(For Informational Purposes Only) Truckee_Biological_Assessment_Amendment_4oct2013.pdf

TRUCKEE MEADOWS FLOOD CONTROL PROJECT

GENERAL REEVALUATION

Amended Biological Assessment of the Recommended Plan

September 3, 2013 Amended October 4, 2013

LOCATION:

Washoe County, Nevada Truckee River

USGS Reno and Vista Quadrangles

Contact Person: Dan Artho Phone Number: 916-557-7723

Introduction

The purpose of this Biological Assessment is to review the U.S. Army Corps of Engineers’ (Corps) proposed Truckee Meadows Flood Control Project Recommended Plan in sufficient detail to determine to what extent the proposed action may affect any of the threatened, endangered, proposed, or candidate species listed below. This Biological Assessment is prepared in accordance with legal requirements set forth under Section 7 of the Endangered Species Act (16 U.S.C. 1536 [c]), and follows the standards established in the U.S. Army Corps of Engineers Procedures for Implementing NEPA (ER 200-2-2) and the Endangered Species Act (ER 1105-2-100).

The species list received on April 8, 2013 (Consultation Tracking Number 08ENVD00-2013-SLI- 0164) identified the species considered in this document and listed below.

Threatened, Endangered, Proposed Threatened or Proposed Endangered Species

Carson wandering skipper (Pseudocopaeodes eunus obscurus) Endangered

Cui-ui (Chasmistes cujus) Endangered

Lahontan cutthroat trout (Oncorhynchus clarki henshawi) (LCT) Threatened

The species list also identified two Candidate species, Webber’s ivesia (Ivesia webberi), and Greater sage grouse (Centrocerius urophasianus). Although consultation is not required for Candidate species, the project is not expected to affect these species because suitable habitat is lacking in the project area.

Critical Habitat

The action addressed within this biological assessment does not fall within designated critical habitat for any of the above listed species.

Consultation to Date

Species lists were requested and received from the U.S. Fish and Wildlife Service’s Nevada Office (USFWS) numerous times since 1998. The latest list was received on April 8, 2013.

On May 22, 2013, the Corps delivered a copy of the draft Environmental Impact Statement (EIS) to the USFWS offices in Reno, along with digital copies of the draft General Reevaluation Report and its technical appendices.

On June 27, 2013, the Corps sent a letter requesting concurrence from the USFWS on their initial determination of may affect, not likely to adversely affect the threatened Lahontan cutthroat trout and endangered cui-ui, and no effect on the Carson wandering skipper.

Supplemental information was provided via e-mail to the USFWS on August 19, 2013.

On August 22, 2013, the USFWS sent a letter (File No. 2013-I-0317) responding to the Corps’ concurrence request, indicating that they cannot concur with the determination of not likely to adversely affect the Endangered Species Act listed species.

Pursuant to the August 22, 2013 letter, the Corps re-examined their evaluations of project-related effects to listed species. A Biological Assessment that documented the re-evaluation and provided a determination of may affect, likely to adversely affect LCT and cui-ui for the proposed action was submitted to USFWS on September 4, 2013 along with a letter requesting formal consultation under Section 7 of the Endangered Species Act.

This amended Biological Assessment provides clarification on construction activities and potential direct and indirect effects of the proposed action in response to comments received from USFWS during subsequent phone conversations and an email dated September 16, 2013.

Description of the Proposed Action

Background

The Truckee Meadows Flood Control Project was authorized under the Water Resources Development Act of 1988, Pub. L. No. 100-676, § 3(a)(10), 102 Stat. 4012. However, the project was deferred during the preconstruction engineering and design (PED) phase when changes in real estate costs made the project economically infeasible. In 1996, the local communities requested that flooding problems in Truckee Meadows be reevaluated. The reevaluation study assessed the feasibility of modifying the congressionally authorized project to reduce the risk of flood damages in the Truckee Meadows project area while avoiding or minimizing adverse effects.

Using the Federal water resources planning process, the Corps identified a National Economic Development Plan (NED Plan) that reasonably maximizes net economic benefits consistent with protecting the Nation’s environment. Based on the reevaluation, the NED Plan is Alternative 3- Floodplain Terrace Plan. In addition, basic recreation features were formulated based on opportunities provided by the NED Plan. The NED Plan combined with basic recreation features was the Tentatively Selected Plan discussed in the draft EIS. This plan is now the Recommended Plan that will be forwarded to Congress for possible authorization. The Corps is the Federal lead agency, and the Truckee River Flood Management Authority (TRFMA) is the local sponsor for the project.

Recommended Plan (Alternative 3-Floodplain Terrace Plan) Design Features

The Recommended Plan is located in the Truckee Meadows area of Washoe County, Nevada, along approximately 6 miles of the Truckee River and adjacent floodplains, between Highway 395 downstream to the eastern end of the Sparks industrial area (Plate 1).

The Recommended Plan proposes to:

Construct 9,650 linear feet of on-bank (6,500 feet) and in-channel (3,150 feet) floodwalls, and 31,000 linear feet of levees along the north and south banks of the Truckee River. This work would also include a gravel levee maintenance road/recreational trail.

Excavate 1.7 miles of new floodplain terraces along the south bank of the Truckee River from Greg Street to East McCarran Boulevard.

Place 3,100 feet of North Truckee Drain in twin 11.5-foot by 10-foot concrete box culverts south of I-80, including a 200-foot extension to the Peoples’ Drain.

