces of dirt and prevent them from entering the channel; dirt clods will be removed prior to re-watering the channel. As this project does not propose any new channel construction, the amount of suspended sediment particles within the stream is expected to be very minor after construction.  Vegetation removal will be limited to the minimum extent needed to complete the repairs. Upon completion of all construction activities, areas disturbed by staging activities, and/or road access will be re-seeded with native grasses.  No loss of wetlands or sensitive aquatic sites will occur.  Isolate in-water work areas prior to culvert installation. Dewater work area as necessary for construction and to minimize turbidity. Do not discharge turbid water into streams.  Pumps used to dewater stream channel sections will be screened or otherwise equipped or placed to prevent fish entrainment/impingement.  Fish species, condition and size class data will be compiled and reported to the IPNF’s fisheries biologist and other appropriate Forest Service staff, as well as the appropriate regulatory agencies.  Fish crowding, rescue, and removal will be conducted by or under the supervision of a fisheries biologist experienced with work area isolation to ensure the safe handling of fish.  Comply with applicable Clean Water Act permits for work in wetlands or streams.  Restrict construction vehicles and equipment to roads and designated work areas.  Return temporary disturbance areas for culvert and road work to pre-construction contours.  Dispose of waste material generated from road work in a stable upland site approved by a geotechnical engineer or other qualified personnel. Smooth disposal site to match adjacent grades.  Conduct soil-disturbing activities during dry conditions to the greatest extent practicable.  Outslope roads (e.g., 2 percent to 5 percent), maintaining natural drainage patterns and minimizing interceptions and concentration of upgradient runoff when practicable.  Design culverts for the 100-year storm event to minimize future maintenance needs.  Develop and implement a spill prevention and spill response plan.

16 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project  Store, fuel, and maintain all vehicles and other heavy equipment (when not in use) in a designated upland staging area located a minimum of 150 feet away from any stream, waterbody, or wetland or where any spilled material cannot enter natural or manmade drainage conveyances.  Biodegradable hydraulic fluids will be used in machinery where appropriate, and will be used in the excavator.  A Fueling and Spill Recovery Plan will be developed prior to construction that will include specific best management practices (BMPs) to prevent spills and to prepare workers to react quickly should an incident occur.  Confirm equipment is clean (e.g., power-washed) and that it does not have fluid leaks prior to contractor mobilization of heavy equipment to site. Inspect equipment and tanks for drips or leaks daily and make necessary repairs within 24 hours.  In the event of a spill, immediately contain the spill, eliminate the source, and deploy appropriate measures to clean and dispose of spilled materials in accordance with Federal, State, and local regulations.  A Stormwater Pollution Prevention Plan will also be developed to identify potential sources and reduce pollutants in stormwater discharges from the construction site.  Maintain emergency spill control materials, such as oil booms and spill response kits, on- site at each work area at all times and have them ready for immediate deployment. Construction personnel will be trained in their proper use.  Install cross-drains where needed.

2.2 Analytical Framework for the Jeopardy Determination

2.2.1 Jeopardy Determination In accordance with policy and regulation, the jeopardy analysis in this Opinion relies on four components: 1. The Status of the Species, which evaluates the bull trout’s rangewide condition, the factors responsible for that condition, and its survival and recovery needs. 2. The Environmental Baseline, which evaluates the condition of the bull trout in the action area, the factors responsible for that condition, and the relationship of the action area to the survival and recovery of the bull trout. 3. The Effects of the Action, which determines the direct and indirect impacts of the proposed Federal action and the effects of any interrelated or interdependent activities on the bull trout. 4. Cumulative Effects, which evaluates the effects of future, non-Federal activities reasonably certain to occur in the action area on the bull trout.

17 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project In accordance with policy and regulation, the jeopardy determination is made by evaluating the effects of the proposed Federal action in the context of the bull trout’s current status, taken together with cumulative effects, to determine if implementation of the proposed action is likely to cause an appreciable reduction in the likelihood of both the survival and recovery of the bull trout in the wild. Recovery Units (RUs) for the bull trout were defined in the final Recovery Plan for the Coterminous United States Population of [the] Bull Trout (USFWS 2015a, entire). Pursuant to Service policy, when a proposed Federal action impairs or precludes the capacity of a RU from providing both the survival and recovery function assigned to it, that action may represent jeopardy to the species. When using this type of analysis, the biological opinion describes how the proposed action affects not only the capability of the RU, but the relationship of the RU to both the survival and recovery of the listed species as a whole. The jeopardy analysis for the bull trout in this biological opinion considers the relationship of the action area and affected core areas (discussed below under the Status of the Species section) to the RU and the relationship of the RU to both the survival and recovery of the bull trout as a whole as the context for evaluating the significance of the effects of the proposed Federal action, taken together with cumulative effects, for purposes of making the jeopardy determination. Within the above context, the Service also considers how the effects of the proposed Federal action and any cumulative effects impact bull trout local and core area populations in determining the aggregate effect to the RU(s). Generally, if the effects of a proposed Federal action, taken together with cumulative effects, are likely to impair the viability of a core area population(s), such an effect is likely to impair the survival and recovery function assigned to a RU(s) and may represent jeopardy to the species (USFWS 2005a, 70 FR 56258).

2.3 Status of the Species This section presents information about the regulatory, biological and ecological status of the bull trout and its critical habitat that provides context for evaluating the significance of probable effects caused by the proposed action.

2.3.1 Listing Status The coterminous United States population of the bull trout was listed as threatened on November 1, 1999 (USFWS 1999, 64 FR 58910-58933). The threatened bull trout occurs in the Klamath River Basin of south-central Oregon; the Jarbidge River in Nevada; the Willamette River Basin in Oregon; Pacific Coast drainages of Washington, including Puget Sound; major rivers in Idaho, Oregon, Washington, and Montana, within the Columbia River Basin; and the St. Mary-Belly River, east of the Continental Divide in northwestern Montana (Bond 1992, p. 2; Brewin and Brewin 1997, p. 215; Cavender 1978, pp. 165-166; Howell and Buchanan 1992, entire; Leary and Allendorf 1997, pp. 716-719; USFWS 1999, 64 FR 58910). The final listing rule for the United States coterminous population of the bull trout discusses the consolidation of five Distinct Population Segments (DPSs) into one listed taxon and the application of the jeopardy standard under section 7 of the Act relative to this species, and

18 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project established five interim recovery units for each of these DPSs for the purposes of Consultation and Recovery (USFWS 1999, 64 FR 58930). The 2010 final bull trout critical habitat rule (USFWS 2010, 75 FR 63898-64070) identified six draft recovery units based on new information that confirmed they were needed to ensure a resilient, redundant, and representative distribution of bull trout populations throughout the range of the listed entity. The final bull trout recovery plan (RP) (USFWS 2015a, pp. 36-43) formalized these six recovery units: Coastal, Klamath, Mid-Columbia, Columbia Headwaters, Saint Mary, and Upper Snake. The final recovery units replace the previous five interim recovery units and will be used in the application of the jeopardy standard for section 7 consultation procedures.

2.3.2 Reasons for Listing and Emerging Threats Throughout its range, the bull trout is threatened by the combined effects of habitat degradation, fragmentation, and alterations associated with dewatering, road construction and maintenance, mining, grazing, the blockage of migratory corridors by dams or other diversion structures, poor water quality; incidental angler harvest; entrainment (a process by which aquatic organisms are pulled through a diversion or other device) into diversion channels; and introduced non-native species (USFWS 1999, 64 FR 58910). Poaching and incidental mortality of bull trout during other targeted fisheries are additional threats. Since the time of coterminous listing the species (64 FR 58910) and designation of its critical habitat (USFWS 2004a, 69 FR 59996; USFWS 2005a, 70 FR 56212; USFWS 2010, 75 FR 63898) a great deal of new information has been collected on the status of bull trout. The Service’s Science Team Report (Whitesel et al. 2004, entire), the bull trout core areas templates (USFWS 2005b, entire; 2009, entire), Conservation Status Assessment (USFWS 2005a, entire), and 5-year Reviews (USFWS 2008, entire; USFWS 2015h, entire) have provided additional information about threats and status. The final RP lists many other documents and meetings that compiled information about the status of bull trout (USFWS 2015a, p. 3). As did the prior 5-year review (2008), the 2015 5-year status review maintains the listing status as threatened based on the information compiled in the final bull trout RP (USFWS 2015a, entire) and the Recovery Unit Implementation Plans (RUIPs) (USFWS 2015b-g, entire). When first listed, the status of bull trout and its threats were reported by the Service at subpopulation scales. In 2002 and 2004, the draft recovery plans (USFWS 2002a, entire; 2004a, entire; 2004b, entire) included detailed information on threats at the recovery unit scale (i.e. similar to subbasin or regional watersheds), thus incorporating the metapopulation concept with core areas and local populations. In the 5-year Reviews, the Service established threats categories (i.e. dams, forest management, grazing, agricultural practices, transportation networks, mining, development and urbanization, fisheries management, small populations, limited habitat, and wild fire) (USFWS 2008, pp. 39-42; USFWS 2015h, p. 3). In the final RP, threats and recovery actions are described for 109 core areas, forage/migration and overwintering areas, historical core areas, and research needs areas in each of the six recovery units (USFWS 2015a, p 10). Primary threats are described in three broad categories: Habitat, Demographic, and Nonnative Fish for all recovery areas within the coterminously listed range of the species.

19 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project The 2015 5-year status review references the final RP and the RUIPs and incorporates by reference the threats described therein (USFWS 2015h, pp. 2-3). Although significant recovery actions have been implemented since the time of listing, the 5-year review concluded that the listing status should remain as “threatened” (USFWS 2015h, p. 3). New or Emerging Threats The 2015 RP (USFWS 2015a, entire) describes new or emerging threats such as climate change and other threats. Climate change was not addressed as a known threat when bull trout was listed. The 2015 bull trout RP and RUIPs summarize the threat of climate change and acknowledge that some bull trout local populations and core areas may not persist into the future due to anthropogenic effects such as climate change. The RP further states that use of best available information will ensure future conservation efforts that offer the greatest long-term benefit to sustain bull trout and their required coldwater habitats (USFWS 2015a, pp. vii, 17-20). Mote et al. (2014, pp. 487-513) summarized climate change effects in the Pacific Northwest to include rising air temperature, changes in the timing of streamflow related to changing snowmelt, increases in extreme precipitation events, lower summer stream flows, and other changes. A warming trend in the mountains of western North America is expected to decrease snowpack, hasten spring runoff, reduce summer stream flows, and increase summer water temperatures (Poff et al. 2002, p. 34; Koopman et al. 2009, entire; Point Reyes Bird Observatory Conservation Science 2011, p. 13). Lower flows as a result of smaller snowpack could reduce habitat, which might adversely affect bull trout reproduction and survival. Warmer water temperatures could lead to physiological stress and could also benefit nonnative fishes that prey on or compete with bull trout. Increases in the number and size of forest fires could also result from climate change (Westerling et al. 2006, p. 940) and could adversely affect watershed function by resulting in faster runoff, lower base flows during the summer and fall, and increased sedimentation rates. Lower flows also may result in increased groundwater withdrawal for agricultural purposes and resultant reduced water availability in certain stream reaches occupied by bull trout (USFWS 2015c, p. B-10). Although all salmonids are likely to be affected by climate change, bull trout are especially vulnerable given that spawning and rearing are constrained by their location in upper watersheds and the requirement for cold water temperatures (Rieman et al. 2007, p. 1552). Climate change is expected to reduce the extent of cold water habitat (Isaak et al. 2015, p. 2549, Figure 7), and increase competition with other fish species (lake trout, brown trout, brook trout, and northern pike) for resources in remaining suitable habitat. Several authors project that brook trout, a fish species that competes for resources with and predates on the bull trout, will continue increasing their range in several areas (an upward shift in elevation) due to the effects from climate change (e.g., warmer water temperatures) (Wenger et al. 2011, p. 998, Figure 2a; Isaak et al. 2014, p. 114).

2.3.3 Species Description Bull trout (Salvelinus confluentus), member of the family Salmonidae, are char native to the Pacific Northwest and western Canada. The bull trout and the closely related Dolly Varden (Salvelinus malma) were not officially recognized as separate species until 1980 (Robins et al. 1980, p. 19). Bull trout historically occurred in major river drainages in the Pacific Northwest

20 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project from the southern limits in the McCloud River in northern California (now extirpated), Klamath River basin of south central Oregon, and the Jarbidge River in Nevada to the headwaters of the Yukon River in the Northwest Territories, Canada (Cavender 1978, pp. 165-169; Bond 1992, pp. 2-3). To the west, the bull trout’s current range includes Puget Sound, coastal rivers of British Columbia, Canada, and southeast Alaska (Bond 1992, pp. 2-3). East of the Continental Divide bull trout are found in the headwaters of the Saskatchewan River in Alberta and the MacKenzie River system in Alberta and British Columbia (Cavender 1978, pp. 165-169; Brewin and Brewin 1997, pp. 209-216). Bull trout are wide spread throughout the Columbia River basin, including its headwaters in Montana and Canada.

