C05__Attachment_3_-_ESA_Section_7(a)(2)_Biological_Opinion__08-20-18.pdf

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TABLE OF CONTENTS

INTRODUCTION

1.1 Background

1.2 Consultation History

1.3 Proposed Federal Action

1.3.1 Chinook Salmon Program

1.3.2 Steelhead Program

1.3.3 Monitoring and Evaluation Activities

ENDANGERED SPECIES ACT:

2.1 Analytical Approach

2.2 Rangewide Status of the Species and Critical Habitat

2.2.1 Species Description and General Life History

2.2.2 Status of SONCC Coho Salmon

2.2.3 Status of SONCC Coho Salmon Critical Habitat

2.2.4 Factors Responsible for the Decline of Species and Degradation of Critical Habitats 8

2.3 Action Area

2.4 Environmental Baseline

2.4.1 SONCC Coho Salmon Population Units in the Action Area

2.4.2 Status of SONCC Coho Salmon Population Units in the Action Area

2.4.3 Status of SONCC Coho Salmon Critical Habitat in the Action Area

2.4.4 Factors Affecting SONCC Coho Salmon Population Units and Critical Habitat in the

Action Area

2.4.5 Climate Change in the Action Area

2.5 Effects of the Action

2.5.1 Effects of the TRH Steelhead Program on SONCC Coho Salmon

2.5.2 Effects of the TRH Chinook Salmon Program on SONCC Coho Salmon

2.5.3 Effects of the Proposed Action on SONCC Coho Salmon Critical Habitat

2.6 Cumulative Effects

2.6.1 Iron Gate Hatchery Chinook salmon and Steelhead production

2.6.2 Control of wildland fires on non-federal lands

2.6.3 Residential development and existing residential infrastructure

2.6.4 Cannabis Regulation

2.6.5 Recreation (including hiking, camping, fishing, and hunting)

2.7 Integration and Synthesis

2.8 Conclusion

2.9 Incidental Take Statement

2.9.1 Amount or Extent of Take

2.9.2 Effect of the Take

2.9.3 Reasonable and Prudent Measures

2.9.4 Terms and Conditions

2.10 Conservation Recommendations

2.11 Reinitiation of Consultation

2.12 “Not Likely to Adversely Affect” Determinations iii

2.12.1 Effects on Southern Resident Killer Whales DPS

2.12.2 Effects on the Southern DPS of North American Green Sturgeon

2.12.3 Effects on Southern DPS of Eulachon

MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

ESSENTIAL FISH HABITAT RESPONSE

3.1 Essential Fish Habitat Affected by the Project

3.2 Adverse Effects on Essential Fish Habitat

3.3 Essential Fish Habitat Conservation Recommendations

3.4 Supplemental Consultation

DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW ..41

4.1 Utility

4.2 Integrity

4.3 Objectivity

REFERENCES

INTRODUCTION

This Introduction section provides information relevant to the other sections of this document and is incorporated by reference into Sections 2 and 3 below.

1.1 Background

NOAA’s National Marine Fisheries Service (NMFS) prepared the biological opinion (opinion) and incidental take statement (ITS) portions of this document in accordance with section 7(b) of the Endangered Species Act (ESA) of 1973 (16 USC 1531 et seq. ), and implementing regulations at 50 CFR 402.

We also completed an essential fish habitat (EFH) consultation on the proposed action, in accordance with section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and

Management Act (MSA) (16 U.S.C. 1801 et seq.) and implementing regulations at 50 CFR 600.

We completed pre-dissemination review of this document using standards for utility, integrity, and objectivity in compliance with applicable guidelines issued under the Data Quality Act

(DQA) (section 515 of the Treasury and General Government Appropriations Act for Fiscal Year

2001, Public Law 106-554). The document will be available through NMFS’ Public Consultation

Tracking System (https://pcts.nmfs.noaa.gov/pcts-web/homepage.pcts). A complete record of this consultation is on file at the Arcata, California NMFS office.

1.2 Consultation History

On March 2, 2018, NMFS received a formal consultation request and a biological assessment from the Bureau of Reclamation (Reclamation) for the artificial propagation of Steelhead and

Chinook salmon at the Trinity River Hatchery (TRH) near Lewiston, California.

On March 15, 2018, NMFS sent Reclamation a letter informing them that formal consultation initiated on March 2, 2018.

On July 11, 2018, Reclamation clarified several references to weirs in the BA via an email to

NMFS. These clarifications are reflected in section 1.3 of this document.