Cap two junction structures of the Peoples’ Drain.

Remediate under-seepage with seepage berms, drainage blankets, impervious berms, and relief wells.

Manage interior drainage with a 14-cubic foot per second (cfs) pumping station upstream of Glendale Boulevard and new flap or vertical sluice gates at all existing storm drains.

Construct 1,700 linear feet of bioengineered bank scour protection and 10,000 linear feet of rock riprap bank scour protection.

Install bridge abutment and pier scour protection at Greg Street, Rock Boulevard, and East McCarran Boulevard bridges.

Revegetate 60 acres along 1.7 miles of new floodplain terraces with riparian vegetation on the south bank of the Truckee River from Greg Street to East McCarran Boulevard.

Relocate approximately 14,100 feet of existing recreational trails along segments of the current trail alignment.

Construct four canoe/kayak launch points at Fisherman’s Park, Glendale Park, Cottonwood Park, and the trail access at the end of Sparks Boulevard.

Install 50 new picnic tables on the north and south sides of the river, including 36 tables within the recreation focus area of the proposed plan between Rock Boulevard and McCarran Boulevard.

Construct 13 fishing access locations on the north and south sides of the river, from Highway 395 to Cottonwood Park.

Construct 18,600 linear feet of new paved (9,700 feet) and unpaved (8,900 feet) recreation trail.

Construct a community park at the current location of the Excel Building on Mill Street.

The park would include a parking lot, playground, public restroom, medium-sized picnic shelter, and access to new recreation trails.

Install a small-sized picnic shelter at the current Sagewinds property.

A map of the project features is included as Plate 2.

If authorized, the project would proceed to the PED phase of design before initiation of construction. Construction would begin in 2015 at the earliest, and continue for 5 years, with an additional 3 years of vegetation establishment and monitoring to ensure success of plantings.

Staging

The contractor’s staging areas would be located at existing open agricultural areas south of the Truckee River and open areas along the bikeway north of the Truckee River, near existing bridges. The staging areas would likely be no more than 0.5 acre in size at any one location.

The staging areas would have temporary fencing placed around the perimeters and around any sensitive vegetation within their confines.

Temporary work area easements would be required to allow for the movement of construction equipment to and within the construction site. In general, these temporary easements would be 15 feet in width and extend from the landside and/or waterside edge of the permanent easements. In-channel floodwalls would require temporary work area easements on both the waterside and landside. A 15-foot temporary easement would be located within the channel on the waterside of the floodwall.

The Corps will require Best Management Practices (BMPs) at any stockpile site (e.g., stockpile protection, silt fencing). The Corps will require the construction contractor to avoid native plant species (including cottonwood trees and willows) where possible. However, some disturbance to and loss of existing riparian trees and other vegetation is anticipated within staging areas.

In-channel Construction Methods

All in-channel construction would take place during low flow and after peak fish migration activities in the river. In-channel construction will be carried out in the dry. The bank and bed excavation within the river encroachment area will be accomplished with a tracked hydraulic excavator and medium loader dump trucks. Heavy equipment access to the river will be limited as much as possible. Native stream bed material would be placed on top of the material used to fill the excavations to a depth of 12 to 24 inches. The contractor will be required to clean all imported rock and gravel, if needed, to be used in the river prior to placement such that it is free of particulate matter.

In-Channel Construction Season. All in-channel construction activities will take place between July 1 and September 30 of Construction Years 1, 2, and 3. This would include construction of in-channel floodwalls (approximately 3,150 linear feet), scour protection along levees and floodwalls not set back from the river channel (approximately 7,800 linear feet), and bridge pier and abutment scour protection along Greg Street, Rock Boulevard, and East McCarran Boulevard bridges.

River Diversion. To initiate in-channel construction, the Truckee River will be temporarily diverted to enable work in a dry river bed. River flows will either be diverted to a temporary bypass channel, through a pipe of sufficient size, or along one side of the existing channel using a diversion structure such as K-rails supplemented with impervious liners and sandbags. The upstream barrier/coffer dam (e.g., K-rails and sandbags) will be located approximately 300 feet upstream of the features to be constructed during that season. The downstream barrier/coffer dam will be located approximately 300 feet downstream of the in-channel features to be constructed for that season. In addition, screened subsurface pumps will be used to keep construction areas dewatered during this period by removing water that infiltrates below the coffer dams. Locations for inlets and outlets of bypass channels, if used, will be selected to have the least impact on riparian vegetation.

Up to 3 separate diversions may be established per construction year, starting from downstream to upstream. The longest area of diversion is not expected to exceed 3,500 feet.

Dewatering/Rewatering activities. All initial activities associated with de-watering will be coordinated in advance between the Corps, its Contractor, USFWS, and NDOW to facilitate fish salvage. Installation of the upstream hydraulic barrier is to take place gradually to allow fish escapement from the affected area. Water levels will then gradually recede to minimize fish stranding, with a target rate of 3 inches per hour.

The Corps will re-water the project area after the periods of in-channel construction for each Construction Year in such a way as to minimize sediment mobilization. Hydraulic barriers will be removed in a systematic fashion, starting from the downstream portion of the work area. All construction debris will be removed prior to rewatering. River flows will be gradually returned to minimize sediment mobilization.