2.3.4 Life History Bull trout exhibit resident and migratory life history strategies throughout much of the current range (Rieman and McIntyre 1993, p. 2). Resident bull trout complete their entire life cycle in the streams where they spawn and rear. Migratory bull trout spawn and rear in streams for 1 to 4 years before migrating to either a lake (adfluvial), river (fluvial), or, in certain coastal areas, to saltwater (anadromous) where they reach maturity (Fraley and Shepard 1989, p. 1; Goetz 1989, pp. 15-16). Resident and migratory forms often occur together and it is suspected that individual bull trout may give rise to offspring exhibiting both resident and migratory behavior (Rieman and McIntyre 1993, p. 2). Bull trout have more specific habitat requirements than other salmonids (Rieman and McIntyre 1993, p. 4). Watson and Hillman (1997, p. 248) concluded that watersheds must have specific physical characteristics to provide habitat requirements for bull trout to successfully spawn and rear. It was also concluded that these characteristics are not necessarily ubiquitous throughout these watersheds, thus resulting in patchy distributions even in pristine habitats. Bull trout are found primarily in colder streams, although individual fish are migratory in larger, warmer river systems throughout the range (Fraley and Shepard 1989, pp. 135-137; Rieman and McIntyre 1993, p. 2; Rieman and McIntyre 1995, p. 288; Buchanan and Gregory 1997, pp. 121- 122; Rieman et al. 1997, p. 1114). Water temperature above 59°F is believed to limit bull trout distribution, which may partially explain the patchy distribution within a watershed (Fraley and Shepard 1989, p. 133; Rieman and McIntyre 1995, pp. 255-296). Spawning areas are often associated with cold water springs, groundwater infiltration, and the coldest streams in a given watershed (Pratt 1992, p. 6; Rieman and McIntyre 1993, p. 7; Rieman et al. 1997, p. 1117). Goetz (1989, pp. 22, 24) suggested optimum water temperatures for rearing of less than 50°F and optimum water temperatures for egg incubation of 35 to 39°F. All life history stages of bull trout are associated with complex forms of cover, including large woody debris, undercut banks, boulders, and pools (Goetz 1989, pp. 22-25; Pratt 1992, p. 6; Thomas 1992, pp. 4-5; Rich 1996, pp. 35-38; Sexauer and James 1997, pp. 367-369; Watson and Hillman 1997, pp. 247-249). Jakober (1995, p. 42) observed bull trout overwintering in deep beaver ponds or pools containing large woody debris in the Bitterroot River drainage, Montana, and suggested that suitable winter habitat may be more restrictive than summer habitat. Bull trout prefer relatively stable channel and water flow conditions (Rieman and McIntyre 1993, p. 6). Juvenile and adult bull trout frequently inhabit side channels, stream margins, and pools with

21 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project suitable cover (Sexauer and James 1997, pp. 368-369). The size and age of bull trout at maturity depend upon life history strategy. Growth of resident fish is generally slower than migratory fish; resident fish tend to be smaller at maturity and less fecund (Goetz 1989, p. 15). Bull trout normally reach sexual maturity in 4 to 7 years and live as long as 12 years. Bull trout are iteroparous (they spawn more than once in a lifetime), and both repeat- and alternate-year spawning has been reported, although repeat-spawning frequency and post-spawning mortality are not well documented (Leathe and Graham 1982, p. 95; Fraley and Shepard 1989, p. 135; Pratt 1992, p. 8; Rieman and McIntyre 1996, p. 133). Bull trout typically spawn from August to November during periods of decreasing water temperatures. Migratory bull trout frequently begin spawning migrations as early as April, and have been known to move upstream as far as 155 miles (mi) to spawning grounds (Fraley and Shepard 1989, p. 135). Depending on water temperature, incubation is normally 100 to 145 days (Pratt 1992, p. 1) and, after hatching, juveniles remain in the substrate. Time from egg deposition to emergence may exceed 200 days. Fry normally emerge from early April through May depending upon water temperatures and increasing stream flows (Pratt 1992, p. 1). The iteroparous reproductive system of bull trout has important repercussions for the management of this species. Bull trout require two-way passage up and downstream, not only for repeat spawning, but also for foraging. Most fish ladders, however, were designed specifically for anadromous semelparous (fishes that spawn once and then die, and therefore require only one-way passage upstream) salmonids. Therefore, even dams or other barriers with fish passage facilities may be a factor in isolating bull trout populations if they do not provide a downstream passage route. Bull trout are opportunistic feeders with food habits primarily a function of size and life history strategy. Resident and juvenile migratory bull trout prey on terrestrial and aquatic insects, macro zooplankton and small fish (Boag 1987, p. 58; Goetz 1989, pp. 33-34; Donald and Alger 1993, pp. 239-243). Adult migratory bull trout are primarily piscivores, known to feed on various fish species (Fraley and Shepard 1989, p. 135; Donald and Alger 1993, p. 242).

2.3.5 Population Dynamics Population Structure As indicated above, bull trout exhibit both resident and migratory life history strategies. Both resident and migratory forms may be found together, and either form may produce offspring exhibiting either resident or migratory behavior (Rieman and McIntyre 1993, p. 2). Resident bull trout complete their entire life cycle in the tributary (or nearby) streams in which they spawn and rear. The resident form tends to be smaller than the migratory form at maturity and also produces fewer eggs (Goetz 1989, p. 15). Migratory bull trout spawn in tributary streams where juvenile fish rear 1 to 4 years before migrating to either a lake (adfluvial form), river (fluvial form) (Fraley and Shepard 1989, p. 138; Goetz 1989, p. 24), or saltwater (anadromous form) to rear as subadults and to live as adults (Brenkman and Corbett 2005, entire; McPhail and Baxter 1996, p. i). Bull trout normally reach sexual maturity in 4 to 7 years and may live longer than 12 years. Repeat- and alternate-year spawning has been reported, although repeat-spawning frequency and post-spawning mortality are not well documented (Fraley and Shepard 1989, p. 135; Leathe and Graham 1982, p. 95; Pratt 1992, p. 8; Rieman and McIntyre 1996, p. 133).

22 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Bull trout are naturally migratory, which allows them to capitalize on temporally abundant food resources and larger downstream habitats. Resident forms may develop where barriers (either natural or manmade) occur or where foraging, migrating, or overwintering habitats for migratory fish are minimized (Brenkman and Corbett 2005, pp. 1075-1076; Goetz et al. 2004, p. 105; Starcevich et al. 2012, p. 10; Barrows et al. 2016, p. 98). For example, multiple life history forms (e.g., resident and fluvial) and multiple migration patterns have been noted in the Grande Ronde River (Baxter 2002, pp. 96, 98-106) and Wenatchee River (Ringel et al. 2014, pp. 61-64). Parts of these river systems have retained habitat conditions that allow free movement between spawning and rearing areas and the mainstem rivers. Such multiple life history strategies help to maintain the stability and persistence of bull trout populations to environmental changes. Benefits of connected habitat to migratory bull trout include greater growth in the more productive waters of larger streams, lakes, and marine waters; greater fecundity resulting in increased reproductive potential; and dispersing the population across space and time so that spawning streams may be recolonized should local populations suffer a catastrophic loss (Frissell 1999, pp. 861-863; MBTSG 1998, p. 13; Rieman and McIntyre 1993, pp. 2-3). In the absence of the migratory bull trout life form, isolated populations cannot be replenished when disturbances make local habitats temporarily unsuitable. Therefore, the range of the species is diminished, and the potential for a greater reproductive contribution from larger size fish with higher fecundity is lost (Rieman and McIntyre 1993, p. 2). Whitesel et al. (2004, p. 2) noted that although there are multiple resources that contribute to the subject, Spruell et al. (2003, entire) best summarized genetic information on bull trout population structure. Spruell et al. (2003, entire) analyzed 1,847 bull trout from 65 sampling locations, four located in three coastal drainages (Klamath, Queets, and Skagit Rivers), one in the Saskatchewan River drainage (Belly River), and 60 scattered throughout the Columbia River Basin. They concluded that there is a consistent pattern among genetic studies of bull trout, regardless of whether examining allozymes, mitochondrial DNA, or most recently microsatellite loci. Typically, the genetic pattern shows relatively little genetic variation within populations, but substantial divergence among populations. Microsatellite loci analysis supports the existence of at least three major genetically differentiated groups (or evolutionary lineages) of bull trout (Spruell et al. 2003, p. 17). They were characterized as: i. “Coastal”, including the Deschutes River and all of the Columbia River drainage downstream, as well as most coastal streams in Washington, Oregon, and British Columbia. A compelling case also exists that the Klamath Basin represents a unique evolutionary lineage within the coastal group. ii. “Snake River”, which also included the John Day, Umatilla, and Walla Walla rivers. Despite close proximity of the John Day and Deschutes Rivers, a striking level of divergence between bull trout in these two systems was observed. iii. “Upper Columbia River” which includes the entire basin in Montana and northern Idaho. A tentative assignment was made by Spruell et al. (2003, p. 25) of the Saskatchewan River drainage populations (east of the continental divide), grouping them with the upper Columbia River group. Spruell et al. (2003, p. 17) noted that within the major assemblages, populations were further subdivided, primarily at the level of major river basins. Taylor et al. (1999, entire) surveyed bull trout populations, primarily from Canada, and found a major divergence between inland and coastal populations. Costello et al. (2003, p. 328) suggested the patterns reflected the existence

23 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project of two glacial refugia, consistent with the conclusions of Spruell et al. (2003, p. 26) and the biogeographic analysis of Haas and McPhail (2001, entire). Both Taylor et al. (1999, p. 1166) and Spruell et al. (2003, p. 21) concluded that the Deschutes River represented the most upstream limit of the coastal lineage in the Columbia River Basin. More recently, the USFWS identified additional genetic units within the coastal and interior lineages (Ardren et al. 2011, pp. 519-523). Based on a recommendation in the USFWS’s 5-year review of the species’ status (USFWS 2008, p. 45), the USFWS reanalyzed the 27 recovery units identified in the 2002 draft bull trout recovery plan (USFWS 2002a, p. 48) by utilizing, in part, information from previous genetic studies and new information from additional analysis (Ardren et al. 2011, entire). In this examination, the USFWS applied relevant factors from the joint USFWS and NMFS Distinct Population Segment (DPS) policy (USFWS and NMFS 1996, 61 FR 4722-4725) and subsequently identified six draft recovery units that contain assemblages of core areas that retain genetic and ecological integrity across the range of bull trout in the coterminous United States. These six recovery units were used to inform designation of critical habitat for bull trout by providing a context for deciding what habitats are essential for recovery (USFWS 2010a, 75 FR 63898). These six recovery units, which were identified in the final bull trout recovery plan (USFWS 2015a) and described further in the RUIPs (USFWS 2015b-g) include: Coastal, Klamath, Mid-Columbia, Columbia Headwaters, Saint Mary, and Upper Snake. Population Dynamics Although bull trout are widely distributed over a large geographic area, they exhibit a patchy distribution, even in pristine habitats (Rieman and McIntyre 1993, p. 4). Increased habitat fragmentation reduces the amount of available habitat and increases isolation from other populations of the same species (Saunders et al. 1991, entire). Burkey (1989, entire) concluded that when species are isolated by fragmented habitats, low rates of population growth are typical in local populations and their probability of extinction is directly related to the degree of isolation and fragmentation. Without sufficient immigration, growth for local populations may be low and probability of extinction high (Burkey 1989, entire). A metapopulation is an interacting network of local populations with varying frequencies of migration and gene flow among them (Meefe and Carroll 1994, pp. 189-190). For inland bull trout, metapopulation theory is likely most applicable at the watershed scale where habitat consists of discrete patches or collections of habitat capable of supporting local populations; local populations are for the most part independent and represent discrete reproductive units; and long-term, low-rate dispersal patterns among component populations influences the persistence of at least some of the local populations (Rieman and Dunham 2000, entire). Ideally, multiple local populations distributed throughout a watershed provide a mechanism for spreading risk because the simultaneous loss of all local populations is unlikely. However, habitat alteration, primarily through the construction of impoundments, dams, and water diversions has fragmented habitats, eliminated migratory corridors, and in many cases isolated bull trout in the headwaters of tributaries (Rieman and Clayton 1997, pp. 10-12; Dunham and Rieman 1999, p. 645; Spruell et al. 1999, pp. 118-120; Rieman and Dunham 2000, p. 55). Human-induced factors as well as natural factors affecting bull trout distribution have likely limited the expression of the metapopulation concept for bull trout to patches of habitat within the overall distribution of the species (Dunham and Rieman 1999, entire). However, despite the

24 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project theoretical fit, the relatively recent and brief time period during which bull trout investigations have taken place does not provide certainty as to whether a metapopulation dynamic is occurring (e.g., a balance between local extirpations and recolonizations) across the range of the bull trout or whether the persistence of bull trout in large or closely interconnected habitat patches (Dunham and Rieman 1999, entire) is simply reflective of a general deterministic trend towards extinction of the species where the larger or interconnected patches are relics of historically wider distribution (Rieman and Dunham 2000, pp. 56-57). Research does, however, provide genetic evidence for the presence of a metapopulation process for bull trout, at least in the Boise River Basin of Idaho (Whiteley et al. 2003, entire). Whitesel et al. (2004 pp. 14-23) summarizes metapopulation models and their applicability to bull trout).

2.3.6 Status and Distribution The following is a summary of the description and current status of the bull trout within the six recovery units (RUs) (shown in Figure 1, below). A comprehensive discussion is found in the Service’s 2015 RP for the bull trout (USFWS 2015a, entire) and the 2015 RUIPs (USFWS 2015b-g, entire). Each of these RUs is necessary to maintain the bull trout’s distribution, as well as its genetic and phenotypic diversity, all of which are important to ensure the species’ resilience to changing environmental conditions. Coastal Recovery Unit The Coastal RUIP describes the threats to bull trout and the site-specific management actions necessary for recovery of the species within the unit (USFWS 2015b, entire). The Coastal RU is located within western Oregon and Washington. The RU is divided into three regions: Puget Sound, Olympic Peninsula, and the Lower Columbia River Regions. This RU contains 20 core areas comprising 84 local populations and a single potential local population in the historic Clackamas River core area where bull trout had been extirpated and were reintroduced in 2011, and identified four historically occupied core areas that could be re-established (USFWS 2015a, p. 47; USFWS 2015b, p. A-2). Core areas within Puget Sound and the Olympic Peninsula currently support the only anadromous local populations of bull trout. This RU also contains ten shared FMO habitats which are outside core areas and allows for the continued natural population dynamics in which the core areas have evolved (USFWS 2015b, p. A-5). There are four core areas within the Coastal RU that have been identified as current population strongholds: Lower Skagit, Upper Skagit, Quinault River, and Lower Deschutes River (USFWS 2015a, p.79). These are the most stable and abundant bull trout populations in the RU. Most core areas in the Puget Sound region support a mix of anadromous and fluvial life history forms, with at least two core areas containing a natural adfluvial life history (Chilliwack River core area [Chilliwack Lake] and Chester Morse Lake core area). Overall demographic status of core areas generally improves as you move from south Puget Sound to north Puget Sound. Although comprehensive trend data are lacking, the current condition of core areas within the Puget Sound region are likely stable overall, although some at depressed abundances. Most core areas in this region still have significant amounts of headwater habitat within protected and relatively pristine areas (e.g., North Cascades National Park, Mount Rainier National Park, Skagit Valley Provincial Park, Manning Provincial Park, and various wilderness or recreation areas).