On July 16, 2018, NMFS and Reclamation agreed to a 45 day extension for completing the biological opinion due to complexities associated with the consultation.

1.3 Proposed Federal Action

“Action” means all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies (50 CFR 402. 02). TRH produces ESA listed Southern

Oregon/Northern California Coast (SONCC) coho salmon and non ESA listed Upper Klamath-

Trinity Rivers (UKTR) spring-run Chinook salmon, UKTR fall-run Chinook salmon, and

Klamath Mountains Province steelhead. The purpose of the TRH Chinook Salmon and Steelhead programs are to mitigate for lost spawning and rearing habitat and harvest opportunities resulting from damming the Trinity River by the Trinity River Project (Trinity and Lewiston dams), completed in 1963. TRH is owned by Reclamation, which is responsible for funding the operation and maintenance of the hatchery. The California Department of Fish and Wildlife

(CDFW) is responsible for carrying out day-to-day operations, fish culture, personnel management, and other aspects related to hatchery operations.

For the purposes of this Biological Opinion, the proposed federal action is the release of 4.3 million Chinook salmon juveniles and 448,000 steelhead juveniles annually into the Trinity

River at TRH in Lewiston, California. NMFS is conducting a separate analysis of the effects of the TRH Coho Salmon Program on ESA listed SONCC coho salmon as part of the section 4d review of the TRH Coho Salmon Hatchery and Genetics Management Plan. As such, the effects of the TRH Coho Salmon Program are not analyzed as part of the effects of the proposed action in this Biological Opinion.

1.3.1 Chinook Salmon Program

The United States Fish and Wildlife Service (USFWS) and the California Department of Fish and Game (CDFG) (1956), now the California Department of Fish and Wildlife (CDFW), estimated that 3,000 spring-run, 8,000 summer-run and 24,000 fall-run Chinook salmon passed above the Lewiston Dam site prior to dam construction. Total annual adult production goals

(catch plus those escaping fisheries) for TRH were further defined in 1980 to be 6,000 spring-run

Chinook salmon and 70,000 fall-run Chinook salmon. Escapement goals to the hatchery were described by USFWS (1983) as 3,000 spring-run Chinook salmon and 9,000 fall-run Chinook salmon. Hatchery production goals are based on achieving juvenile release numbers, not adult production levels. The hatchery program currently releases 1.3 million yearling and 3 million sub-yearling spring- and fall-run Chinook salmon each year. Hatchery spring- and fall-run

Chinook salmon juveniles pose predation, competition and disease risks to natural-origin juvenile SONCC coho salmon (see Sections 8.4.1 and 8.4.4).

Under the proposed action, the existing fall-run Chinook salmon program would continue to release 2 million sub-yearlings (“fingerlings”, at 90 fish per pound [fpp]) in June and 900,000 yearlings (“yearlings”, at 10 fpp) in October. Fall-run Chinook salmon are marked at a rate of 25 percent (constant fractional marking) with an adipose fin clip and coded-wire tag, and released at the hatchery site (CA HSRG 2012).

The existing spring-run Chinook salmon program releases 1 million sub-yearlings (“fingerlings”, at 90 fpp) in June and 400,000 yearlings (at 10 fpp) in October. Spring-run Chinook Salmon are marked at a rate of 25 percent (constant fractional marking) with an adipose fin clip and coded-wire tag, and released at the hatchery site (CA Hatchery Scientific Review Group (HSRG) 2012).

1.3.2 Steelhead Program

USFWS and CDFG (1956), now CDFW, estimated that an average of 10,000 Steelhead passed above the Lewiston Dam site prior to dam construction. The escapement goals are 10,000 adult hatchery Steelhead returning to TRH and 40,000 wild adult Steelhead returning to the Trinity

River (USFWS 1983).

Under the proposed action, the TRH Steelhead program would continue to be operated as an integrated program. Under the integrated strategy, natural-origin adults are included in the broodstock in a systematic manner to minimize genetic divergence of hatchery fish from a natural population. The goal is to have the natural environment drive the mean fitness of hatchery produced fish, instead of the hatchery environment. In response to concerns associated with hatchery Steelhead predation on SONCC Coho Salmon (see Section 8.3.1), TRH has incorporated the following actions into its existing Steelhead hatchery program, which also address recovery actions in the SONCC Coho Salmon recovery plan (NMFS 2014). Many of these actions are intended to create quality smolts. The HSRG (2004) noted that the definition of a quality hatchery smolt is equivalent to the definition of a quality natural smolt, which is a metamorphosed, anadromous salmonid that exhibits rapid downstream migration, increased hypo-osmoregulatory capability (enhanced seawater tolerance), sustained growth in the ocean, and high survival to adulthood.