Fish Salvage. The capture and relocation of fish from within dewatered areas will be conducted by the Corps in coordination with NDOW and USFWS. Capture methods may include the use of electrofishing equipment and dip nets. Fish salvage operations will be timed to occur during the coolest part of the day, and fish will be returned to the river downstream of the project area with minimal handling. Fish salvage will target all species and life stages that can be safely captured and handled; in most cases, this will include fingerling- and adult-sized fish.

In-channel Floodwall Construction Activities. For in-channel floodwall designs, the larger footing/heel is located on the landside of the flood wall. The floodwalls would be constructed of reinforced concrete with a patterned architectural finish. Excavation would be 4 to 4.5 feet below the existing grade and backfilled with compacted native soil. Footings would be founded 3 to

3.5 feet below the final grade. The toe of the footings would be located at least 4 feet from the top of channel bank.

As indicated in Figure 1, scour protection for in-channel floodwalls consists of standard riprap protection with a vertical placement extending from 2 feet above the top of footing to the computed total scour depth. In-channel floodwall protection riprap will be placed primarily under the channel bottom, with the riprap slope to be 1.5 horizontal to 1 vertical in order to minimize construction limits and riprap extent. Native stream bed material would be placed on top of the material used to fill the excavations to a depth of 12 to 24 inches. The contractor will be required to clean all imported rock and gravel, if needed, to be used in the river prior to placement such that it is free of particulate matter.

Figure 1. In-channel Floodwall Scour Protection Typical Drawing.

Riprap Revetment Scour Protection Activities. For on-bank levees adjacent to the river bank, placement of riprap will be extended from the top of levees to the maximum scour depth. On-bank floodwalls adjacent to the river bank would have riprap extended from 2 feet above the top of the floodwall footing to the maximum scour depth.

Bioengineered Scour Protection Activities. For locations that have levees and floodwalls sufficiently set back from the river bank but that demonstrate sufficient long-term scour potential along the river bank, bioengineered scour protection features would be installed to maintain the integrity of the levee or floodwall. Stream bank soil bioengineering would be used to stabilize the channel boundary and improve riparian function wherever feasible in the study area. A combination of native vegetation cuttings, sprouted seedlings, and fibrous material made from coconut fibers (coir) would be used. A typical cross-section of a bioengineered scour protection area is shown in Figure 2.

Figure 2. Bioengineered Scour Protection Typical Cross-section.

To protect the bank toe from scour, riprap planted with live willow stakes would be used. The riprap would be installed from two feet above the average low water line down to the minimum scour elevation. Three live willow stakes will be planted for every lineal foot of riprap revetment to improve site aesthetics and habitat conditions. Vegetated coir matting will extend from the top of the riprap to two feet above the design high water elevation. The mats can be vegetated prior to installation or hydro-seeded after installation.

Bridge Pier and Abutment Scour Protection Activities. Pier riprap would be placed to at least the contraction scour depth. The top of riprap around piers would be flush with the channel bottom. The depth of rock for sloping abutments extends to the maximum scour depth. Typical cross-sections for bridge abutment and pier scour protection are shown in Figure 3.

Figure 3. Bridge Pier and Abutment Scour Protection Typical Cross-sections.

Avoidance Measures

In order to avoid or minimize project effects on LCT, the following measures would be implemented by the Corps, its local partner, and/or the construction contractor:

1. All soils would be stabilized within 14 days of completed work. Hydromulch would be secured with an organic tackifier that is safe for use in aquatic environments.

2. Construction equipment would be limited to the actual area being disturbed, and vehicles would not travel in areas to be left in their natural state.

3. Short-term staging of soil material would be surrounded by a silt fence, fiber rolls, or other perimeter.

4. Long-term staging of soil material (longer than 1 week) would be placed away from the stream, vegetated, and surrounded by a berm perimeter to control runoff and erosion.

5. Existing vegetation would be left in place to the maximum extent possible.

6. Bare ground would be watered to reduce erosion from wind and stormwater runoff.

7. The contractor would be required to conduct water quality tests specifically for increases in turbidity and sedimentation caused by construction activities. Water samples for determining background levels would be collected in the Truckee River and its tributaries within the general vicinity of the construction sites. Testing to establish background levels would be performed at least once a day when construction activity is in progress. The contractor would monitor turbidity and settleable solids at least daily and turbidity at least hourly when a turbidity plume is visible. If turbidity limits are exceeded, the contractor would slow the rate of earthwork or use other means to comply with the requirements, including stopping construction activities until the plume has cleared.

8. Sediment barriers would be installed on graded or other disturbed slopes, as needed, to prevent sediment from leaving the project sites and entering nearby surface waters.

9. The contractor would have a designated area for vehicle and equipment maintenance that is self-contained to protect groundwater, surface water, and soils from contamination.

10. Dewatering water would be discharged into a meadow a sufficient distance from the stream to ensure no direct discharge back to the stream.

11. Suitable stream crossings would be constructed and/or existing and appropriate access would be used to avoid damage to the streambanks and bed.

12. Banks would be revegetated at the end of each construction season. Hydromulch would be secured with an organic tackifier that is safe for use in aquatic environments.

13. Construction traffic would be restricted to predetermined routes.

14. Construction activities immediately in and adjacent to the river channel would be done during low flows (i.e., between July 1 and September 30) while maintaining downstream water flow. De-watering associated with construction would not occur during the spring season to avoid migration periods of native fish (especially Federally listed fish species).