25 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Within the Olympic Peninsula region, demographic status of core areas is poorest in Hood Canal and Strait of Juan de Fuca, while core areas along the Pacific Coast of Washington likely have the best demographic status in this region. The connectivity between core areas in these disjunct regions is believed to be naturally low due to the geographic distance between them. Internal connectivity is currently poor within the Skokomish River core area (Hood Canal) and is being restored in the Elwha River core area (Strait of Juan de Fuca). Most core areas in this region still have their headwater habitats within relatively protected areas (Olympic National Park and wilderness areas). Across the Lower Columbia River region, status is highly variable, with one relative stronghold (Lower Deschutes core area) existing on the Oregon side of the Columbia River. The Lower Columbia River region also contains three watersheds (North Santiam River, Upper Deschutes River, and White Salmon River) that could potentially become re-established core areas within the Coastal Recovery Unit. Adult abundances within the majority of core areas in this region are relatively low, generally 300 or fewer individuals. The current condition of the bull trout in this RU is attributed to the adverse effects of climate change, loss of functioning estuarine and nearshore marine habitats, development and related impacts (e.g., flood control, floodplain disconnection, bank armoring, channel straightening, loss of instream habitat complexity), agriculture (e.g., diking, water control structures, draining of wetlands, channelization, and the removal of riparian vegetation, livestock grazing), fish passage (e.g., dams, culverts, instream flows) residential development, urbanization, forest management practices (e.g., timber harvest and associated road building activities), connectivity impairment, mining, and the introduction of non-native species. The RP identifies three categories of primary threats1: Habitat (upland/riparian land management, instream impacts, water quality), demographic (connectivity impairment, fisheries management, small population size), and nonnatives (nonnative fishes). Of the 20 core areas in the Coastal RU, only one (5 percent), the Lower Deschutes River, has no primary threats identified (USFWS 2015b, Table A-1). Conservation measures or recovery actions implemented in this RU include relicensing of major hydropower facilities that have provided upstream and downstream fish passage or complete removal of dams, land acquisition to conserve bull trout habitat, floodplain restoration, culvert removal, riparian revegetation, levee setbacks, road removal, and projects to protect and restore important nearshore marine habitats. For more information on conservation actions see section 2.3.1.7 below. Klamath Recovery Unit The Klamath RUIP describes the threats to bull trout and the site-specific management actions necessary for recovery of the species within the unit (USFWS 2015c, entire). This RU is located

1 Primary Threats are factors known or likely (i.e., non-speculative) to negatively impact bull trout populations at the core area level, and accordingly require actions to assure bull trout persistence to a degree necessary that bull trout will not be at risk of extirpation within that core area in the foreseeable future (4 to 10 bull trout generations, approximately 50 years).

26 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project in southern Oregon and northwestern California. The Klamath RU is the most significantly imperiled RU, having experienced considerable extirpation and geographic contraction of local populations and declining demographic condition, and natural re-colonization is constrained by dispersal barriers and presence of nonnative brook trout (USFWS 2015a, p. 39). This RU currently contains three core areas and eight local populations (USFWS 2015a, p. 47; USFWS 2015c, p. B-1). Nine historic local populations of bull trout have become extirpated (USFWS 2015c, p. B-1). All three core areas have been isolated from other bull trout populations for the past 10,000 years (USFWS 2015c, p. B-3). The current condition of the bull trout in this RU is attributed to the adverse effects of climate change, habitat degradation and fragmentation, past and present land use practices, agricultural water diversions, nonnative species, and past fisheries management practices. Identified primary threats for all three core areas include upland/ riparian land management, connectivity impairment, small population size, and nonnative fishes (USFWS 2015c, Table B-1). Conservation measures or recovery actions implemented include removal of nonnative fish (e.g., brook trout, brown trout, and hybrids), acquiring water rights for instream flows, replacing diversion structures, installing fish screens, constructing bypass channels, installing riparian fencing, culvert replacement, and habitat restoration. For more information on conservation actions see section 2.3.1.7 below. Saint Mary Recovery Unit The St. Mary RUIP describes the threats to bull trout and the site-specific management actions necessary for recovery of the species within the unit (USFWS 2015g). The Saint Mary RU is located in Montana but is heavily linked to downstream resources in southern Alberta, Canada. Most of the Saskatchewan River watershed which the St. Mary flows into is located in Canada. The United States portion includes headwater SR habitat and the upper reaches of FMO habitat. This RU contains four core areas (St. Mary River, Slide Lake, Cracker Lake, and Red Eagle Lake), and eight local populations (USFWS 2015g, p. F-1) in the U.S. headwaters. Current status of bull trout in the Saint Mary River complex core area (U.S.) is considered strong. The three simple core areas (Slide Lake, Cracker Lake, and Red Eagle Lake) appear to be self-sustaining and fluctuating within known historical population demographic bounds. Note: the NatureServe status assessment tool ranks this RU as imperiled (Figure 2). The current condition of the bull trout in this RU is attributed primarily to the outdated design and operations of the Saint Mary Diversion operated by the Bureau of Reclamation (e.g., entrainment, fish passage, instream flows), and, to a lesser extent habitat impacts from development and nonnative species. Of the four core areas, the three simple core areas (all lakes) have no identified primary threats (USFWS 2015g, Table F-1). Columbia Headwaters Recovery Unit The Columbia Headwaters RUIP describes the threats to bull trout and the site-specific management actions necessary for recovery of the species within the unit (USFWS 2015e, entire). The Columbia Headwaters RU is located in western Montana, northern Idaho, and the northeastern corner of Washington. The RU is divided into five geographic regions: Upper Clark Fork, Lower Clark Fork, Flathead, Kootenai, and Coeur d’Alene Geographic Regions (USFWS 2015e, pp. D-2 – D-4). This RU contains 35 bull trout core areas; 15 of which are complex core areas as they represent larger interconnected habitats and 20 simple core areas as

27 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project they are isolated headwater lakes with single local populations. The 20 simple core areas are each represented by a single local population, many of which may have persisted for thousands of years despite small populations and isolated existence (USFWS 2015e, p. D-1). Fish passage improvements within the RU have reconnected some previously fragmented habitats (USFWS 2015e, p. D-1), while others remain fragmented. Unlike the other RUs in Washington, Idaho and Oregon, the Columbia Headwaters RU does not have any anadromous fish overlap. Therefore, bull trout within the Columbia Headwaters RU do not benefit from the recovery actions for salmon (USFWS 2015e, p. D-41). Conclusions from the 2008 5-year review (USFWS 2008, Table 1) were that 13 of the Columbia Headwaters RU core areas were at High Risk (37.1 percent), 12 were considered At Risk (34.3 percent), 9 were considered at Potential Risk (25.7 percent), and only 1 core area (Lake Koocanusa; 2.9 percent) was considered at Low Risk. Simple core areas, due to limited demographic capacity and single local populations were generally more inherently at risk than complex core areas under the model. While this assessment was conducted nearly a decade ago, little has changed in regard to individual core area status in the interim (USFWS 2015e, p. D-7). The current condition of the bull trout in this RU is attributed to the adverse effects of climate change, mostly historical mining and contamination by heavy metals, expanding populations of nonnative fish predators and competitors, modified instream flows, migratory barriers (e.g., dams), habitat fragmentation, forest practices (e.g., logging, roads), agriculture practices (e.g. irrigation, livestock grazing), and residential development. Of the 34 occupied core areas, nine (26 percent) have no identified primary threats (USFWS 2015e, Table D-2). Conservation measures or recovery actions implemented include habitat improvement, fish passage, and removal of nonnative species. Mid-Columbia Recovery Unit The Mid-Columbia RUIP describes the threats to bull trout and the site-specific management actions necessary for recovery of the species within the unit (USFWS 2015d, entire). The Mid- Columbia RU is located within eastern Washington, eastern Oregon, and portions of central Idaho. The Mid-Columbia RU is divided into four geographic regions: Lower Mid-Columbia, Upper Mid-Columbia, Lower Snake, and Mid-Snake Geographic Regions. This RU contains 24 occupied core areas comprising 142 local populations, two historically occupied core areas, one research needs area, and seven FMO habitats (USFWS 2015a, p. 47; USFWS 2015d, p. C-1 – C4). The current demographic status of bull trout in the Mid-Columbia Recovery Unit is highly variable at both the RU and geographic region scale. Some core areas, such as the Umatilla, Asotin, and Powder Rivers, contain populations so depressed they are likely suffering from the deleterious effects of small population size. Conversely, strongholds do exist within the RU, predominantly in the Lower Snake geographic area. Populations in the Imnaha, Little Minam, Clearwater, and Wenaha Rivers are likely some of the most abundant. These populations are all completely or partially within the bounds of protected wilderness areas and have some of the most intact habitat in the recovery unit. Status in some core areas is relatively unknown, but all indications in these core areas suggest population trends are declining, particularly in the core areas of the John Day Basin. More detailed description of bull trout distribution, trends, and survey data within individual core areas is provided in Appendix II of the RUIP (USFWS 2015d).

28 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project The current condition of the bull trout in this RU is attributed to the adverse effects of climate change, agricultural practices (e.g., irrigation, water withdrawals, livestock grazing), fish passage (e.g. dams, culverts), nonnative species, forest management practices, and mining. Of the 24 occupied core areas, six (25 percent) have no identified primary threats (USFWS 2015d, Table C-2). Conservation measures or recovery actions implemented include road removal, channel restoration, mine reclamation, improved grazing management, removal of fish barriers, and instream flow requirements. Upper Snake Recovery Unit The Upper Snake RUIP describes the threats to bull trout and the site-specific management actions necessary for recovery of the species within the unit (USFWS 2015f, entire). The Upper Snake RU is located in central Idaho, northern Nevada, and eastern Oregon. The Upper Snake RU is divided into seven geographic regions: Salmon River, Boise River, Payette River, Little Lost River, Malheur River, Jarbidge River, and Weiser River. This RU contains 22 core areas and 206 local populations (USFWS 2015a, p. 47), with almost 60 percent being present in the Salmon River Region. The population trends for the 22 core areas in the Upper Snake RU are summarized in Table E-2 of the Upper Snake RUIP (USFWS 2015f, pp. E-5 – E-7): six are classified as increasing, two are stable; two are likely stable; three are unknown, but likely stable; two are unknown, but likely decreasing; and, seven are unknown. The current condition of the bull trout in this RU is attributed to the adverse effects of climate change, dams, mining, forest management practices, nonnative species, and agriculture (e.g., water diversions, grazing). Of the 22 occupied core areas, 13 (59 percent) have no identified primary threats (USFWS 2015f, Table E-3). Conservation measures or recovery actions implemented include instream habitat restoration, instream flow requirements, screening of irrigation diversions, and riparian restoration. Status Summary The Service applied the NatureServe status assessment tool2 to evaluate the tentative status of the six RUs. The tool rated the Klamath RU as the least robust, most vulnerable RU and the Upper Snake RU the most robust and least vulnerable recovery unit, with others at intermediate values (Figure 2).

2 This tool consists of a spreadsheet that generates conservation status rank scores for species or other biodiversity elements (e.g. bull trout Recovery Units) based on various user inputs of status and threats (see USFWS 2015, p. 8 and Faber-Langendoen et al. 2012, entire, for more details on this status assessment tool).

29 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project

Figure 2. NatureServe status assessment tool scores for each of the six bull trout recovery units. The Klamath RU is considered the least robust and most vulnerable, and the Upper Snake RU the most robust and least vulnerable (from USFWS 2015, Figure 2).

2.3.7 Conservation Needs The 2015 RP for bull trout established the primary strategy for recovery of bull trout in the coterminous United States: (1) conserve bull trout so that they are geographically widespread across representative habitats and demographically stable in six RUs; (2) effectively manage and ameliorate the primary threats in each of six RUs at the core area scale such that bull trout are not likely to become endangered in the foreseeable future; (3) build upon the numerous and ongoing conservation actions implemented on behalf of bull trout since their listing in 1999, and improve our understanding of how various threat factors potentially affect the species; (4) use that information to work cooperatively with our partners to design, fund, prioritize, and implement effective conservation actions in those areas that offer the greatest long-term benefit to sustain bull trout and where recovery can be achieved; and (5) apply adaptive management principles to implementing the bull trout recovery program to account for new information (USFWS 2015a, p. 24.). Information presented in prior draft recovery plans published in 2002 and 2004 (USFWS 2002a, entire; 2004b, entire; 2004c, entire) provided information that identified recovery actions across the range of the species and to provide a framework for implementing numerous recovery actions by our partner agencies, local working groups, and others with an interest in bull trout conservation. Many recovery actions were completed prior to finalizing the RP in 2015. The 2015 RP (USFWS 2015a, entire) integrates new information collected since the 1999 listing regarding bull trout life history, distribution, demographics, conservation successes, etc., and integrates and updates previous bull trout recovery planning efforts across the coterminous range of the bull trout. The Service has developed a recovery approach that: (1) focuses on the identification of and effective management of known and remaining threat factors to bull trout in each core area; (2) acknowledges that some extant bull trout core area habitats will likely change (and may be lost) over time; and (3) identifies and focuses recovery actions in those areas where success is likely to meet our goal of ensuring the certainty of conservation of genetic diversity, life history features, and broad geographical representation of remaining bull trout populations so that the protections of the Act are no longer necessary (USFWS 2015a, p. 45-46).