The juvenile release number will not exceed 448,000 yearling steelhead for 6 years, commencing in 2014. (Prior to 2014 production was 800,000 yearlings). Predation risk and redd superimposition impacts on natural Coho Salmon are to be evaluated to determine future production levels.

A feeding schedule designed to mimic wild fish physiological development (i.e., minimal winter growth with rapid spring growth).

Feeding the fish a high protein diet to ensure health and growth.

Prior to release, manually grading fish to remove fish < 5 fpp and > 7 fpp (target release size of 210 mm).

Implementing a volitional release strategy (i.e., fish are not forced from raceways).

Fish will be volitionally released from April 15 to April 30 (i.e., near the time of the new moon).

Releasing quality hatchery Steelhead smolts is expected to enhance emigration rates (travel time in days),to the ocean and reduce the rate at which the smolts residualize (fail to migrate) in the

Trinity River , which in turn is expected to result in reduced competition and potential predation effects to Coho Salmon juveniles. The effectiveness of program actions to reduce competition and predation risks to Coho Salmon would be determined by monitoring:

The size and number of Steelhead released each year (448,000, 6 fpp).

Emigration rates from release location at the hatchery to existing juvenile trapping facilities in the mainstem Trinity River at Willow Creek (performance criterion: < 14 days).

Number of hatchery Steelhead residing in the first five miles below Lewiston Dam

(performance criterion: <100 residual Steelhead per mile).

All Steelhead would be marked with an adipose fin clip and released at the hatchery site.

Unspawned adults are recycled to the river below the ladder between September and December

(while trap is being operated for other species); fish in excess of broodstock needs are returned to the river on each spawning day.

1.3.3 Monitoring and Evaluation Activities

Monitoring and effectiveness activities associated with the Trinity River Hatchery programs include the following:

Monitor the life history characteristics of hatchery-origin and natural-origin adult Coho

Salmon through analysis of hatchery and natural fish returns at weirs and the TRH.

Monitor adult holding survival, egg-to-fry, fry-to-parr, and parr-to-smolt survival at the

TRH.

Monitor the proportion of natural origin recruit (NOR) broodstock (pNOB) in the Upper

Trinity River Coho Salmon population.

Continue to monitor the health of hatchery-produced smolts.

Continue to monitor the size and condition of fish released from the TRH.

Monitor outmigration rates of hatchery releases using outmigrant trapping in the mainstem Trinity River.

Continue to monitor estimates of Smolt to Adult Returns (SAR) of hatchery production.

Continue to monitor estimates of the proportion of hatchery fish spawning on the spawning grounds.

Monitor existing harvest rate, and consider changes to future harvest rates in the context of Coho Salmon recovery.

Prevention of disease is an important aspect of TRH operations. This starts when adults enter the holding ponds, includes careful handling of adults and eggs during spawning and incubation, and continues through release of the fish. Specifically, this includes gentle handling of all life stages, the use of disinfectant agents for equipment and clothing used in the raceways such as brushes, nets, crowders, and waders. Hatchery staff also maintains detailed records on water flows, temperatures, densities, mortality, feeding behaviors, and fish growth. Attention is also given to other environmental conditions which enhance the health of the fish such as cleaning, feed quality, dissolved oxygen, shade/cover, etc. Operations are conducted to minimize the use of therapeutic drugs and chemicals and to comply with conditions of the National Pollutant

Discharge Elimination System (NPDES) permit as well as Food and Drug Administration laws and regulations.

Reclamation requested an Essential Fish Habitat Consultation under the Magnuson Stevens

Fishery Conservation and Management Act (MSA). For the MSA, a Federal action means any action authorized, funded, or undertaken, or proposed to be authorized, funded, or undertaken by a Federal Agency (50 CFR 600. 910). We have provided an MSA consultation on the proposed action in Part 3 of this Biological Opinion.

“Interrelated actions” are those that are part of a larger action and depend on the larger action for their justification. “Interdependent actions” are those that have no independent utility apart from the action under consideration (50 CFR 402. 02). There are no interrelated or interdependent actions related to the proposed action that are expected to affect SONCC Coho Salmon or their critical habitat.