Personnel and equipment would be on-hand to conduct fish rescues, if needed, placing fish outside areas of construction. Fish salvage operations would be coordinated with the USFWS and Nevada Division of Wildlife at least 24 hours prior to implementation.

15. Equipment would be operated slowly and deliberately to minimize potential injury and mortality of juvenile and adult fish during excavation and placement of fill materials within the active channel. The contractor would be instructed to operate an excavator bucket or equipment to “tap” the surface of the water before submerging an excavator bucket or placing fill gravel below the water surface.

16. Dewatering the existing channel would be conducted slowly and deliberately to prevent the mortality of juvenile or adult LCT.

17. Excavation within the stream channel would be limited to the extent possible. If all the excavated materials are not relocated to another portion of the project area, it would be completely removed from the floodplain so it does not reenter the river during the next high flow event. These materials would be located on previously disturbed upland areas to the extent possible.

18. Erosion control and maintenance measures would be implemented on a site-specific basis.

Pertinent materials would be certified weed-free.

19. Excess spoil materials would be properly stored. Measures would be implemented to ensure that spoil material does not enter the Truckee River, Steamboat Creek, or adjacent wetlands.

20. A spill prevention and containment countermeasure plan that addresses all potential mechanisms of contamination would be developed. Suitable containment materials would be on-hand in the event of a spill. All discarded material and any accidental spills would be removed and disposed of at approved sites.

21. Instream time and the number of stream crossings for heavy equipment would be minimized to the extent possible. Stream crossings would be perpendicular to the stream and in designated areas using gently sloping and stable banks.

22. Equipment and vehicles operated within the floodway would be checked and maintained daily to prevent leaks of fuels, lubricants, and other fluids to the river.

23. Temporary roads would be constructed to the minimal number, width, and total length consistent with construction activities. Roads would be minimized in sensitive areas (e.g., riparian). Water bars and other erosion controls would be installed for permanent roads or trails.

24. Coordination efforts with the USFWS, Nevada Division of Wildlife, and Pyramid Lake Paiute Tribe would continue throughout the PED phase with emphasis on features directly affecting fish and wildlife resources.

25. Measures for monitoring and associated adaptive management would be implemented to verify the performance of revegetation, construction best management practices (BMP’s), and other conservation features. Lessons learned from the earlier phases of construction would be applied to later phases.

26. Fish entrainment would be avoided by implementation of typical dendritic drainage patterns within the floodplain terraces, allowing fish to leave as waters recede.

27. The Corps would use biotechnical bank stabilization methods to the extent possible in areas adjacent to the Truckee River and Steamboat Creek.

28. Invasive perennials such as whitetop species would be treated with herbicide prior to any revegetation efforts. For revegetation areas adjacent to the river and wetlands, perennial invasive species would be hand-pulled. Re-growth would be treated with weed herbicide using a wick applicator.

29. Equipment would be cleaned of all seeds and vegetative material before entering and leaving the construction area to prevent the spread of invasive plants.

30. Equipment would be cleaned and inspected before entering and leaving the construction area to prevent the spread of New Zealand mud snails.

In order to avoid or minimize short-term effects to water temperature resulting from temporary loss of riparian shading, the following measures would be implemented:

1. Project construction would be phased over a 5-year period to allow for transitional effects to the overall project area so that only a portion of the riparian shading would be lost per year.

During each successive year, riparian plantings would mature over the course of project construction.

2. Planting some mature trees in critical areas would be considered to provide short-term benefits while younger riparian vegetation matures.

3. Water temperatures would be monitored during the first year of construction, and short-term avoidance and minimization efforts would be adapted for successive years based on changes measured.

Restoration

All disturbed area caused by the installation of in-channel floodwalls and scour protection features will be revegetated to the extent possible within the requirements of the Corps’ levee/floodwall vegetation guidance. The majority of the plantings will consist of Fremont cottonwood (Populus fremontii). Other species expected to be included in the revegetation plan would be Western choke cherry (Prunus virginiana), Pacific willow (Salix lasiandra), Scouler’s willow (Salix sconleriana), buffalo berry (Sheperdia rotundifolia), golden currant (Ribes aurem), and a broadcast riparian seed mix. Additional specifications on revegetation would be coordinated with NDOW and USFWS.

In addition, as part of the environmentally sustainable design approach to flood risk management, the floodplain terraces to be excavated would be replanted with 12.4 acres of native riparian forest habitat and 49.9 acres of native willow/mixed willow scrub habitat. This replanting, in conjunction with implementation of bioengineered scour protection measures, where feasible, would establish up to 9,000 linear feet of shaded riparian aquatic habitat along the river.

Operation and Maintenance Actions

For the Truckee Meadows reach, operation and maintenance is required for floodwalls, levees, interior drainages, relief wells, seepage remediation and bank protection. The requirements include inspecting and maintaining the floodwalls and interior drainage features regularly and inspecting and maintaining levees and keeping them free from vegetation growth that could reduce reliability. Inspections and maintenance activities near the Reno-Tahoe International

Airport must be coordinated in advance. The bank protection would be inspected annually prior to flood season and maintained in accordance with the operation and maintenance agreement with TRFMA.

Access for O&M activities would be provided by a 10-foot-wide maintenance road located on the levee crest or landside of floodwalls. See the Engineering Appendix to the GRR for more information. During floods, the levees and floodwalls would be patrolled continuously to locate possible boils or unusual wetness that signals a problem in the structure.