30 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project To implement the recovery strategy, the 2015 RP establishes three categories of recovery actions for each of the six RUs (USFWS 2015a, pp. 50-51): 1. Protect, restore, and maintain suitable habitat conditions for bull trout. 2. Minimize demographic threats to bull trout by restoring connectivity or populations where appropriate to promote diverse life history strategies and conserve genetic diversity. 3. Prevent and reduce negative effects of nonnative fishes and other nonnative taxa on bull trout. 4. Work with partners to conduct research and monitoring to implement and evaluate bull trout recovery activities, consistent with an adaptive management approach using feedback from implemented, site-specific recovery tasks, and considering the effects of climate change. Bull trout recovery is based on a geographical hierarchical approach. Bull trout are listed as a single DPS within the five-state area of the coterminous United States. The single DPS is subdivided into six biological-based recovery units: (1) Coastal Recovery Unit; (2) Klamath Recovery Unit; (3) Mid-Columbia Recovery Unit; (4) Columbia Headwaters Recovery Unit (5) Upper Snake Recovery Unit; and (6) Saint Mary Recovery Unit (USFWS 2015a, p. 23). A viable recovery unit should demonstrate that the three primary principles of biodiversity have been met: representation (conserving the genetic makeup of the species); resiliency (ensuring that each population is sufficiently large to withstand stochastic events); and redundancy (ensuring a sufficient number of populations to withstand catastrophic events) (USFWS 2015a, p. 33). Each of the six recovery units contain multiple bull trout core areas, 109 total, which are non- overlapping watershed-based polygons, and each core area includes one or more local populations. Currently there are 109 occupied core areas, which comprise 611 local populations (USFWS 2015a, pp. 3, 47, Appendix F). There are also six core areas where bull trout historically occurred but are now extirpated, and one research needs area where bull trout were known to occur historically, but their current presence and use of the area are uncertain (USFWS 2015a, p. 3). Core areas can be further described as complex or simple (USFWS 2015a, p. 3-4). Complex core areas contain multiple local bull trout populations, are found in large watersheds, have multiple life history forms, and have migratory connectivity between SR habitat and FMO habitats. Simple core areas are those that contain one bull trout local population. Simple core areas are small in scope, isolated from other core areas by natural barriers, and may contain unique genetic or life history adaptations. A core area is a combination of core habitat (i.e., habitat that could supply all elements for the long-term security of bull trout) and a core population (a group of one or more local bull trout populations that exist within core habitat) and constitutes the basic unit on which to gauge recovery within a recovery unit. Core areas require both habitat and bull trout to function, and the number (replication) and characteristics of local populations inhabiting a core area provide a relative indication of the core area’s likelihood to persist. A core area represents the closest approximation of a biologically functioning unit for bull trout. Core areas are presumed to reflect the metapopulation structure of bull trout.

31 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project A local population is a group of bull trout that spawn within a particular stream or portion of a stream system (USFWS 2015a, p. 73). A local population is considered to be the smallest group of fish that is known to represent an interacting reproductive unit. For most waters where specific information is lacking, a local population may be represented by a single headwater tributary or complex of headwater tributaries. Gene flow may occur between local populations (e.g., those within a core population), but is assumed to be infrequent compared with that among individuals within a local population.

2.4 Environmental Baseline of the Action Area This section assesses the effects of past and ongoing human and natural factors that have led to the current status of the species, its habitat and ecosystem in the action area. Also included in the environmental baseline are the anticipated impacts of all proposed Federal projects in the action area that have already undergone section 7 consultations, and the impacts of state and private actions which are contemporaneous with this consultation.

2.4.1 Status of Bull Trout in the Action Area The action area is located in the Lower Clark Fork geographic region of the Columbia Headwaters Recovery Unit. The Lower Clark Fork Geographic Region comprises two complex core areas: Lake Pend Oreille and Priest Lake. The Project will take place in the Lake Pend Oreille core area. Because of the systematic and jurisdictional complexity (three States and a Tribal entity) and the current degree of migratory fragmentation caused by five mainstem dams, the threats and recovery actions in the Lake Pend Oreille (LPO) core area are very complex and are described in three parts. LPO-A is upstream of Cabinet Gorge Dam, almost entirely in Montana, and includes the mainstem Clark Fork River upstream to the confluence of the Flathead River as well as the portions of the lower Flathead River (e.g., Jocko River) on the Flathead Indian Reservation. LPO-B is the Pend Oreille lake basin proper and its tributaries, extending between Albeni Falls Dam downstream from the outlet of Lake Pend Oreille and Cabinet Gorge Dam just upstream of the lake; almost entirely in Idaho. LPO-C is the lower basin (i.e., lower Pend Oreille River), downstream of Albeni Falls Dam to Boundary Dam (1 mile upstream from the Canadian border) and bisected by Box Canyon Dam; including portions of Idaho, eastern Washington, and the Kalispel Reservation. Historically, and for current purposes of bull trout recovery, migratory connectivity among these separate fragments remains a primary objective. The action area is located within LPO-B of the Lake Pend Oreille core area.

32 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project

Figure 2. Map showing the three parts that comprise the Lake Pend Oreille (LPO) core area. The action area is located in LPO-B between Cabinet Gorge Dam and Albeni Falls Dam.

Lake Pend Oreille Core Area The Lake Pend Oreille (LPO) core area is one of the largest, most complex, and best- documented bull trout core areas in the Columbia Headwaters Recovery Unit, encompassing 95,000-acres (the largest and deepest natural lake in Idaho) and extending into western Montana. Bull trout in the interconnected LPO watershed appear to be entirely adfluvial (USFWS 2012, pp. 24) and are widely distributed throughout the core area. Adult bull trout movement into spawning streams tends to occur over several months and several seasons. Adults from local populations that have greater distances to travel from the lake to spawning streams and must migrate through larger river and tributary networks generally begin their migration earlier in the year. This must be done as migratory habitats may become inhospitable in the summer and fall due to elevated water temperatures and low flows (e.g., Priest River, Lightning Creek, and the Pack River), and these bull trout typically begin their migration as early as April or May through June to early July (DuPont et al. 2007, p. 1272; USFWS 2012, p. 24). Adult bull trout in direct tributaries to the lake (e.g., Trestle and Gold Creek), that have migration distances of a few hundred meters to several kilometers typically migrate from late August through October (Downs and Jakubowski 2003, p. 78). However, these smaller tributary streams tend to have relatively cool water temperatures during the summer months and adult bull trout have been documented moving into them during this time (Downs and Jakubowski 2006, p. 80). Adult bull

33 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project trout tend to migrate back into Lake Pend Oreille fairly rapidly after spawning, typically from September through October (Downs and Jakubowski 2003, p. 77). As with adult bull trout, juvenile migration from natal streams to foraging, migration, and overwintering habitat in LPO tends to occur over several months and several seasons. Juvenile outmigration occurs as early as March and continues into June as well as throughout the fall and winter months (Downs et al. 2006, pp. 193-194). To monitor bull trout population trends, an extensive redd count monitoring program in the LPO core area has been developed by IDFG and has been implemented since 1983 (USFWS in litt. 2008, p. 2). Despite the difficulties in identifying direct impacts from various factors, redd surveys provide one of the only mechanisms for long-term evaluation of adult bull trout abundance (Hardy et al. 2010, p. 10). Bull trout redd surveys have been conducted in 25 tributary streams or rivers reaches since 1983 in this portion of the core area with redds documented in at least 22 of the tributaries in most years (IDFG in litt. 2015). Redd survey data is collected annually from six index tributary streams (IDFG 2012, pp. 159-160): East Fork Lightning Creek, Johnson Creek, Trestle Creek, North Gold Creek, Gold Greek and Grouse Creek. Bull trout index redd counts have ranged from 273 to 794 throughout the 33-year period of record (averaging 509 redds per year). In addition to data collected from index streams, surveys have documented bull trout redds in 16 additional tributary streams including: Lightning Creek, Savage Creek, Char Creek, Porcupine Creek, Wellington Creek, Rattle Creek, Morris Creek, Strong Creek, Granite Creek, Sullivan Springs, West Gold Creek, Middle Fork East River, Uleda Creek, Pack River, Caribou Creek, and Hellroaring Creek. In the 8 years after listing (1999-2006), index stream redd counts ranged between 462 and 794, averaging 606 per year. Since the record high redd counts in 2006, index redd counts have generally declined over the last 9 years (2007-2015), ranging between 297 and 597, and averaging 404, a decline of roughly 33 percent since the 1999-2006 average. Based on annual redd counts which began in 1983 as an indicator of the core area population trend for index streams in the LPO core area, the population was steadily increasing through 2006, but has been declining in recent years. However, overall redd count data for all streams indicate that the core area population is still relatively strong with a 10-year average (2006-2015) of roughly 800 bull trout redds. Using an estimate of 3.2 bull trout per redd counted (IDFG 2012, p. 154), it is estimated that on average, the annual adult bull trout spawner escapement for surveyed streams in the core area is 2,550 adult bull trout. Furthermore, two separate bull trout population estimates within the lake in 1998 and 2008 were 12,134 fish greater than 40 centimeters (cm) and 12,513 fish greater than 35 cm, respectively (Vidergar 2000, p. 17; Dux, pers. comm. 2015). A 2011 population estimate found that the abundance of bull trout in the lake greater than 40 cm to be 11,744 fish, although there was high variance with this estimate likely due to study limitations (IDFG in litt. 2012).

34 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project

Figure 3. Number of bull trout redds in the Lake Pend Oreille Core Area (tributaries to Lake Pend Oreille basin proper including Priest River).

Status and Distribution of Bull Trout within the Action Area The action area is located within the Lightning Creek drainage within the Lake Pend Oreille (LPO) core area (Figure 5). Bull trout are known to reside in the Lightning Creek drainage in Idaho, which is considered an important spawning and rearing drainage for bull trout. The bull trout population in Lightning Creek is connected to the LPO core area population except during intermittent periods of no surface flow in the lower portion of Lightning Creek. This disconnection generally occurs during summer months after adult bull trout have migrated from LPO through the lower reaches of Lightning Creek into its upper reaches and tributaries. It is unknown if some bull trout from the Lightning Creek drainage are impacted from the intermittent connectivity during their upstream or downstream migrations. The Lightning Creek drainage is also used by a variety of native and nonnative species, including westslope cutthroat trout, rainbow trout, brown trout, brook trout, kokanee salmon, and mountain whitefish.

35 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project

Figure 4. Lightning Creek (red box) is a tributary to the Clark Fork River, which flows into Lake Pend Oreille in northern Idaho. Map source: Irving 1986, p. 6.

Bull trout are known to spawn in the mainstem of Lightning Creek, as well as seven of its tributaries: Morris, Savage, Char, Porcupine, Wellington, East Fork, and Rattle creeks (Pratt 1985; USFWS 2002b), with a significant percentage of bull trout spawning occurring in East Fork Creek. In 1983, the basin supported more bull trout spawning activity than any other tributary system in the Lake Pend Oreille key watershed, exceeding even Trestle Creek. However, historical redd count information provided by IDFG from 1983-2017 shows a recent declining trend of redd counts observed in Lightning Creek and its tributaries (Table 1), with the exception of redd surveys from 2017.

36 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Table 1. Redd counts within the Lightning Creek drainage, Idaho from 1983 through 2017. Surveys are conducted annually by the Idaho Department of Fish and Game. Lightning Lightning East Savage Char Porcupine Wellington Rattle Morris Drainage Year Cr. Fork* Cr. Cr. Cr. Cr. Cr. Cr. Total 1983 28 110 36 18 37 21 51 301 1984 9 24 12 9 52 18 32 156 1985 46 132 29 11 32 15 21 -- 286 1986 14 8 0 1 7 10 -- 40 1987 4 59 0 2 9 2 35 -- 111 1988 79 79 1989 100 100 1990 29 29 1991 0 1992 11 32 1 9 4 9 10 76 1993 2 27 6 37 6 4 8 90 1994 5 28 6 13 1 9 0 62 1995 0 3 0 2 2 1 1 9 1996 6 49 0 14 0 5 10 84 1997 0 22 0 1 0 2 2 27 1998 3 64 0 16 0 1 15 99 1999 16 44 4 17 4 22 13 1 121 2000 4 54 2 11 4 8 12 1 96 2001 7 36 4 2 0 7 67 0 123 2002 8 58 15 8 0 7 33 7 136 2003 8 38 7 7 5 8 37 1 111 2004 9 77 15 14 10 7 34 1 167 2005 22 50 7 15 14 6 34 3 151 2006 9 51 25 20 8 29 21 16 179 2007 3 34 0 1 8 9 2 0 57 2008 10 38 8 5 8 10 24 6 109 2009 11 85 5 1 15 4 62 6 189 2010 0 26 6 4 11 7 43 9 106 2011 20 64 1 9 13 6 65 0 178 2012 1 11 0 2 5 59 0 78 2013 1 26 5 4 4 5 8 3 56 2014 4 22 6 2 15 11 63 14 137 2015 11 17 5 0 0 8 5 0 46 2016 19 1 0 14 3 5 3 45 2017 3 80 9 0 10 5 20 32 169 10-year Average 7 39 5 3 9 6 35 7 111

Bull trout in the interconnected LPO watershed appear to be entirely adfluvial (USFWS 2012, p. 24). In the LPO basin, bull trout make spawning migrations into tributaries, including Lightning Creek, from LPO as early as May (Downs et al. 2006, p.191) with juvenile outmigration from upstream tributaries into LPO occurring as early as March (Downs et al. 2006, p. 196). Fall migrations occur as post spawning adults return to LPO. While post spawning outmigrations peak in August and September in Trestle Creek (Downs et al. 2006, p. 193), Dunham et al. (2001, p. 347) documented peak spawning in East Fork Lightning Creek in early October, suggesting a slightly later post spawn outmigration for the Lightning Creek drainage. Adult

37 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project outmigration is concurrent with a second pulse of juveniles moving downstream into the lake (Downs et al. 2006, p. 193-194). While juvenile outmigration peaks in October, bull trout monitoring data in nearby Granite and Trestle creeks suggest that juvenile bull trout continue to migrate out of natal streams between October and February (Bouwens, pers. comm. 2016). Bull trout are known to reside in the Lightning Creek drainage, and it is considered an important spawning and rearing drainage. The upper reach of Lightning Creek (where the project is located) provides SR habitat for bull trout, and the lower reach (below the East Fork Lightning Creek tributary) is designated foraging, migratory, and overwintering (FMO) habitat. Bull trout use the action area year-round for early-life rearing. As such, juvenile bull trout are likely to be present, and adult bull trout may be staging for spawning when the project is implemented. We can estimate the number of bull trout present in the Project area during Project implementation. In 2012, the Idaho Department of Fish and Game (IDFG) conducted monitoring surveys on LPO tributaries in an effort to follow general trends in fish abundance, species composition, and distribution (IDFG 2013, p. 2). Surveys were not conducted in the immediate action area; however, data was compiled in the lower sections of East Fork Lightning Creek, Porcupine Creek, and Rattle Creek, which are in close proximity to the action area. Utilizing the IDFG dataset, the Service took the mean of the density estimates for the three nearby survey locations for both juveniles and subadults/adults to estimate bull trout density within the action area (Table 2). This resulted in a density of 5 juveniles per 1,076 square feet and 0.5 subadults/adults per 1,076 square feet.