ENDANGERED SPECIES ACT:

BIOLOGICAL OPINION AND INCIDENTAL TAKE STATEMENT

The ESA establishes a national program for conserving threatened and endangered species of fish, wildlife, plants, and the habitat upon which they depend. As required by section 7(a)(2) of the ESA, each Federal agency must ensure that its actions are not likely to jeopardize the continued existence of endangered or threatened species, or adversely modify or destroy their designated critical habitat. Per the requirements of the ESA, Federal action agencies consult with

NMFS and section 7(b)(3) requires that, at the conclusion of consultation, NMFS provides an opinion stating how the agency’s actions would affect listed species and their critical habitats. If incidental take is reasonably certain to occur, section 7(b)(4) requires NMFS to provide an ITS that specifies the impact of any incidental taking and includes non-discretionary reasonable and prudent measures (RPMs) and terms and conditions to minimize such impacts.

Reclamation has determined that the proposed action is not likely to adversely affect the Distinct

Population Segment (DPS) of Southern Resident Killer Whales, the Southern DPS of Eulachon, the Southern DPS of North American Green Sturgeon, or their critical habitats. Our concurrence is documented in the "Not Likely to Adversely Affect" Determinations section 2.12.

2.1 Analytical Approach

This biological opinion includes both a jeopardy analysis and/or an adverse modification analysis. The jeopardy analysis relies upon the regulatory definition of “to jeopardize the continued existence of” a listed species, which is “to engage in an action that would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species”

(50 CFR 402. 02). Therefore, the jeopardy analysis considers both survival and recovery of the species.

This biological opinion relies on the definition of "destruction or adverse modification," which

“means a direct or indirect alteration that appreciably diminishes the value of critical habitat for the conservation of a listed species. Such alterations may include, but are not limited to, those that alter the physical or biological features essential to the conservation of a species or that preclude or significantly delay development of such features” (81 FR 7214).

The designation of critical habitat for SONCC Coho Salmon uses the term primary constituent element (PCE) or essential features. The new critical habitat regulations (81 FR 7414) replace this term with physical or biological features (PBFs). The shift in terminology does not change the approach used in conducting a ‘‘destruction or adverse modification’’ analysis, which is the same regardless of whether the original designation identified PCEs, PBFs, or essential features.

In this biological opinion, we use the term PBF to mean PCE or essential feature, as appropriate for the specific critical habitat.

We use the following approach to determine whether a proposed action is likely to jeopardize listed species or destroy or adversely modify critical habitat:

Identify the range-wide status of the species and critical habitat expected to be adversely affected by the proposed action.

Describe the environmental baseline in the action area.

Analyze the effects of the proposed action on both species and their habitat using an

“exposure-response-risk” approach.

Describe any cumulative effects in the action area.

Integrate and synthesize the above factors by: (1) Reviewing the status of the species and critical habitat; and (2) adding the effects of the action, the environmental baseline, and cumulative effects to assess the risk that the proposed action poses to species and critical habitat.

Reach a conclusion about whether species are jeopardized or critical habitat is adversely modified.

If necessary, suggest a Reasonable and Prudent Alternative (RPA) to the proposed action.

2.2 Rangewide Status of the Species and Critical Habitat

This opinion examines the status of SONCC Coho Salmon that would be adversely affected by the proposed action. Their status is determined by the level of extinction risk that the listed species faces, based on parameters considered in documents such as recovery plans, status reviews, and listing decisions. This informs the description of the species’ likelihood of both survival and recovery. The species status section also helps to inform the description of the current “reproduction, numbers, or distribution” of the species as described in 50 CFR 402.02.

This opinion also examines the condition of critical habitat throughout the designated area, evaluates the conservation value of the various watersheds and coastal and marine environments that make up the designated area, and discusses the current function of the essential PBFs that help to form that conservation value.

In this biological opinion, NMFS assesses four population viability parameters to help us understand the status of the SONCC Coho Salmon Evolutionarily Significant Unit (ESU) and its ability to survive and recover. These population viability parameters are: abundance, population productivity, spatial structure, and diversity (McElhaney et al. 2000). While there is insufficient information to evaluate these population viability parameters in a thorough quantitative sense, NMFS has used existing information, including the Recovery Plan for SONCC Coho Salmon

(NMFS 2014) to determine the general condition of each population and factors responsible for the current status of the ESU. We use these population viability parameters as surrogates for numbers, reproduction, and distribution, the criteria found within the regulatory definition of jeopardy (50 CFR 402.20).

2.2.1 Species Description and General Life History

Most Coho Salmon have a 3‐year life history, though some may spend more than one year in freshwater, which can make the analysis of age at return and cohort structure challenging

(Bennett et al. 2015). The adults typically migrate from the ocean and into bays and estuaries towards their freshwater spawning grounds in late summer and fall, and spawn by mid-winter.