Environmental Baseline

Action Area

The Action Area for the Recommended Plan is defined as the terrestrial footprint of the flood risk management features construction area as well as the aquatic habitat in the Truckee River from the farthest upstream portion of levee and floodwall alignments along the river down to Pyramid Lake. The Action Area also includes the terrestrial footprint of the flood risk management features construction area along the North Truckee Drain as well as the aquatic habitat in the drainage canal from Interstate 80 downstream to its confluence with the Truckee River. The listed species are not found in the North Truckee Drain; only in the Truckee River and Pyramid Lake. However, construction activities along the drain could temporarily increase sediment load into the drain and the river.

Status of the Species in the Action Area and Species Accounts

Based on the lists of threatened and endangered species that may occur in the project area, field visits, literature searches, and availability of habitat, the Corps has determined that the Federally listed species with the potential to be directly or indirectly affected by the Recommended Plan are the threatened LCT and endangered cui-ui. The Corps has also determined there would be No Effect on the endangered Carson wandering skipper.

Carson Wandering Skipper

The habitat of the Carson wandering skipper butterfly is characterized as grassland habitats on alkaline substrates. These habitats are typified by the presence of saltgrass (Distichlis spicata) meadows in proximity to nectar sources in open areas near springs or water. The range of the Carson wandering skipper is restricted to four extant populations occurring within a small geographic range extending from south of Carson City, Nevada, through Washoe County, to southeastern Lassen County, California. No critical habitat has been designated for the Carson wandering skipper. There are locations in the project area where salt grass is a dominant component of the plant community. However, these locations are unlikely to provide the appropriate habitat needs for the Carson wandering skipper due to their small aerial extent, fragmentation, previous disturbances from agricultural practices, invasions of white top (Lepidium latifolium), and Russian thistle (Salsola kali), and lack of alkaline soils. As a result, the project will have No Effect on the Carson wandering skipper.

Lahontan Cutthroat Trout

Status. LCT was listed by the USFWS in 1970 (35 FR 16047) as endangered. Subsequently, LCT was reclassified as threatened in 1975 in order to facilitate management and allow State regulated angling (40 FR 29863). In 1995, the USFWS released its recovery plan for LCT, encompassing six river basins within the historic range of this subspecies (USFWS, 1995).

Critical habitat has not been designated for LCT.

Classification. LCT is an inland subspecies (one of 14 recognized subspecies of cutthroat trout in the western U.S.) endemic to the Lahontan basin of northern Nevada, eastern California, and southern Oregon. LCT historically occurred in most cold waters of the Lake Lahontan basin, including: (1) large alkaline terminal lakes (e.g., Pyramid Lake and Walker Lake); ( 2) oligotrophic alpine lakes (e.g., Lake Tahoe and Independence Lake), slow meandering low-gradient rivers (e.g., Humboldt River), moderate gradient montane rivers (e.g., Truckee, Carson, and Walker Rivers), and small headwater tributary streams (e.g., Donner and Prosser Creeks)

(USFWS, 2003).

The USFWS recognizes three geographic management units (GMU) of LCT based on morphological, meristic, allozyme, and mitochondrial genetic differences. These include: (1) Western Lahontan basin composed of the Truckee, Carson, and Walker River basins; (2) Northwestern Lahontan basin composed of the Quinn River, Black Rock Desert, and Coyote Lake basins; and (3) Humboldt River basin (USFWS, 1995). These GMU designations have been confirmed most recently with data from microsatellite markers, and more extensive and systematic sampling of extant LCT populations (Peacock and Kirchoff, 2007). The proposed project area is within the Truckee River basin; therefore, this evaluation is specific to the Truckee River basin portion of the Western Lahontan basin GMU.

Distribution. In the Truckee River basin, LCT historically occupied about 360 miles of suitable stream (fluvial) habitat and 284,000 acres of lake (lacustrine) habitat (Gerstung, 1986a). Lake Tahoe is the source for the Truckee River, which flows into Pyramid Lake. Pyramid Lake is a remnant of pluvial Lake Lahontan which, as a terminal lake, supports a highly alkaline and nitrogen-limited ecosystem. Native LCT populations in Pyramid Lake migrated more than 100 miles up the Truckee River through Lake Tahoe to headwaters in its tributaries to spawn (LaRivers, 1962). The Truckee River drainages historically provided spawning habitat and undoubtedly formed networked ecosystems that supported all life stages prior to water diversions and introduction of non-native fishes in the 20th century (Western Native Trout Initiative, 2007). However, by 1939, the native Lake Tahoe LCT population was extirpated as a result of damage to spawning tributaries. By 1944, the original Pyramid Lake LCT population was extirpated after losing access to its Truckee River spawning grounds due to Derby diversion dam and other factors (e.g., pollution, commercial harvest, and exotic fish introductions (Gerstung, 1988).

Today, there are no extant fluvial LCT populations native to the Truckee River watershed (Peacock and Kirchoff, 2007). Native fluvial LCT populations have been displaced by competition and predation from introduced brown and brook trout, and from hybridization with rainbow trout stocked for recreational fishing (Western Native Trout Initiative, 2007).

Independence Lake (outside the project area) supports the only extant native lacustrine LCT population, but it does not show a strong phylogenetic relationship with Truckee River basin historical samples or any other western basin population (Peacock and Kirchoff, 2007).