Table 2. Tributary monitoring results by stream, abundance, and density estimates sampled in 2012 (IDFG 2013, entire) and mean density estimates for the Project area.

Tributary Stream Width (ft) Juvenile Subadult/ Juveniles/ Subadult & Count Adult 1,076 ft² Adult/1,076 ft² Count

E. Fork 21.75 22 5 3.3 0.8 Lightning

Porcupine 16.6 13 3 2.6 0.6

Rattle 23.13 64 1 9.1 0.1

Mean of 3 ------5.0 0.5 tributaries

The project will include six in-stream diversion areas, totaling 715 feet in length and up to 35 feet in width, for a total area of 25,025 square feet. For juvenile and subadult/adult bull trout within the action area, utilizing the previously calculated densities of 5 juveniles per 1,076 square feet and 0.5 subadults/adults per 1,076 square feet and extrapolating those for the action area, we estimate (rounded up to the nearest whole number) that 117 juveniles and 12 subadult/adult bull trout will occur within the stream diversion areas. This estimate was derived

38 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project by comparing the estimated total area of the stream diversion areas (25,025 square feet) and dividing that by 1,076 square feet and then multiplying by the density estimates of 5 and 0.5 subadult/adult bull trout. During stream isolation activities, the Service anticipates that 129 bull trout (117 juvenile and 12 subadult/adults) will occur within the stream diversion area.

2.4.2 Factors Affecting Bull Trout in the Action Area Bull trout in general are vulnerable to human-induced factors that increase water temperature and sediment loads, change flow regimes, block migration routes, and establish nonnative trout, particularly brook trout (USFWS 2012, p. 32) and/or lake trout. As part of the Bull Trout Problem Assessment for the Lake Pend Oreille Key Watershed (Panhandle Bull Trout Technical Advisory Team 1998, entire), threats and limiting factors to bull trout were assessed. Limiting factors for bull trout in the Pend Oreille basin include lake and stream habitat conditions; outside influences on the species including competition, hybridization, prey availability, and predation (including human predation); and biological constraints inherent to the species (USFWS 2012, p. 32). The construction and operation of dams on the Clark Fork River (Cabinet Gorge) and Pend Oreille River (Albeni Falls) impact bull trout water quality (sediment, temperature, and nutrients), and habitat availability (spawning and rearing) and quantity within the Pend Oreille Core Area. These dams have likely permanently altered bull trout migration routes to tributary streams historically supporting the migratory form of bull trout. The action area has experienced changes since the completion of Albeni Falls Dam (USFWS 2012, p. 32). LPO water levels are artificially manipulated by the Albeni Falls Dam and vary seasonally. Due to the bi-annual draw down of LPO, the shallow area at the confluence of Lightning Creek and the Clark Fork River is routinely exposed, creating conditions that are not conducive to native riparian/shoreline vegetation or native in-water aquatic vegetation. As discussed in the Conservation Needs section of this Opinion (section 2.3.1.7), the Service drafted RUIPs for each recovery unit, including the Columbia Headwaters RU, identifying primary threats known to negatively impact bull trout populations at the core level, as well as conservation recommendations. The Columbia Headwaters RUIP identified upland and riparian land management threats (USFWS 2015e, p. D16). These include legacy effects from forest roads, logging, and fires that increase sediment and caused riparian and in-stream degradation, loss of large woody debris, and pool reductions in FMO and some SR habitat (e.g., Lightning and Grouse creeks, and Pack River). The Lightning Creek Watershed Assessment (PWA 2004, pp. 78-81) identified mechanisms that may be affecting bull trout abundance specifically within the Lightning Creek watershed, including trapping or migration barriers caused by the intermittent drying of stream reaches; decreased egg survival caused by high levels of fine sediments in spawning reaches; reduced summer rearing capacity due to reduced flows, simplified habitat structure, or increased water temperatures resulting from lack of riparian integrity; juvenile displacement or mortality resulting from lack of woody debris or other refuge structures in winter rearing habitat; and nonnative fishes. The introduction of nonnative fish species affects the population abundance and potentially the distribution of bull trout within the action area. Brook trout and lake trout are present in many of

39 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project the tributaries within the system, and may present the greatest threat to bull trout (USFWS in litt. 2008, p. 16). Brook trout hybridize with bull trout and lake trout prey on juvenile bull trout, with both species potentially competing for forage with bull trout. The impact of lake trout upon the bull trout population that utilize the action area is not fully understood; however, there is concern over the apparently rapidly expanding population abundance and distribution of lake trout within the LPO system. Additionally, the presence of nonnative walleye (Sander vitreus) near the mouth of the Clark Fork River may also affect bull trout, although their impacts to bull trout near the action area and LPO are not fully understood. Climate change is expected to impact bull trout across its range. Recent climate modeling by Isaak et al. (2015) indicates that, while suitable bull trout habitat will remain in all core areas within the Columbia Headwaters RU by 2040, some core areas will show a reduction in habitat suitability. The Lake Pend Oreille Core Area has been identified as one of seven core areas within the Columbia Headwaters RU that show little loss in the spatial extent of suitable habitat by 2040. However, modeling shows a sharp decline in the availability of SR habitat by 2080. This is likely due to reduced snow pack and increased incidence of rain-on-snow events due to their lower elevation and the influence of a maritime climate. Bull trout resiliency to climate change in the LPO core area is dependent on cold water refugia provided by the lake and ultimately may depend on the persistence of suitable SR habitat (USFWS 2015e, p. D40). Also discussed in the Conservation Needs section of this Opinion, a large body of research has documented the potential impacts to bull trout as a result of increases in air temperature and the subsequent increases in water temperature associate with climate change. The action area serves primarily as SR habitat so threats due to climate change are a concern. Additionally, unusually high winter flows resulting from increased winter precipitation in the form of rain rather than snow threaten to displace recently emerged juveniles and could increase the number of juveniles present in the action area during Project implementation. Lightning Creek is currently impacted by high sedimentation in the lower drainage. Reduced flows in summer months may result in an inability for adfluvial bull trout to migrate between spawning and rearing sites in the upper Lightning Creek drainage and overwinter sites in Lake Pend Oreille, thereby reducing the total number of adult immigrants. However, due to the short timeframe for Project implementation, it is unlikely that climate change will significantly alter the number of bull trout in the action area during Project implementation.

2.5 Effects of the Proposed Action Effects of the action consider the direct and indirect effects of an action on the listed species and/or critical habitat, together with the effects of other activities that are interrelated or interdependent with that action. These effects are considered along with the environmental baseline and the predicted cumulative effects to determine the overall effects to the species. Direct effects are defined as those that result from the proposed action and directly or immediately impact the species or its habitat. Indirect effects are those that are caused by, or will result from, the proposed action and are later in time, but still reasonably certain to occur. An interrelated activity is an activity that is part of the proposed action and depends on the proposed action for its justification. An interdependent activity is an activity that has no independent utility apart from the action under consultation.

40 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project 2.5.1.1 Direct and Indirect Effects of the Proposed Action The status of local adfluvial bull trout populations within the LPO core area may be affected by impacts to individuals moving through or utilizing habitat within the action area during Project implementation. The Project area is within the upper reach of Lightning Creek, and is utilized by bull trout as SR habitat. As such, bull trout are likely to occur within the Project area during Project implementation. The proposed Project has the potential to affect juvenile and subadult/adult bull trout present in the area through (1) fish capture, handling, and relocation; (2) noise; (3) sediment and turbidity; and (4) chemical contamination. Fish capture, handling, and relocation While partial stream diversion will occur during the Service-recommended in-water work windows when the likelihood of encountering bull trout and other salmonids is low, there is still a possibility of juvenile and subadult/adult bull trout presence in Lightning Creek during the stream diversion activities. The FHWA will assume that bull trout will be present in the stream at the Project sites and will attempt to remove any juvenile and subadult/adult bull trout from the reach during installation of the stream diversion berms and dewatering. It is possible that juvenile and subadult/adult bull trout could become stranded as a portion of the channel is being dewatered and diverted. It is also possible that juvenile and subadult/adult bull trout could be injured or killed during efforts to capture and relocate them. Handling stress and the use of dip nets may result in some injury and death. Individual fish could be harmed should descaling or other injury occur during dip netting or handling. Thus, juvenile and subadult/adult bull trout may be injured or killed during capture and removal from the work zone. The Service anticipates that not all bull trout will be captured during relocation activities and mortalities may result as a result of stranding. We estimate that roughly 5 percent of the bull trout in the diversion areas will not be captured during the multiple pass rescue efforts along the stream margins and within the diversion berms (USFWS 2004). In this Opinion, the Service is following assumptions provided in the USFWS biological opinion for fish passage restoration activities in eastern Oregon and Washington (USFWS 2004). Assumptions include:  5 percent stranded fish rate.  95 percent capture rate with electrofishing. o Of the 95 percent captured during electrofishing, there could be a 25 percent electroshocking injury/mortality rate. The Service estimates that 129 bull trout may be present in the isolated areas (117 juvenile and 12 adult bull trout). Project estimates include (rounded to the nearest whole number):  6 bull trout could be killed due to stream dewatering and stranding in the substrate (5 percent multiplied by 129 bull trout).  123 bull trout could be captured and handled during electrofishing activities (95 percent multiplied by 129 bull trout).  Of these 123 bull trout captured through electrofishing, 31 bull trout could be injured or killed during fish handling (25 percent multiplied by 123 bull trout).

41 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project In summary, the Service estimates that 129 bull trout may be present in the isolated areas. Of these, 6 bull trout may be killed as a result of stranding and 31 bull trout may be injured or killed as a result of fish handling. The remaining 92 bull trout will be harassed as a result of the relocation activities. To minimize the potential for and magnitude of adverse effects to bull trout, a qualified fisheries biologist will be present during the isolation of the work areas, and will conduct and/or supervise the capture and relocation activities. Removal and relocation of entrapped bull trout will be conducted via backpack electroshocker and dip nets (per protocol established by NMFS 2000, pp. 1-5). Electrofishing attempts will use the minimum voltage, pulse width, and rate settings necessary to immobilize fish. Fish capture and removal operations will be planned and conducted so as to minimize the amount and duration of handling. Captured fish will be kept in water to the maximum extent possible during seining/netting, handling, and transfer for release. In the event fish are observed dying or in distress, all activities that may exacerbate these suboptimal conditions will cease and remedial actions will be taken as necessary. As explained above, bull trout are likely to be present in the Project area during Project implementation. Bull trout may experience behavioral effects due to crowding, or may be killed or injured due to salvage or stranding. However, because fish removal will be limited to a 715- foot section of stream, will occur outside of the peak juvenile outmigration and adult migration, and because of a number of minimization measures described in the Assessment (FHWA 2017, pp. 12-13) including oversight of capture, handling, and relocation activities by a fisheries biologist, the number of bull trout that might be injured or killed, or suffer behavioral effects has been minimized to a reasonable extent. Noise (i.e., construction activities) All bank stabilization work will be completed in the dry, dewatered area following fish removal activities and construction of a diversion berm. However, the presence of large machinery adjacent to streams where bull trout are present would result in increased noise levels from construction equipment, vibration, and disturbances associated with increased human presence. The general increase in human activity associated with construction activities may disturb and displace bull trout in the action area. Machinery would operate throughout the day adjacent to the rivers intermittently with actual activity near and within the dewatered areas. The Fisheries Hydrostatic Working Group (FHWG) established a disturbance threshold for bull trout of 150 decibels (dB) (FHWG 2008). A study (FHWA 2008) regarding construction noise evaluated the impacts to fish from peak noise levels ranging from 170 to 255 dB and found that typical construction equipment similar to that proposed for this Project (e.g., excavator, crane, concrete pump, and trucks) produces noise ranging from 82 to 85 dB at 50 feet. Because the dB levels of construction equipment would be below the threshold criteria of 150 dB for behavioral effects to bull trout, the Service does not anticipate injury due to noise from construction equipment. The construction noise, vibration, and human presence may cause bull trout to avoid the action area during Project implementation, which may result in delayed migration. However, construction activities would only occur during daylight hours, and bull trout typically migrate during the night when construction noise, vibration, and human presence would not present a disturbance. Fish passage will be available at all times. For those bull trout that may be holding in the action area during the day, it is unknown if these stressors would cause fish to temporarily