Adults die after spawning. The eggs are buried in nests, called redds, in the rivers and streams where the adults spawn. The eggs incubate in the gravel until fish hatch and emerge from the gravel the following spring as fry. These 0+ age fish typically rear in freshwater for about 15 months before migrating to the ocean. The juveniles go through a physiological change during the transition from fresh to salt water called smoltification. Coho salmon typically rear in the ocean for two growing seasons, returning to their natal streams as 3‐year old fish to renew the cycle. Male jacks return at age 2, after spending approximately six months at sea, providing important genetic material across cohorts, such that each cohort does not become reproductively isolated from the others.

2.2.2 Status of SONCC Coho Salmon

Although long-term data on Coho Salmon abundance are scarce, the available evidence from short-term research and monitoring efforts indicate that spawner abundance has declined since the last status review for populations in this ESU (Williams et al. 2016). In fact, most of the 30 independent populations in the ESU are at high risk of extinction because they are below or likely below their depensation threshold, which can be thought of as the minimum number of adults needed for survival of a population.

The distribution of SONCC Coho Salmon within the ESU is reduced and fragmented, as evidenced by an increasing number of previously occupied streams from which SONCC Coho

Salmon are now absent (NMFS 2001, Good et al. 2005, Williams et al. 2011, Williams et al.

2016). Extant populations can still be found in all major river basins within the ESU (70 FR

37160). However, extirpations, loss of brood years, and sharp declines in abundance (in some cases to zero) of SONCC Coho Salmon in several streams throughout the ESU indicate that the

SONCC Coho Salmon spatial structure is more fragmented at the population-level than at the

ESU scale. The genetic and life history diversity of populations of SONCC Coho Salmon is likely very low and is inadequate to contribute to a viable ESU, given the significant reductions in abundance and distribution. A viable ESU contains populations that exist as a metapopulation that as an entity is naturally self-sustaining into the foreseeable future, no longer needs the protection of the Endangered Species Act, and therefore can be “delisted” – taken off the list of threatened and endangered species.

2.2.3 Status of SONCC Coho Salmon Critical Habitat

One factor affecting the range wide status and aquatic habitat at large is climate change.

Information since these species were listed suggests that the earth’s climate is warming, and that this change could significantly impact ocean and freshwater habitat conditions, which affect survival of all three species of listed salmonids subject to this consultation. In the coming years, climate change will reduce the ability to recover some salmon species in most or all of their watersheds. Coho salmon are particularly vulnerable to climate change due to their need for year-round cool water temperatures, as they rear for one or more years in freshwater, unlike some other salmonid species (Moyle 2002). By increasing air and water temperatures, climate change is expected to decrease the amount and quality of habitat Coho Salmon, reducing the productivity of populations and exacerbating the decline of the species. Climate change effects on stream temperatures within Northern California are already apparent. For example, in the

Klamath River, Bartholow (2005) observed a 0. 5°C per decade increase in water temperature since the early 1960’s, and model simulations predict a further increase of 1-2°C over the next 50 years (Perry et al. 2011).

In coastal and estuarine ecosystems, the threats from climate change largely come in the form of sea level rise and the loss of coastal wetlands. Sea levels will likely rise exponentially over the next 100 years, with possibly a 50-80 cm rise by the end of the 21st century (IPCC 2007). This rise in sea level will alter the habitat in estuaries and either provide increased opportunity for feeding and growth or in some cases will lead to the loss of estuarine habitat and a decreased potential for estuarine rearing. Marine ecosystems face an entirely unique set of stressors related to global climate change, all of which may have deleterious impacts on growth and survival while at sea. In general, the effects of changing climate on marine ecosystems are not well understood given the high degree of complexity and the overlapping climatic shifts that are already in place (e.g., El Niño, La Niña, Pacific Decadal Oscillation) and will interact with global climate changes in unknown and unpredictable ways. Overall, climate change is believed to represent a growing threat, and will challenge the resilience of salmonids in Northern

California, including SONCC Coho Salmon.