Out-of-basin fish believed to have originated from the Truckee River basin have been planted throughout the Truckee River watershed by CDFG, NDOW, USFWS, and the PLPT under experimental conditions for recovery (USFWS, 1995) and as part of the recreational fishery in Nevada (Western Native Trout Initiative, 2007). It is estimated that less than 0.3 percent (%) of lake habitat and about 2.2% of stream habitat in the Truckee River basin are currently occupied by self-sustaining LCT. This habitat includes 7 small headwater tributaries with a total of 8 miles that support self-sustaining river populations (Interior & State, 2008). These populations are found in Independence Creek, Pole Creek, Upper Truckee River, Bronco Creek, Hill Creek, and West Fork Gray Creek. The lake populations are found in Pyramid and Independence Lakes.

Only Independence Lake has a naturally reproducing population.

Currently, spawning opportunities and permanent rearing habitat for LCT in the lower Truckee River do not exist due to seasonally high water temperatures, unsuitable spawning habitat, high sediment loads, and diversion of water before LCT eggs can hatch and fish migrate back to the lake. Cooperative efforts are ongoing to enhance the lower Truckee River system and improve riparian and riverine habitat. This includes the implementation of a more natural flow regime in support of riparian forests and active restoration in various segments of the river.

Life History. Like most cutthroat trout species, LCT is an obligatory stream spawner, which means that LCT predominantly use tributary streams as spawning sites. Spawning typically occurs from April through July throughout the range of LCT, depending on stream elevation, stream discharge, and water temperature (USFWS, 1995). Fish may exhibit three different strategies depending upon conditions, outmigration as fry, as juveniles, or remaining in the river as residents (Neville-Arsenault, 2003). According to Snyder, dependent upon river flow, trout were rather common throughout the entire course of the Truckee River before the river suffered from anthropogenic effects (Snyder, 1917). Seasonal increases in river flow stimulated mass movement of large trout from lakes; as river flows decreased, large trout were less abundant in various reaches of the river. It is likely that a certain proportion of the hatched lacustrine form of LCT stayed in the tributaries and became acclimated to the local habitats and exhibited life history characteristics more typical of fluvial species (USFWS, 2003).

Habitat. Specific habitat requirements of LCT vary seasonally and with life stage. Generally, fluvial LCT inhabit small streams characterized by cool water, pools in close proximity to cover and velocity breaks, well vegetated and stable stream banks, and relatively silt-free, rocky substrate in riffle-run areas (USFWS, 1995). Fluvial populations of cutthroat trout including LCT appear to be intolerant of competition or predation by non-native salmonids, and rarely coexist with them (Dunham, Rahn, Schroeter, and Breck, 2000; USFWS, 1995).

In contrast, lacustrine LCT have adapted to a wide variety of lake habitats that range from small alpine lakes to large desert waters. Unlike most freshwater fish species, some LCT tolerate alkalinity and total dissolved solid levels as high as 3,000 mg/L and 10,000 mg/L, respectively (Koch et al., 1979). LCT are noted for their ability to live in streams where water temperatures during the summer may exceed 27 °C for short periods and fluctuate as much as 14 to 20 °C daily (Dunham et al., 1999; USFWS, 1995). Although LCT can survive prolonged exposure to temperatures of nearly 25 °C, growth ceases when temperatures exceed 22 to 23 °C (Dickerson and Vinyard, 1999). LCT in the lower Truckee River are likely to avoid this reach as temperatures increase and flows decrease during summer and early fall (July to October).

Management. The recovery plan issued in 1995 by the USFWS identified five conditions contributing to the decline and affecting the potential recovery in the Truckee River basin: (1) reduction and alteration of streamflow and discharge; (2) alteration of stream channels and morphology; (3) degradation of water quality; (4) reduction of Pyramid Lake elevation; and (5) introduction of non-native fish species. Several actions were recommended including: (1) developing an ecosystem plan for the Truckee River basin to determine long-rang options relating to water and other uses in the basin; (2) evaluating lacustrine population viability; and

(3) evaluating possible remnant “Pyramid Lake strain” LCT in other waters for transplanting.

According to the recovery plan’s objectives, LCT may be considered for delisting when management is implemented to sustain identified numbers of self-sustaining viable populations.

Habitat should be secured to ensure the benefits of management to allow LCT a 95% chance of persisting for 100 years or more. Viable populations are considered to be ones that have been established for five or more years and have three or more age classes of self-sustaining LCT as determined through monitoring. The Truckee river basin targets this objective for existing populations in seven fluvial and two lacustrine systems. In addition, LCT reintroduction should be conducted to establish a minimum of six additional populations. (USFWS, 1995)

In 2003, the Truckee River Recovery Implementation Team1 developed a short-term action plan for LCT in the Truckee River basin which focuses on gathering information about habitat requirements and implementing demonstration projects and research (Interior & State, 2008).

The action plan identifies tasks intended to eliminate or minimize threats that affect LCT in the Truckee River and through continued implementation of this process, ensure the long-term persistence of the species. Major issues include: (1) reduction and alteration of stream flow and discharge; (2) alteration of stream channels and morphology; (3) degradation of water quality;

(4) reduction of Pyramid Lake elevation and concentration of chemical components; and (5) introductions of non-native fish species.