42 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project move away or if fish would remain present. If bull trout move to avoid noise, vibration, or increased human presence, similar habitat is available both upstream and downstream of the action area and it is assumed that bull trout would move into the nearest similar habitat. Therefore, the Service does not consider these effects to be a significant disruption to normal feeding, holding, or sheltering behavior; therefore, effects to bull trout from project implementation, including noise, vibration, and human presence, would be insignificant. Turbidity and sedimentation Suspended sediment entering the stream channel could negatively impact bull trout in the immediate vicinity of the Project area. Suspended sediment could enter the stream channel from construction and removal of the in-stream diversion berms, and associated re-watering of the diversion areas. Sediment is a very important stressor to salmonids and can affect them both directly and indirectly. Bull trout are highly susceptible to sediment inputs and, of all salmonids, require the lowest turbidity and suspended sediment levels for spawning, incubation, and juvenile rearing (USFWS 1998). The potential negative impacts of increased suspended sediment on bull trout and other salmonids have been well documented (e.g., Bakke et al. 2002, p.1; Newcombe and MacDonald 1991, pp. 72-73; Newcombe and Jensen 1996, pp. 700-715; Bash et al. 2001, p. 24). Increases in suspended sediment have been shown to affect salmonid behavior in several ways. Social and feeding behaviors can be disrupted by increased levels of suspended sediment (Berg and Northcote 1985, p. 1410). Fish may avoid high concentrations of suspended sediments altogether (Hicks et al. 1991, pp. 483-485). Even small increases in suspended sediment may reduce feeding efficiency and growth rates of some salmonids (Sigler et al. 1984, p. 142). Based on their experiments with juvenile rainbow trout, Suttle et al. (2004, p. 973) concluded that “fine sediment deposition, even at low concentrations, can decrease growth and survival of juvenile salmonids.” They found “no threshold below which fine-sediment addition is harmless.” Turbidity can cause lethal, sublethal, and behavioral effects in juvenile, subadult and adult salmonids depending on the duration and intensity (Newcombe and Jensen 1996, pp. 700-715). Increased turbidity levels in the action area may result in temporary displacement of fish from preferred habitat or potential sublethal effects such as gill flaring, coughing, avoidance, and increase in blood sugar levels. The magnitude of these stress responses is generally higher when turbidity is increased and particle size decreased (Gregory and Northcote 1993, p. 1393). When the particles causing turbidity settle out of the water column in quiescent zones (slow moving pools, stream margins), they can contribute to sediment accumulation on the stream margins. Sediment release due to diversion berm construction and removal may result in temporary, localized increases in suspended sediment and turbidity. Sediment release due to re-watering (i.e., during diversion berm removal) may result in temporary increases in suspended sediment/turbidity. Re-watering diversion sites have been shown to produce a turbidity plume visible as much as 1000 feet downstream from the repair site that dissipates within a few hours (USFWS 2014, pp. 71-72). It is expected that construction and removal of the diversion berms could create a similar effect. Within the first 1,000 feet, bull trout may be killed or injured and may suffer behavioral effects, but effects will be insignificant beyond 1,000 feet. However, a turbidity monitoring plan will be in place during all in-stream work and the turbidity exceedance trigger would be 50 NTU for 2 consecutive hours above background conditions, as measured at the downstream end of the action area, which is the standard established by the State

43 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project of Idaho Water Quality Standards. The 50 NTU level is based on data from Lloyd et al. 1987 (in Bash et al. 2001, p. 67) suggesting that salmonids reacted negatively by beginning to move away from areas when the turbidity reaches 50 NTU. Should turbidity levels exceed 50 NTUs above background for more than 2 consecutive hours, work will be halted and construction methods adjusted to ensure that future exceedances do not occur. Fish removal will occur within the diversion berm area prior to construction, so effects to bull trout occupying the diversion area would be discountable. Bull trout that are present downstream of the diversion berm or downstream as the berm is deconstructed may experience temporary displacement from their preferred habitat or potential sublethal effects identified above. However, the Service has determined that effects to any bull trout will be insignificant because construction, removal, and subsequent re-watering will occur slowly, and turbidity monitoring and action-specific responses to excessive turbidity would ensure turbidity does not exceed 50 NTUs above background for more than 2 hours. These measures will ensure turbidity plumes are short-term in duration and will dissipate relatively quickly. Displaced bull trout would simply move downstream to adjacent habitat. Bull trout can travel as much as 156 miles per day during their migration (Swanberg 1996), so displacement downstream of 1,000 feet will not result in undue energetic demands that would lead to long-term adverse effects. Chemical Contamination Petroleum-based contaminants such as fuel, oil, and some hydraulic fluids contain poly-cyclic aromatic hydrocarbons, which can cause chronic sublethal effects to aquatic organisms (USFWS 2014, p. 77). Fuels and petroleum products are moderately to highly toxic to salmonids, depending on concentrations and exposure time. Free oil and emulsions can adhere to gills and interfere with respiration, and heavy concentrations of oil can suffocate fish. Evaporation, sedimentation, microbial degradation, and hydrology act to determine the fate of fuels entering fresh water (USFWS 2014, p. 77). Ethylene glycol (the primary ingredient in antifreeze) has been shown to result in sublethal effects to rainbow trout at concentrations of 20,400 milligrams per liter (Staples et al. 2001, p. 377). Brake fluid is also a mixture of glycols and glycol ethers, and has about the same toxicity as antifreeze. Impacts to water quality through chemical contamination could affect bull trout. Heavy machinery use in or near stream channels raises the potential of an accidental spill of fuel, lubricants, hydraulic fluid, and similar contaminants in the riparian conservation area, or directly into the water where they could adversely affect habitat, injure or kill aquatic food organisms, or directly impact bull trout. Machinery work would occur from the streambank and not within the active channel, which would significantly reduce the likelihood of toxic materials entering live water. Petroleum spill response and containment materials will be kept on site during construction to ensure rapid and adequate response to petroleum releases from the construction site. Additionally, any fuels and chemical supplies associated with construction activities will be stored no closer than 100 feet away from the live stream channel and all fueling will take place a minimum of 100 feet from the live stream channel (FHWA 2017, p. 13). If a spill occurs, amounts likely would be small because they would be associated with individual vehicles or equipment and not associated with larger fuel transport and related transfer operations. In addition, it is unlikely that any machinery or equipment fluids would be spilled in volumes or concentrations large enough to harm bull trout in or downstream of the area. Due to these and other Project minimization measures

44 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project described in the Assessment (FHWA 2017, pp. 12-13), the effects to bull trout associated with accidental chemical contamination are expected to be insignificant. 2.5.1.2 Effects of Interrelated or Interdependent Actions An interrelated activity is an activity that is part of the proposed action and depends on the proposed action for its justification. An interdependent activity is an activity that has no independent utility apart from the action under consultation. No effects from interrelated or interdependent actions are anticipated.

2.6 Cumulative Effects The implementing regulations for section 7 define cumulative effects to include the effects of future State, Tribal, local or private actions that are reasonably certain to occur in the action area considered in this Opinion. Future Federal actions that are unrelated to the proposed action are not considered in this section because they require separate consultation pursuant to section 7 of the Act. The Service is not aware of non-Federal plans proposed within the action area that will cumulatively affect bull trout.

2.7 Conclusion The Service has reviewed the current status of the bull trout, the environmental baseline in the action area, effects of the proposed action, and cumulative effects, and it is our conclusion that the proposed action is not likely to jeopardize the species’ continued existence. Furthermore, the Project will not impact the distribution of bull trout in the core area. While we do expect some individual bull trout will be adversely affected, we expect numbers to be low, and thus, we do not anticipate that this will translate to local population-level affects. The Service concludes that direct adverse effects and behavioral effects to bull trout in the action area would result from crowding and capture, handling, and relocation activities that will occur during the construction of the diversion berms. Adverse effects in the form of potential injury or death are expected during construction of the diversion berms as a result of fish salvage or stranding during dewatering. Adverse effects in the form of harassment may result in behavioral effects from crowding during berm construction. Based on the fact that project implementation will occur during the Service’s recommended work window (i.e. fish handling), we do not expect significant numbers of bull trout to be present in the action area. Passage around the project areas will be available at all times, and all work will be performed during daylight hours. In addition, many of the anticipated effects should be minimized, but not precluded, by the minimization measures (FHWA 2017, pp. 12-13) incorporated into the Project. When implemented correctly, these measures will significantly reduce potential impacts to bull trout, but some adverse effects are still expected. The Service expects that the numbers and distribution of bull trout in the action area, the Lake Pend Oreille Core Area, or in the Columbia Headwaters Recovery Unit will not be significantly changed as a result of this Project; Project impacts will not appreciably reduce the likelihood of either the survival or recovery of bull trout. The proposed action may have some adverse effects

45 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project to a small number of bull trout; however, these effects are not likely to cause a measurable response to bull trout at the local population, core area, or coterminous U.S. scales. It is the Service’s opinion that the proposed action would not jeopardize the coterminous population of bull trout. Our conclusions are based on the following: 1. This action will not prevent the ability of bull trout to migrate between Lake Pend Oreille and SR habitat in Lightning Creek and its tributary streams, as fish passage will be available at all times during Project implementation. Work will occur only during daylight hours while bull trout typically migrate at night. 2. In-water work (berm construction and deconstruction) will occur over no more than 2 non-consecutive days at each of the six project locations during Service-identified work windows that are specifically designed to minimize the number of bull trout present in the area, thus minimizing potential effects such as exposure to crushing, turbidity, and migratory delays. 3. Fish capture, handling, and relocation activities will be conducted according to established protocols that are specifically designed to minimize impacts to salmonids and activities will be overseen by fisheries biologists. Furthermore, a fish biologist will ensure minimization measures are implemented and that any site-specific adjustments to Project activities are protective of bull trout. 4. The minimization measures specifically identified for the implementation of this Project reduce the potential for causing short-term adverse effects to bull trout.

2.8 Incidental Take Statement Section 9 of the Act and Federal regulations pursuant to section 4(d) of the Act prohibit the take of endangered and threatened fish species without specific exemption. Take is defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt to engage in any such conduct. Harm in the definition of take in the Act means an act which actually kills or injures wildlife. Such act may include significant habitat modification or degradation that results in death or injury to listed species by significantly impairing essential behavioral patterns, including breeding, feeding, or sheltering. Harass is defined by the Service as an intentional or negligent act or omission which creates the likelihood of injury to listed species by annoying it to such an extent as to significantly disrupt normal behavior patterns which include, but are not limited to, breeding, feeding, or sheltering. Incidental take is defined as take that is incidental to, and not the purpose of, the carrying out of an otherwise lawful activity. Under the terms of section 7(b)(4) and section 7(o)(2), taking that is incidental to and not intended as part of the agency action is not considered to be prohibited taking under the Act provided that such taking is in compliance with the terms and conditions of this Incidental Take Statement. The FHWA has a continuing duty to regulate the activity covered by this incidental take statement. If the FHWA fails to assume and implement the terms and conditions the protective coverage of section 7(o)(2) may lapse. In order to monitor the impact of incidental take, the

46 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project FHWA must report the progress of the action and its impact on the species to the Service as specified in the incidental take statement [50 CFR §402.14(i)(3)].

2.8.1 Form and Amount or Extent of Take Anticipated Based on bull trout redd survey data and other population sampling activities conducted by the IDFG, bull trout have been documented utilizing Lightning Creek throughout the watershed and in the immediate Project vicinity. Data on migration timing, spawning and early life rearing habitat, temperature regimes, population monitoring, and habitat quality and quantity demonstrates that bull trout presence in the action area during implementation of the proposed Project is possible. The project site locations occur in designated bull trout SR habitat. Juveniles are expected to be present in SR habitat year-round and adult bull trout could be migrating upstream through the action area on their way to begin staging for spawning. The majority of the in-water work will occur within the Service’s recommended in-water work window (July 15 through August 31). All diversion berms and fish handling will be completed by the end of the in-water work window (August 31), and all in-water work will be completed by September 15. Project implementation will occur during daylight hours when bull trout are less likely to move through the area. These factors further reduce the likelihood of high numbers of bull trout present during Project implementation. During stream isolation activities, the Service anticipates that, of these, up to 129 bull trout (117 juvenile and 12 subadult/adult) may be present within the six isolated diversion areas. As partial segments of the channel are dewatered, some bull trout are expected to evacuate the area of their own volition while others will remain and require capture, handling, and release. The Service anticipates that not all bull trout will be captured during relocation activities and may result in mortalities as a result of stranding. We estimate that roughly 5 percent of the bull trout will not be captured during the multiple pass rescue efforts along the stream margins and within the diversion berms (USFWS 2004). Given that trained fisheries biologists will be conducting the fish salvage activities, we anticipate stranding of bull trout to be no more than 5 percent, and injury and/or mortality of bull trout from fish salvage activities is expected to be no more than 25 percent. The amount of take is partitioned as discussed in the Effects of the Proposed Action section of this Opinion. The Service, therefore, estimates that implementation of the proposed Project will take, in the form of harassment, 92 bull trout. The Service estimates that implementation of the proposed Project will take, in the form of harm (i.e. mortality) due to stranding, 6 bull trout. Additionally, the Service estimates take, in the form of harm (injury and/or mortality) due to fish handling, 31 bull trout.

2.8.2 Effect of the Take In the accompanying Opinion, the Service determined that this level of anticipated take is not likely to jeopardize the continued existence of the bull trout across its range.

47 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project 2.8.3 Reasonable and Prudent Measures The Service concludes that the following reasonable and prudent measures (RPMs) are necessary and appropriate to minimize the take of bull trout caused by the proposed action activities. 1. Minimize the potential for incidental take resulting from dewatering and fish removal activities, and construction of the diversion berms. 2. Minimize the potential for incidental take resulting from project-related sediment effects.

2.8.4 Terms and Conditions In order to be exempt from the prohibitions of section 9 of the Act, the FHWA must comply with the following terms and conditions, which implement the RPMs described above: To implement RPM #1 (dewatering and fish removal activities): 1. Fish capture, handling, and relocation will be conducted by a fisheries biologist experienced with work area isolation to ensure the safe handling of fish. All fish removal activities will be completed by the end of the Service’s recommended in-water work window (August 31). 2. Dewater the stream channel in a slow controlled fashion to allow the maximum number of bull trout to safely exit the stream of their own volition. To implement RPM #2 (sediment) 1. Re-water the stream channel in a slow, controlled fashion to limit the intensity, duration, and extent of the turbidity plumes produced.

2.8.5 Reporting and Monitoring Requirement In order to monitor the impacts of incidental take, the Federal agency or any applicant must report the progress of the action and its impact on the species to the Service as specified in the incidental take statement [(50 CFR 402.14 (i)(3)]. 1. The FHWA will prepare a report for the Service that summarizes the number and species of fish handled during all fish crowding and dewatering activities. 2. During Project implementation, the FHWA will promptly notify the Service’s Idaho Fish and Wildlife Office in Spokane of any emergency or unanticipated situations arising that may be detrimental for bull trout relative to the proposed activity. 3. The FHWA will provide a copy of the results of turbidity monitoring from this project. Reports can be submitted electronically to Megan Kosterman ([email protected]) or mailed to this office.

2.9 Conservation Recommendations Section 7(a)(1) of the Act directs Federal agencies to utilize their authorities to further the purposes of the Act by carrying out conservation programs for the benefit of endangered and threatened species. Conservation recommendations are discretionary agency activities to

48 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project minimize or avoid adverse effects of a proposed action on listed species or critical habitat, to help implement recovery programs, or to develop new information on listed species. The Service recommends that the FHWA: 1. Identify and pursue opportunities to improve habitat in spawning and rearing tributaries within the Lightning Creek watershed.