2.2.4 Factors Responsible for the Decline of Species and Degradation of Critical Habitats

The factors that caused declines include hatchery practices, ocean conditions, habitat loss due to dam building, degradation of freshwater habitats due to a variety of agricultural and forestry practices, water diversions, urbanization, over-fishing, mining, climate change, and severe flood events exacerbated by land use practices (Good et al. 2005, Williams et al. 2016). Sedimentation and loss of spawning gravels associated with poor forestry practices and road building are particularly chronic problems that can reduce the productivity of salmonid populations. Late

1980s and early 1990s droughts and unfavorable ocean conditions were identified as further likely causes of decreased abundance of SONCC Coho Salmon (Good et al. 2005). From 2014 through 2016, the drought in California reduced stream flows and increased temperatures, further exacerbating stress, disease, and decreasing the quantity and quality of spawning and rearing habitat available to SONCC Coho Salmon. Ocean conditions have been unfavorable in recent years (2014 to present) due to El Niño conditions and the warm water “Blob” which impacted the U.S. west coast, and reduced ocean productivity and forage for SONCC Coho Salmon.

2.3 Action Area

Action Area means 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). For this proposed action, the Action Area includes TRH (Section 8, Township 40°43'11. 61"N, Range 122°48'4. 90"W), Trinity River, and the

Klamath River from its confluence with the Trinity to its mouth in the Pacific Ocean (Figure 2). The

Action Area also includes the nearshore portions of Pacific Ocean at the mouth of the Klamath River.

Figure 1. Map of the proposed Action Area (Trinity River basin) and associated anadromous fish hatcheries in the region.

2.4 Environmental Baseline

The “environmental baseline” includes the past and present impacts of all Federal, state, or private actions and other human activities in the action area, the anticipated impacts of all proposed Federal projects in the action area that have already undergone formal or early section

7 consultation, and the impact of state or private actions which are contemporaneous with the consultation in process (50 CFR 402.02).

2.4.1 SONCC Coho Salmon Population Units in the Action Area

There are three Trinity River population units and one Klamath River population unit that are in the action area (Table 2-2). Although they migrate through the lower Klamath River portion of the action area, the population units of the Interior-Klamath Stratum will have little exposure to the proposed action. Williams et al. (2006) identified the boundaries of the affected population units based on precipitation and flow patterns, among other factors (Table 2-1).

Table 2-2. Population unit boundaries for SONCC Coho Salmon populations in the action area.

Population Unit Boundaries Adult population needed for recovery

Upper Trinity River Confluence of North Fork Trinity

River (inclusive) upstream to

Ramshorn Creek (inclusive).

5,800

Lower Trinity River Confluence of Klamath River upstream to confluence with North

Fork Trinity River (non-inclusive).

3,600

South Fork Trinity

River

South Fork Trinity River to the confluence of the Trinity River.

Lower Klamath

River

Mouth of Klamath River upstream to confluence with Trinity River.

5,900

The Upper Trinity River, Lower Trinity River, and Lower Klamath River Population Units are

“core” population units, and need to achieve a robust level of adult spawners for recovery of the

ESU (Table 2-3; NMFS 2014). The South Fork Trinity River Population Unit is not considered a core population unit, and needs to achieve only an amount of adult spawners required to be functionally independent for the recovery of the ESU (Table 2-4; NMFS 2014). Therefore, the

Action Area is very important to the survival and recovery of the ESU because the ESU cannot recover without three of the four population units in the Action Area being recovered.

Population units in the Trinity River have a high conservation value. As mentioned above, at least two of them must be viable for the diversity stratum to be viable and for the ESU to be viable. The Upper-Trinity Population unit is unique within the Trinity River system as these

Coho Salmon are currently the longest migrating adult Coho Salmon in the stratum. While Coho

Salmon likely used to migrate as far as Hayfork Creek on the South Fork Trinity River, habitat degradation and water utilization on that river has restricted the spatial structure of the population unit. The run timing of the Upper Trinity River population unit is earlier (September and October) than those fish in the Lower Trinity Population unit (November through January).

Within the Interior-Trinity diversity stratum, the Upper Trinity River population unit and the

Lower Trinity River population unit capture both the coastal winter returning run timing and the inland fall returning run timing. This aids in protecting the diversity stratum from both drought and flood by extending the time during which adults enter the Trinity River. The upper Trinity

River population unit may serve as an important “source” population for the Lower Trinity and

South Fork Trinity populations which may act as “sinks.” The Upper Trinity River population unit also protects the ESU against range shrinkage by maintaining an inland population that is one of the furthest east migrating population units in the ESU. The discharge of the Lower

Trinity River is more dominated by rain while discharge of the Upper Trinity River is more of a rain-snowmelt mix. These population units have developed different life history strategies to take advantage of this difference. The Lower Klamath River Population unit is important in order for populations in the Central Coastal Basins Diversity Stratum to maintain connectivity with other populations to the north and south along the California and Oregon coasts. This population unit has access to a wide range of diverse off channel pond and slough habitat types, which aids in a diversity of life history strategies, which protects it and the ESU against environmental change, catastrophes, and natural disasters.