A large component of species management in the Truckee River involves hatchery supplementation. In Nevada, LCT are stocked in the Truckee River by the USFWS and NDOW, in cooperation with the Pyramid Lake Paiute Tribe (PLPT). Since the extirpation of the original Pyramid Lake strain of LCT, the Pyramid Lake fishery has been maintained by a hatchery stocking program currently operated by the PLPT Fishery Program and the USFWS. In Pyramid Lake, the contemporary LCT strain, derived from four strains (Heenan, Walker, Summit and Independence Lakes) (Coleman and Johnson, 1988), has been maintained by hatcheries operated by the PLPT. This strain has developed into a sport fishery in Pyramid Lake that is an important source of revenue for the PLPT. These fish are imprinted to the hatchery rather than to the Truckee River, which means spawning fish are more likely to return to an artificial spawning channel created at Sutcliffe, Nevada (on the west side of Pyramid Lake), than to migrate up the river. The population does not naturally reproduce but rather depends on hatchery propagation for maintenance. These fish have also been used as the source for NDOW’s hatchery, which also stocks LCT in various locations on the Truckee River with increased frequency over the years (NDOW 2001, 2002, 2003, 2004, 2005). This has been done concurrent with the State’s de-emphasis on stocking of and use of sterile (triploid) rainbow trout in a continued attempt to reduce the hybridization risks between LCT and rainbow trout.

Recent genetic work using microsatellite DNA analysis suggests transplanted LCT populations found in Bettridge and Morrison Creeks in the Pilot Peak mountains along the Utah-Nevada border originated from the Truckee River basin, deemed the “Pilot Peak” strain (Peacock and Kirchoff, 2007). This strain has become the focus of production at the USFWS’s Lahontan National Fish Hatchery, which raises and stocks these fish in the Truckee River and other locations. The bulk of the trout stocked in 2005 were LCT, of which 34,333 were Pyramid strain raised at the Mason Valley Hatchery, and 48,046 were Pilot Peak strain raised at the Lahontan National Fish Hatchery. In addition, over 2,000 large LCT (>18 inches) from Pyramid Lake were also stocked as part of the mark-recapture tagging and telemetry studies (Table 1). These LCT were found in the river up to 49 days after stocking. Although not originally planned for stocking into the Truckee in 2005, the Pilot Peak strain LCT that were stocked became available after disease testing from the California/Nevada Fish Health Lab returned results indicating some fish

Composed of representatives from USFWS, USGS Biological Resources Division, U.S. Forest Service, BIA, USBOR, CDFG, PLPT, Trout Unlimited, Otis Bay Consultants, and UNR.

tested positive for bacterial kidney disease (Renibacterium salmoninarum). As a result, the State of California denied their importation so the Lahontan National Fish Hatchery consulted with NDOW to stock the fish into the Truckee in Nevada. After consultation with the PLPT, their release was approved. Sixty-four percent of the Pilot Peak LCT were stocked below the East McCarran Bridge (the lower Truckee) to take advantage of the low fish densities and reduced competition with other salmonids.

Table 1. Stocking Summary for LCT Planted in the Truckee River between 1999 and

2005.

Year Number Average Size (in) Number of Adult

LCT1

1999 86,388 6.1 -

2000 52,927 9.0 -

2001 42,700 1.0 -

2002 0 - -

2003 3,047 14.3 1,906

2004 53,846 11.3 1,999

2005 84,379 10.9 2,000 Represents adult LCT collected at Marble Bluff Fish Passage Facility and the Pyramid Lake spawning channel at Sutcliff, NV and planted in the Truckee River (Reno area) as part of radio telemetry studies conducted by NDOW. Source (NDOW 2001, 2002, 2003, 2004, 2005)

Cui-ui

Status. The cui-ui lake sucker (Chasmistes cujus) was listed as a Federally endangered species March 11, 1967 (32 FR 4001). In 1992, the USFWS released its updated recovery plan for cui-ui. The second revision of the cui-ui recovery plan provided a quantifiable recovery objective (based upon probabilistic analysis of simulated cui-ui response to various hydrologic conditions) with site-specific tasks which, if implemented, are expected to achieve recovery (i.e., eventual delisting) of cui-ui (USFWS, 1992). Critical habitat has not been designated for this species.

Classification. The cui-ui is one of four lake sucker species of the genus Chasmistes. The four recognized species are residents of three distinct drainages: cui-ui in the Truckee River basin of western Nevada; shortnose sucker (C. brevirostris) in the Klamath River basin of Oregon and California; June sucker (C. liorus) in Utah Lake; and the now extinct Snake River sucker (C.

muriei) of the upper Snake River in Wyoming (Miller and Smith, 1981). Lake suckers are differentiated from other members of the family Castostomidae by thin lips, the lobes of which are separated and may contain papillae, and by a large terminal, oblique mouth.

Distribution. Cui-ui occupied ancient Lake Lahontan, which covered much of northwest and west-central Nevada during the Pleistocene and more recently until 5,000 to 10,000 years ago.

Climate change lowered the level of Lake Lahontan until only fragmented, remnant waters remained (Pyramid, Winnemucca, Walker, and Honey Lakes). By the beginning of the 20th century, cui-ui were abundant in Pyramid Lake and the adjacent Winnemucca Lake. Cui-ui may have spawned in the lower 40+ miles of the Truckee River. As water diversions from the Truckee River were developed (i.e. Newlands Project), Truckee River inflow to Pyramid Lake diminished substantially. During the 1930’s, the elevation of Pyramid Lake dropped rapidly and a large delta formed at the mouth of the Truckee River, making it frequently impassable to the stream-spawning cui-ui. Winnemucca Lake dried up at this time as well. During many years, the entire Truckee River was diverted during critical spawning migrations of cui-ui and during summer months.