2.10 Reinitiation Notice This concludes formal consultation on the Idaho Panhandle National Forests Roads and Bridges Repair Project. As provided in 50 CFR §402.16, reinitiation of formal consultation is required where discretionary Federal agency involvement or control over the action has been maintained (or is authorized by law) and if: 1. The amount or extent of incidental take is exceeded. 2. New information reveals effects of the agency action that may affect listed species or critical habitat in a manner or to an extent not considered in this Opinion. 3. The agency action is subsequently modified in a manner that causes an effect to the listed species or critical habitat that was not considered in this Opinion. 4. A new species is listed or critical habitat designated that may be affected by the action. In instances where the amount or extent of incidental take is exceeded, any operations causing such take must cease pending reinitiation.

49 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project 3. LITERATURE CITED

3.1 Published Literature Ardren, W.R., P.W. DeHaan , C.T. Smith , E.B. Taylor , R. Leary , C.C. Kozfkay , L. Godfrey, M. Diggs , W. Fredenberg , J. Chan, C.W. Kilpatrick , M.P. Small, and D.K. Hawkins. 2011. Genetic Structure, Evolutionary History, and Conservation Units of Bull Trout in the Coterminous United States, Transactions of the American Fisheries Society, 140:2, 506-525. Bakke, P.D., B. Peck, and S. Hager. 2002. Geomorphic controls on sedimentation impacts. Eos, Transactions, American Geophysical Union 83(47), Fall Meet. Suppl., Abstract Hl lC- 0847, 2002. Poster presented at GU 2002 Fall Meeting, San Francisco, California. Fish and Wildlife Service, Western Washington Fish and Wildlife Office, Lacey, Washington. Bash, J., C. Berman, and S. Bolton. 2001. Effects of turbidity and suspended solids on salmonids. Center for Berg, R.K. and E.K. Priest. 1995. Appendix Table 1: A list of stream and lake fishery surveys conducted by U.S. Forest Service and Montana Fish, Wildlife and Parks fishery biologists in the Clark Fork River Drainage upstream of the confluence of the Flathead River from the 1950s to the present. Montana Fish, Wildlife, and Parks, Job Progress Report, Project F-78-R-1, Helena, Montana. Barrows, M.G., D.R. Anglin, P.M. Sankovich, J.M. Hudson, R.C. Koch, J.J. Skalicky, D.A. Wills and B.P. Silver. 2016. Use of the Mainstem Columbia and Lower Snake Rivers by Migratory Bull Trout. Data Synthesis and Analyses. Final Report. U.S. Fish and Wildlife Service, Columbia River Fisheries Program Office, Vancouver, Washington. 276 pp. Baxter, C.V. 2002. Fish movement and assemblage dynamics in a Pacific Northwest riverscape. Doctor of Philosophy in Fisheries Science. Oregon State University, Corvallis, Oregon. 174 pp. Berg, L. and T.G. Northcote. 1985. Changes in territorial, gill-flaring, and feeding behavior in juvenile coho salmon (Oncorhyncus kisutch) following short-term pulses of suspended sediment. Canadian Journal of Fisheries and Aquatic Sciences 42(8):1410-1417pp. Boag, T.D. 1987. Food habits of bull char, Salvelinus confluentus, and rainbow trout, Salmo gairdneri, coexisting in a foothills stream in northern Alberta. Canadian Field-Naturalist 101(1): 56-62. Bond, C.E. 1992. Notes on the nomenclature and distribution of the bull trout and the effects of human activity on the species. Pages 1-4 in Howell, P.J. and D.V. Buchanan, editors. Proceedings of the Gearhart Mountain Bull Trout Workshop. Oregon Chapter of the American Fisheries Society, Corvallis, Oregon. Brenkman, S.J., and S.C. Corbett. 2005. Extent of anadromy in bull trout and implications for conservation of a threatened species. North American Journal of Fisheries Management 25:1073-1081.

50 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Brewin, P.A. and M.K. Brewin. 1997. Distribution maps for bull trout in Alberta. Pages 206-216 in Mackay, W.C., M.K. Brewin and M. Monita, editors. Friends of the Bull Trout Conference Proceedings. Buchanan, D. M. and S. V. Gregory. 1997. Development of water temperature standards to protect and restore habitat for bull trout and other cold water species in Oregon. Pages 1- 8 in Mackay, W.C., M.K. Brewin and M. Monita, editors. Friends of the Bull Trout Conference Proceedings. Burkey, T.V. 1989. Extinction in nature reserves: the effect of fragmentation and the importance of migration between reserve fragments. Oikos 55:75-81. Cavender, T.M. 1978. Taxonomy and distribution of the bull trout, Salvelinus confluentus (Suckley), from the American Northwest. California Fish and Game 64(3): 139-174. Costello, A.B., T.E. Down, S.M. Pollard, C.J. Pacas, and E.B. Taylor. 2003. The influence of history and contemporary stream hydrology on the evolution of genetic diversity within species: an examination of microsatellite DNA variation in bull trout, Salvelinus confluentus (Pisces: Salmonidae). Evolution 57(2):328-344. Donald, D.B. and D.J. Alger. 1993. Geographic distribution, species displacement, and niche overlap for lake trout and bull trout in mountain lakes. Canadian Journal of Zoology 71: 238-247. Downs, C.C., and R. Jakubowski. 2003. Lake Pend Oreille Clark Fork River fishery research and monitoring: 2002 annual progress report bull trout redd counts and escapement estimates, 1999–2001. Report to the Avista Corporation by the Idaho Department of Fish and Game, Boise, Idaho. Downs, C.C., D. Horan, E. Morgan-Harris, and R. Jakubowski. 2006. Spawning Demographics and Juvenile Dispersal of an Adfluvial Bull Trout Population in Trestle Creek, Idaho. North American Journal of Fisheries Management 16:190-200. Downs C.C., and R. Jakubowski. 2006. Lake Pend Oreille/Clark Fork River Fishery Research and Monitoring 2005 Progress Report. 2005 bull trout redd counts; 2005 Clark Fork River fishery assessment progress report; 2005 Trestle and Twin creeks bull trout outmigration and Lake Pend Oreille survival study; 2005 Johnson and Granite creeks bull trout trapping; 2005 Twin Creek restoration monitoring progress report; 2005 tributary fish population monitoring progress report; 2005 lower Clark Fork River westslope cutthroat trout radio telemetry and genetic study progress report. Report to Avista Corporation from the Idaho Department of Fish and Game, Boise, Idaho. Dunham, J.B. and B.E. Rieman. 1999. Metapopulation structure of bull trout: influences of physical, biotic, and geometrical landscape characteristics. Ecological Applications 9(2):642-655. Dunham, J.B, B.E. Rieman, and K. Davis. 2001. Sources and Magnitude of Sampling Error in Redd Counts for Bull Trout. North American Journal of Fisheries Management 21(2):343-352 DuPont, J.M., R.S. Brown, and D.R. Geist. 2007. Unique allacustrine migration patterns of a bull trout population in the Pend Oreille River drainage, Idaho. North American Journal of Fisheries Management 27(4):1268-1275.

51 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Fisheries Hydroacoustic Working Group (FHWG). 2008. Agreement in Principle for Interim Criteria for Injury to Fish from Pile Driving Activities (June 12, 2008). Fraley, J.J., and B.B. Shepard. 1989. Life history, ecology and population status of migratory bull trout (Salvelinus confluentus) in the Flathead Lake and River system, Montana. Northwest Science 63(4): 133-143. Frissell, C.A. 1999. An ecosystem approach to habitat conservation for bull trout: groundwater and surface water protection. Flathead Lake Biological Station, University of Montana, Open File Report Number 156-99, Polson, MT, January 07, 1999. 46 pp. Goetz, F. 1989. Biology of the bull trout, Salvelinus confluentus, a literature review. Willamette National Forest. Eugene, Oregon. Goetz, F., E.D. Jeanes, and E.M. Beamer. 2004. Bull trout in the nearshore. U.S. Army Corps of Engineers, Preliminary draft, Seattle, Washington, June 2004. 396 pp. Gregory, R.S., and T.G. Northcote. 1993. Surface, planktonic, and benthic foraging by juvenile chinook salmon (Oncorhynchus tshawytscha) in turbid laboratory conditions. Canadian Journal of Fisheries and Aquatic Sciences 50(2):233-240. Haas, G.R., and J.D. McPhail. 2001. The post-Wisconsin glacial biogeography of bull trout (Salvelinus confluentus): a multivariate morphometric approach for conservation biology and management. Canadian Journal of Fisheries and Aquatic Sciences 58:2189-2203. Hardy, R., R. Ryan, M. Liter, M. Maiolie, and J. Fredericks. 2010. Fishery Management Annual Report Panhandle Region 2009. Idaho Department of Fish and Game. December 2010. IDFG 10-112. Howell, P.J., and D.V. Buchanan. 1992. Proceedings of the Gearhart Mountain bull trout workshop. Oregon Chapter of the American Fisheries Society, Corvallis, Oregon. 67 pp. Hicks, B.J., J.D. Hall, P.A. Bisson, and J.R. Sidell. 1991. Response of salmonids to habitat change. In Meehan, W.R., editor. Influences Of Forest And Rangeland Management On Salmonid Fishes and Their Habitats. American Fisheries Society Special Publication 19. 483-518 pp. Idaho Department of Fish and Game (IDFG). 2012. Fishery Management Annual Report, Panhandle Region 2011. Boise, Idaho. 178 pp. Idaho Department of Fish and Game (IDFG). 2013. Idaho Native Salmonid Research and Monitoring Update – 2012. Coeur d’Alene, Idaho. 33 pp. Irving, D.B. 1986. Pend Oreille trout and char life history study. Idaho Department of Fish and Game, in cooperation with Lake Pend Oreille Idaho Club. Boise, Idaho. Isaak, D.J., M.K. Young, D. Nagel, and D. Horan. 2014. Coldwater as a Climate Shield to Preserve Native Trout Through the 21st Century. Pages 110-116 in Carline, R.F., C. LoSapio, editors. Looking back and moving forward. Proceedings of the Wild Trout XI Symposium, Bozeman, Montana. 392 pp. Isaak, D.J., M.K. Young, D.E. Nagel, D.L. Horan, and M.C. Groce. 2015. The cold-water climate shield: delineating refugia for preserving salmonid fishes through the 21st century. Global Change Biology 21:2540-2553.

52 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Jakober, M. 1995. Autumn and winter movement and habitat use of resident bull trout and westslope cutthroat trout in Montana. M.S. Thesis, Montana State University, Bozeman, Montana. Koopman, M.E., R.S. Nauman, B.R. Barr, S.J. Vynne, and G.R. Hamilton. 2009 Projected Future Conditions in the Klamath Basin of Southern Oregon and Northern California. 28 pp. Leary, R.F. and F.W. Allendorf. 1997. Genetic confirmation of sympatric bull trout and Dolly Varden in western Washington. Transactions of the American Fisheries Society 126:715- 720. Leathe, S.A. and P. Graham. 1982. Flathead Lake fish food habits study. E.P.A. through Steering Committee for the Flathead River Basin Environmental Impact Study. McPhail, J.D., and J.S. Baxter. 1996. A review of bull trout (Salvelinus confluentus) life-history and habitat use in relation to compensation and improvement opportunities. Department of Zoology, University of British Columbia, Fisheries Management Report Number 104, Vancouver, British Columbia. 36 pp. Meefe, G.K. and C.R. Carroll. 1994. Principles of conservation biology. Sinauer Associates, Inc. Sunderland, Massachusetts. Montana Bull Trout Scientific Group (MBTSG). 1998. The Relationship Between Land Management Activities and Habitat Requirements of Bull Trout. Helena, Montana. 78 pp. + vi. Mote, P., A.K. Snover, S. Capalbo, S.D. Eigenbrode, P. Glick, J. Littell, R. Raymondi, and S. Reeder. 2014. Northwest. In Climate change impacts in the United States: The third national climate assessment, edited by J.M. Melillo, T.C. Richmond, and G.W. Yohe. Washington, DC: U.S. Global Change Research Program. Online at www.globalchange.gov/nca3-downloads-materials. National Marine Fisheries Service (NMFS). 2000. Guidelines for Electrofishing Waters Containing Salmonids Listed Under the Endangered Species Act. Newcombe, C.P. and J.O.T. Jensen. 1996. Channel suspended sediments and fisheries: a synthesis for quantitative assessment of risk and impact. North American Journal of Fisheries Management 16: 693-727. Newcombe, C.P. and D.D. MacDonald. 1991. Effects of suspended sediments on aquatic ecosystems. North American Journal of Fisheries Management 11: 72-81pp. Panhandle Bull Trout Technical Advisory Team (PBTTAT). 1998. Draft Coeur d'Alene Lake Basin bull trout problem assessment. Prepared for the State of Idaho. 73 pp. Poff, N.L., M.M Brinson, and J.W. Day (Jr.)/ 2002. Aquatic Ecosystems and Global Climate Change: Potential Impacts on Inland Freshwater and Coastal Wetland Ecosystems in the United States. Prepared for the Pew Center on Global Climate Change. 45 pp. Point Reyes Bird Observatory Conservation Science (PRBO). 2011. Projected Effects of Climate Change in California: Ecoregional Summaries Emphasizing Consequences for Wildlife. Version 1.0, February 2011. 59 pp.