2.4.2 Status of SONCC Coho Salmon Population Units in the Action Area.

Limited information about the population size of individual SONCC Coho Salmon population units within the action area is available. No systematic surveys that monitor population sizes in any of the populations are performed. CDFW monitors Coho Salmon run size at a weir near

Willow Creek, California on the lower Trinity River. Because adult Coho Salmon from all three population units of the Interior-Trinity Diversity Stratum pass through the weir site due to its location, it is not known which population of Coho Salmon is captured at the weir. As such, the weir estimates provide an aggregate population estimate for all unmarked Coho Salmon upstream of the weir. All Coho Salmon marked by maxillary bone removal captured at the weir are known to be of TRH origin. The California drought from 2013 to 2017, combined with poor ocean conditions during the same period pushed adult Coho Salmon returns to some of their lowest levels in recent decades (Figure 2-2). The reduced production at TRH also changed the number of returning TRH origin Coho Salmon in recent years (Figure 2-2). Hatchery origin adults often make up 80% or greater of the overall run, though there is indication that this proportion has decreased recently with lower production from TRH.

Figure 2-2. Coho Salmon run size estimates for the Trinity River upstream of the Willow Creek

Weir 1997 to 2016 (Kier et al. 2017).

Upper Trinity River Population Unit

The Upper Trinity River population is at moderate risk of extinction as described in the SONCC coho salmon recovery plan (NMFS 2014). Coho salmon continue to be present in many of the tributary streams in this population unit, but low adult returns in recent years have left some habitat unoccupied. Although there may be robust numbers of spawners occasionally in some years, the overall number of naturally produced Coho Salmon in the Upper Trinity River watershed is low compared to historic conditions, and hatchery fish dominate the run. The Upper Trinity River

Population unit has the greatest degree of temporal and spatial exposure to hatchery fish of any of the population units in the action area. SONCC Coho Salmon in this population unit are exposed to both genetic interactions through breeding with TRH Coho Salmon, as well as ecological interactions

(predation, competition and disease transfer) with hatchery coho salmon, Chinook salmon, and steelhead. This population needs to have adult returns of 5,800 for the SONCC Coho Salmon

ESU to be viable as described in the SONCC coho salmon recovery plan (NMFS 2014).

Lower Trinity River Population Unit

Limited data exists for this population as few surveys have been completed. The limited data available from the U.S. Forest Service and the Hoopa Valley Tribe for the Lower Trinity River population suggests that much of the habitat in the Lower Trinity River is currently unoccupied or only sporadically occupied. Brood year cohorts may be missing and the adult Coho Salmon population is likely less than the depensation threshold of 112 adults. The population growth rate in Lower Trinity River sub-basin has not been quantified. The Lower Trinity population is at high risk of extinction as described in the SONCC coho salmon recovery plan (NMFS 2014).

This population needs to have adult returns of 3,600 for the SONCC Coho Salmon ESU to be viable as described in the SONCC coho salmon recovery plan (NMFS 2014).

South Fork Trinity River Population Unit

The only population estimates for the South Fork Trinity River are based on work by Jong and Mills

(1992) who estimated that 127 adult and jack Coho Salmon returned to the South Fork Trinity River in 1985 and 99 returned in 1990. With 35.8 percent (46) of the adult Coho Salmon captured in 1985 being of hatchery origin, the total wild population was likely under 100 adults during these years

(Jong and Mills 1992). However, in other years, few or no hatchery Coho Salmon were trapped on the South Fork Trinity River (Jong and Mills 1992). Although we have no current population estimates, if we assume abundances are similar to those found in 1985 and 1990, the South Fork

Trinity River population does not meet the depensation threshold of 242 adults and is at high risk of extinction. The population growth rate in South Fork Trinity River basin has not been quantified but is likely negative based on loss of habitat and declining water quality. The South Fork Trinity River population is at high risk of extinction as described in the SONCC coho salmon recovery plan

(NMFS 2014). This population needs to have adult returns of 970 for the SONCC Coho Salmon

ESU to be viable as described in the SONCC coho salmon recovery plan (NMFS 2014).

Lower Klamath River Population Unit

NMFS (2014) determined that based on criteria established by Williams et al. (2008), the Lower

Klamath River population is at high risk of extinction because the spawner abundance has likely been below the depensation threshold of 205 adult Coho Salmon. The productivity of the population, based on the limited information available, appears to be declining (NMFS 2014).