Cui-ui are currently restricted to Pyramid Lake and the lower Truckee River (downstream from Derby Dam). Adults use the lower 12 miles of the Truckee River only during the spawning season and only in years in which there is sufficient attraction flow for them to pass above or around the delta at the mouth of the Truckee River (Scoppettone, Wedemeyer, and Coleman, 1986). Most spawners use the 10-mile reach between Marble Bluff and Numana dams. Fish passage improvements were completed by USBOR at Derby Dam in 2003; however, the fish ladder has not been operated successfully since its completion.

Life History. Cui-ui are obligate stream spawners that spawn in the lower Truckee River, but spend most of their life in Pyramid Lake (Scoppettone, Wedemeyer, and Coleman, 1986). They are long-lived species (45 years or more), able to take advantage of the occasional high water years to reproduce (Scoppettone, Rissler, and Butler, 2000). Spawning runs generally begin in April or May, depending on timing of runoff, river access, water turbidity, and water temperature.

Currently, cui-ui passage above Marble Bluff Dam is facilitated through a lock system that provides passage over the dam. Entrance to the Truckee River (and the Marble Bluff fish facility) from Pyramid Lake is problematic when lake levels drop below elevation 3,812 feet and a delta is exposed. After successful passage, most spawning activity in the river is restricted between Marble Bluff Dam and Numana Dam. Depending on the passage avenue, some also spawn in the Pyramid Lake Fishway or in the Truckee River downstream from Marble Bluff Dam. While most spawners spend only a few days in the river, some may remain up to 16 days. Spawning runs may continue for 4 to 8 weeks, but most fish migrate during a 1- to 2-week period (Coleman, 1986).

Cui-ui predominantly spawn at night, depositing eggs in gravel dominated substrate, at depths of 0.3-1.5 feet with velocities between 0.75 to 2.85 feet/second (Scoppettone, Wedemeyer, Coleman, and Burge, 1983). Fertilized eggs hatch in 1 to 2 weeks, depending upon water temperature, after which yolk-sac larvae remain in the gravel 5 to 10 days prior to emergence (Scoppettone, Wedemeyer, Coleman, and Burge, 1983). The optimum range for larvae is 14.4 to 17.2 °C; survival of newly fertilized eggs decreases markedly in water above 17.2 °C. After the eggs hatch, yolk-sac larvae remain in the gravel 5 to 10 days prior to emergence (Scoppettone, Wedemeyer, Coleman, and Burge, 1983). After emergence, some fry may enter river backwaters and remain there for several weeks; however, a majority is carried by river currents into Pyramid Lake where fry occupy shallow littoral zones.

Management. The management objective of the USFWS, which has the lead responsibility for cui-ui management, is to enhance prospects for cui-ui survival by providing as many opportunities for cui-ui to reproduce as available water resources will allow. To do so, Truckee River discharge into Pyramid Lake must be sufficient to: (1) attract and initiate the spawning run;

(2) maintain spawning, incubation, and rearing habitat in the river; and (3) provide for outmigration of adults and larvae (Buchanan, 1987). In general, the greater the spring discharge (and turbidity), the greater the numbers of cui-ui that enter the river and the higher the survival rate of their larvae (Buchanan and Strekal, 1988).

Recovery efforts for the cui-ui began in 1973 by the USFWS and the PLPT to restore the food and sport fishery. The Marble Bluff Fish Facility, managed by USFWS, was completed to allow migrating cui-ui to bypass the delta (fishway) and Marble Bluff Dam (fish lock). Hatchery propagation also began in 1976 to prevent extinction of the species. The Dave Koch Fish Hatchery is operated and maintained by the PLPT and has produced millions of cui-ui larvae yearly since its inception. The larvae have been released into the lake and Lower Truckee River.

The regulation of water flows in combination with restrictions on the harvest of cui-ui, hatchery programs, and subsequent wet water years, has led to increasing cui-ui numbers (Rood et al., 2003). Fish passage over the Truckee River delta has also improved recently because of rising Pyramid Lake elevations (Interior & State, 2008).

Cui-ui reproduced successfully in 14 of 20 years from 1980 to 1999, a substantial improvement from 1950 to 1979, when cui-ui produced large year classes in only two years (1950 and 1969).

Spawning runs in the 1980s ranged from 5,000 to 36,300 fish and averaged 12,470 fish annually. Cui-ui passage during spawning runs in the mid-to-late 1990s is shown in Table 2.

Record spawning runs were documented between 1996 and 1999, with 585,000 adults in 1999.

In 2000, cui-ui numbers dropped to 183,000 spawners. In 1997 and 1998, the USFWS assisted the USGS’s Biological Resources Division with a semi-quantitative study to estimate larval cui-ui production upstream of Numana Dam. An estimated 236 million larvae were produced upstream from Numana Dam in 1997, compared to 111.5 million in 1998. A comparison of larval samples taken below Numana and Marble Bluff dams in 1998 gives a very rough estimate of the number of adult cui-ui that spawned successfully above Numana Dam that year. Out of approximately 500,000 adults that passed Marble Bluff Dam, roughly 60,000 passed Numana Dam (Interior & State, 2008).

Table 2. Number of Cui-ui Estimated to have Naturally Spawned in the Truckee River between 1994 and 2003.

Year Number of…