53 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Pratt, K. L. 1985. Pend Oreille trout and char life history study. Idaho Department of Fish and Game, Boise, Idaho. 105 pp. Pratt, K.L. 1992. A review of bull trout life history. Pages 5-9 in Howell, P. J. and D. V. Buchanan, editors. Proceedings of the Gearhart Mountain Bull Trout Workshop. Oregon Chapter of the American Fisheries Society, Corvallis, Oregon. Rich, C.F., Jr. 1996. Influence of abiotic and biotic factors on occurrence of resident bull trout in fragmented habitats, western Montana. M.S. thesis. Montana State University, Bozeman, Montana. Rieman, B.E. and J. Clayton. 1997. Wildfire and native fish: Issues of forest health and conservation of sensitive species. Fisheries 22:6-14. Rieman, B.E. and J.B. Dunham. 2000. Metapopulations and salmonids: a synthesis of life history patterns and empirical observations. Ecology of Freshwater Fish 9:51-64. Rieman, B.E., D. Isaak, S. Adams, D. Horan, D. Nagel, C. Luce, and D. Meyers. 2007. Anticipated climate warming effects on bull trout habitats and populations across the Interior Columbia River Basin. Transactions of the American Fisheries Society 136:1552-1565. Rieman, B.E., D.C. Lee and R.F. Thurow . 1997. Distribution, status, and likely future trends of bull trout within the Columbia River and Klamath River basins. North American Journal of Fisheries Management 17(4): 1111-1125. Rieman, B.E. and J.D. McIntyre. 1993. Demographic and habitat requirements for conservation of bull trout. General Technical Report INT-302, Intermountain Research Station, U.S. Department of Agriculture, Forest Service, Boise, Idaho. Rieman, B.E. and J.D. McIntyre. 1995. Occurrence of bull trout in naturally fragmented habitat patches of varied size. Transactions of the American Fisheries Society 124 (3): 285-296. Rieman, B.E. and J.D. McIntyre. 1996. Spatial and temporal variability in bull trout redd counts. North American Journal of Fisheries Management 16: 132-141. Ringel, B.M., J. Neibauer, K. Fulmer, and M.C. Nelson. 2014. Migration patterns of adult bull trout in the Wenatchee River, Washington 2000-2004. U.S. Fish and Wildlife Service, Leavenworth, Washington. 81 pp. with separate appendices. Robins, C.R., R.M. Bailey, C.E. Bond, J.R. Brooker, E.H. Lachner, R.N. Lea and W.B. Scott. 1980. A list of common and scientific names of fishes from the United States and Canada. American Fisheries Society Special Publication 12, Bethesda, Maryland. Ryan, R. and R. Jakubowski. 2012. Idaho native salmonid research and monitoring report, 2011 progress report. Report to Avista Corporation, Spokane, WA. Saunders, D.A., R.J. Hobbs, and C.R. Margules. 1991. Biological consequences of ecosystem fragmentation: A review. Conservation Biology 5:18-32. Sexauer, H.M. and P.W. James. 1997. Microhabitat use by juvenile trout in four streams located in the Eastern Cascades, Washington. Pages 361-370 in Mackay, W.C., M.K. Brown and M. Monita, editors. Friends of the Bull Trout Conference Proceedings.

54 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Sigler, J.W., T.C. Bjornn, and F.H. Everest. 1984. Effects of chronic turbidity on density and growth of steelheads and coho salmon. Transactions of the American Fisheries Society 113:142-150. Spruell, P., B.E. Rieman, K.L. Knudsen, F.M. Utter, and F.W. Allendorf. 1999. Genetic population structure within streams: microsatellite analysis of bull trout populations. Ecology of Freshwater Fish 8:114-121. Spruell, P., A.R. Hemmingsen, P.J. Howell, N. Kanda, and F.W. Allendorf. 2003. Conservation genetics of bull trout: Geographic distribution of variation at microsatellite loci. Conservation Genetics 4:17-29 Staples, C.A, J.B. Williams, G.R. Craig, and K.M. Roberts. 2001. Fate, effects and potential environmental risks of ethylene glycol: a review. Chemosphere 43(3):377-383. Starcevich, S.J., P.J. Howell, S.E. Jacobs, and P.M. Sankovich. 2012. Seasonal movement and distribution of fluvial adult bull trout in selected watersheds in the mid-Columbia River and Snake River basins. PLoS ONE 7(5):e37257. doi:10.1371/journal.pone.0037257 Suttle, K.B., M.E. Power, J.M. Levine, and C. McNeely. 2004. How fine sediment in riverbeds impairs growth and survival of juvenile salmonids. Ecological Applications 14(4):969- 974. Swanberg, T.R. 1996. The movement and habitat use of fluvial bull trout in the Upper Clark Fork River Drainage. Master's thesis, University of Montana. 61 pp. Taylor, B.E., S. Pollard, and D. Louie. 1999. Mitochondrial DNA variation in bull trout (Salvelinus confluentus) from northwestern North America: implications for zoogeography and conservation. Molecular Ecology 8:1155-1170. Thomas, G. 1992. Status of bull trout in Montana. Report prepared for Montana Department of Fish, Wildlife and Parks, Helena, Montana. 83 pp. U.S. Federal Highway Administration (FHWA). 2008. Effective Noise Control During Nighttime Construction – FHWA Work Zone – Mozill. December 22, 2008. http://ops.fhwa.dot.gov/wz/workshops/accessible/Schexnayder_paper.htm (December 2012). U.S. Federal Highway Administration (FHWA). 2017. Idaho Panhandle National Forests Project, Bonner and Boulder Counties, Idaho. Biological Assessement. (December 1, 2017). U.S. Fish and Wildlife Service (USFWS). 1998. Bull Trout Interim Conservation Guidance. 47 pp. U.S. Fish and Wildlife Service (USFWS). 1999. Endangered and Threatened Wildlife and Plants; Determination of Threatened Status for Bull Trout in the Coterminous United States. Fish and Wildlife Service, Department of the Interior. November 1, 1999. 64 FR 58910- 58933. U.S. Fish and Wildlife Service (USFWS). 2002a. Bull trout (Salvelinus confluentus) draft recovery plan (Klamath River, Columbia River, and St. Mary-Belly River distinct population segments). U.S. Fish and Wildlife Service, Portland, Oregon.

55 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project U.S. Fish and Wildlife Service (USFWS). 2002b. Endangered and Threatened Wildlife and Plants; Proposed Designation of Critical Habitat for the Klamath River and Columbia River Distinct Population Segments of Bull Trout and Notice of Availability of the Draft Recovery Plan; Proposed Rule and Notice. November 29, 2002. 67 FR 71236-71284. U.S. Fish and Wildlife Service (USFWS). 2004. Biological Opinion for USDA Forest Service Fish Passage Restoration Activities in Eastern Oregon and Washington 2004-2008. U.S. Fish and Wildlife Service, Region 1. Portland, Oregon, and Western Washington Fish and Wildlife Office, Lacey, Washington. U.S. Fish and Wildlife Service (USFWS). 2004a. Designation of critical habitat for the Klamath River and Columbia River populations of bull trout. October 6, 2004. 69 FR 59996 – 60076. U.S. Fish and Wildlife Service (USFWS). 2004b. Draft Recovery Plan for the Coastal-Puget Sound distinct population segment of bull trout (Salvelinus confluentus). Volume I: Puget Sound Management Unit, 389 + xvii p., and Volume II: Olympic Peninsula Management Unit, 277 + xvi p., Portland, Oregon. U.S. Fish and Wildlife Service (USFWS). 2004c. Draft recovery plan for the Jarbidge River distinct population segment of the bull trout (Salvelinus confluentus). U.S. Fish and Wildlife Service, Portland, Oregon. 132 + xiii p. U.S. Fish and Wildlife Service (USFWS). 2005a. Endangered and threatened wildlife and plants; designation of critical habitat for the bull trout. September 26, 2005. 70 FR 56212-56311. U.S. Fish and Wildlife Service (USFWS). 2005b. Bull trout core area templates - complete core area by core area analysis. U.S. Fish and Wildlife Service, Portland, Oregon. 662 pp. U.S. Fish and Wildlife Service (USFWS). 2005c. Bull trout core area conservation status assessment. W. Fredenberg, J. Chan, J. Young, and G. Mayfield. U.S. Fish and Wildlife Service, Portland, Oregon. 399 pp. U.S. Fish and Wildlife Service (USFWS). 2005d. Recovery Plan Outline: Contiguous United States Distinct Population Segment of the Canada lynx. Unpublished. Montana Field Office, Helena, Montana. 21 pp. U.S. Fish and Wildlife Service (USFWS). 2006. Occupied mapped Lynx Habitat Amendment to the Canada Lynx Conservation Agreement. Unpublished. 5 pp. U.S. Fish and Wildlife Service (USFWS). 2008. Bull trout (Salvelinus confluentus) 5-year review: Summary and evaluation. U.S. Fish and Wildlife Service, Portland, Oregon. U.S. Fish and Wildlife Service (USFWS). 2009. Bull trout core area templates - complete core area by core area re-analysis. W. Fredenberg and J. Chan, editors. U. S. Fish and Wildlife Service. Portland, Oregon. 1895 pp. U.S. Fish and Wildlife Service (USFWS). 2010. Endangered and Threatened Wildlife and Plants; Revised Designation of Critical Habitat for Bull Trout in the Coterminous United States; Final Rule. October 18, 2010. 75 FR 63898-64070. U.S. Fish and Wildlife Service (USFWS). 2012. Biological Opinion for the Montana Rail Link Bridge No. 94.1 Rehabilitation Project. Service Reference number 14420-2011-F-0126. U.S. Fish and Wildlife Service, Spokane, Washington. 53 pp.

56 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project U.S. Fish and Wildlife Service (USFWS). 2014. Idaho Habitat Restoration Programmatic Biological Opinion. Service Reference number: 01EIFWoo-2014-F-0456. U.S. Fish and Wildlife, Boise, Idaho. 117 pp. U.S. Fish and Wildlife Service (USFWS). 2015a. Recovery plan for the coterminous United States population of bull trout (Salvelinus confluentus). U.S. Fish and Wildlife Service, Portland, Oregon. xii + 179 pp. U.S. Fish and Wildlife Service (USFWS). 2015b. Coastal recovery unit implementation plan for bull trout (Salvelinus confluentus). U.S. Fish and Wildlife Service, Lacey, Washington, and Portland, Oregon. 155 pp. U.S. Fish and Wildlife Service (USFWS). 2015c. Klamath recovery unit implementation plan for bull trout (Salvelinus confluentus). U.S. Fish and Wildlife Service, Klamath Falls, Oregon. 35 pp. U.S. Fish and Wildlife Service (USFWS). 2015d. Mid-Columbia recovery unit implementation plan for bull trout (Salvelinus confluentus). U.S. Fish and Wildlife Service, Portland, Oregon. 345 pp. U.S. Fish and Wildlife Service (USFWS). 2015e. Columbia headwaters recovery unit implementation plan for bull trout (Salvelinus confluentus). U.S. Fish and Wildlife Service, Kalispell, Montana, and Spokane, Washington. 179 pp. U.S. Fish and Wildlife Service (USFWS). 2015f. Upper Snake recovery unit implementation plan for bull trout (Salvelinus confluentus). U.S. Fish and Wildlife Service, Boise, Idaho. 113 pp. U.S. Fish and Wildlife Service (USFWS). 2015g. St. Mary recovery unit implementation plan for bull trout (Salvelinus confluentus). U.S. Fish and Wildlife Service, Kalispell, Montana. 30 pp. U.S. Fish and Wildlife Service (USFWS). 2015h. Bull Trout 5-Year Review, Short Form Summary. U.S. Fish and Wildlife Service, Boise, Idaho. 7pp. U.S. Fish and Wildlife Service and National Marine Fisheries Service (USFWS and NMFS). 1996. Policy Regarding the Recognition of Distinct Vertebrate Population Segments Under the Endangered Species Act. February 7, 1996. 61 FR 4722-4725. Vidergar, D.T. 2000. Population estimate, food habits and estimate of consumption of selected predatory fishes in Lake Pend Oreille, Idaho. Master of Science Thesis. University of Idaho, Moscow, Idaho. 99 pp. Watson, G. and T. Hillman. 1997. Factors affecting the distribution and abundance of bull trout: an investigation into hierarchical scales. North American Journal of Fisheries Management 17:237-252. Wenger, S.J., D.J. Isaak, J.B. Dunham, K.D. Fausch, C.H. Luce, H.M Neville, B.E. Rieman, M.K. Young, D.E. Nagel, D.L. Horan, and G.L. Chandler. 2011. Role of climate and invasive species in structuring trout distributions in the interior Columbia River basin, USA. Canadian Journal of Fisheries and Aquatic Sciences 68:988-1008. Westerling, A.L., H.G. Hidalgo, D.R. Cayan, and T.W. Swetnam. 2006. Warming and earlier spring increase western U.S. Forest Wildfire Activity. Science 313:940-943.

57 Erin Chipps, Environmental Protections Specialist 01EIFW00-2018-F-0035 Western Federal Lands Highway Division Idaho Panhandle National Forests Roads and Bridges Repair Project Whiteley, A., P. Spruell and F.W. Allendorf. 2003. Population genetics of Boise Basin bull trout (Salvelinus confluentus). Final Report to Bruce Rieman, Rocky Mountain Research Station. University of Montana Wild Trout and Salmon Genetics Lab, Missoula, Montana. Whitesel, T.A., J. Brostrom, T. Cummings, J. Delavergne, W. Fredenberg, H. Schaller, P. Wilson, and G. Zydlewski. 2004. Bull Trout Recovery Planning: A review of the science associated with population structure and size. Science Team Report #2004-01. U.S. Fish and Wildlife Service, Regional Office, Portland, Oregon.

3.2 In Litteris References Idaho Department of Fish and Game (IDFG). 2012. Lake Pend Oreille Bull Trout Population Estimate Summary. Summary provided by Andy Dux. Idaho Department of Fish and Game, Coeur d’Alene, Idaho. Idaho Department of Fish and Game (IDFG). 2015. Lightning Creek Bull Trout Redd Survey Data. Summary provided by Andy Dux. Idaho Department of Fish and Game, Coeur d’Alene, Idaho. Excel Spreadsheet 1p. U.S. Fish and Wildlife Service (USFWS). 2008. Bull trout core area status assessment: Lake Pend Oreille. Unpublished document, August 13, 2008. 19pp.

3.3 Personal Communications Chipps, E. 2018. Email received by Megan Kosterman (U.S. Fish and Wildlife Service) from Erin Chipps (Western Federal Lands Highway Division) on January 24, 2018 regarding implementation of the Idaho Panhandle National Forest Food Storage Order. Dux, A. 2015. Email sent to Scott Deeds (U.S. Fish and Wildlife Service) from Andy Dux (Idaho Department of Fish and Game) on August 13, 2012, reporting Lake Pend Oreille bull trout population estimates. Bouwens, K. Email received by Scott Deeds (U.S. Fish and Wildlife Service) from Kenneth Bouwens (Idaho Department of Fish and Game) on June 6, 2016, providing data on bull trout migration within Granite Creek, Idaho, 2011-2015.

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