This population needs to have adult returns of 5,900 for the SONCC Coho Salmon ESU to be viable as described in the SONCC coho salmon recovery plan (NMFS 2014).

2.4.3 Status of SONCC Coho Salmon Critical Habitat in the Action Area.

Upper Trinity River Population Unit

The Trinity River Division of the Central Valley Project has caused loss of hydraulic function, habitat loss, and habitat simplification. The juvenile life stage of the Upper Trinity River population unit of SONCC coho salmon is the most limited of the life stages and suitable quality summer and winter rearing habitat is lacking for the population. Loss of flow variability and reduced rearing habitat during the fall and winter months as a result of water storage and flow management is expected to reduce the ability of the habitat in the Upper Trinity River to support winter rearing of juvenile Coho Salmon. Water withdrawals from important tributaries like Weaver and Rush creeks reduce baseflows in the summer and fall months, contributing to low flows and high water temperatures. Variability of the natural flow regime is inherently critical to ecosystem function and native biodiversity (Bunn and Arthington 2002, Beechie et al. 2006). In the summer, flow regimes and the lack of large woody debris (LWD) and off-channel habitat leads to poor hydrologic function, disconnection and diminishment of thermal refugia, and poor water quality in tributaries and the mainstem during dry years. Floodplain disconnection and poor riparian function as a result of reduced flow and variability is being addressed through restoration efforts but will continue to be a limiting factor for the population.

Lower Trinity River Population Unit

There is no critical habitat on the Hoopa Valley Tribe Reservation, which is located in the lower

Trinity River area. Lack of floodplain and channel structure impacts has a major impact on the productivity of this population. Rearing opportunities and capacity are low due to disconnection of the floodplain, a lack of LWD inputs, poor riparian conditions, and sediment accretion. Low-lying areas of streams such as Supply, Mill, and Willow Creek have been channelized, diked, and disconnected from the floodplain. Many tributaries in low-gradient areas of the Lower

Trinity experience similar habitat characteristics due to development of the floodplain, sedimentation and changes in flow. The mainstem river also lacks side channel, backwater, and wetland habitat where juvenile Coho Salmon could find habitat in the winter. A lack of floodplain and channel structure impacts winter rearing because high flow events can displace juveniles from streams and there exists very little low-velocity rearing habitat. Lack of complex habitat also impacts summer rearing due to the loss of predatory refugia, low-flow refugia, and foraging habitat. In some portions of this population unit cannabis farming impacts summer rearing areas for juveniles, due to runoff and pollution, as well as contributing to poor water quality and quantity.

South Fork Trinity River Population Unit

The South Fork originates in the North Yolla Bolly Mountains about 50 miles southwest of Redding and runs northwest for approximately 90 miles before reaching its confluence with the Trinity River.

A large portion of the South Fork Trinity River watershed is publicly owned and managed by the

Shasta-Trinity National Forest. Much of the basin is still recovering from the effects of the 1964 flood that introduced massive volumes of sediment into the South Fork Trinity River and most tributary reaches. Due to the substantial sediment influx, much of the mainstem South Fork Trinity

River and Hayfork Creek still lack deep pool holding habitat for adult salmon (NMFS 2007). In addition, temperatures in the lower South Fork and selected tributaries, particularly the lower portion of Hayfork Creek, have been implicated as being too high to fully support salmon. Deforestation, dewatering, illegal grading, and pollution associated with cannabis farming has significantly altered water quality and fish habitat in this population unit.

Lower Klamath River Population Unit

There is no designated critical habitat for this population unit, as the population boundaries lie entirely within the Yurok Tribe Reservation. Altered sediment supply, lack of floodplain and channel structure, degraded riparian forest conditions and impaired estuary function are the biggest stresses to this population. The juvenile life stage is most limited and quality winter rearing habitat, as well as summer rearing habitat, is lacking for the population. Juvenile summer rearing habitat is impaired from subsurface flow conditions in the tributaries and poor water quality of the mainstem Klamath River. Winter rearing habitat is severely lacking because of channel simplification, disconnection from the floodplain, degraded riparian conditions, poor large wood availability, and an estuary which has been altered and reduced in size due to development, channelization, and diking. Large wood has been removed and is not naturally replacing at the rates required to maintain key components of habitat complexity. Altered sediment supply in many tributaries has hindered fish passage, resulted in poor summer survival, poor spawning and incubation habitat suitability, and the loss and degradation of stream and off-channel habitat. Most potential spawning reaches have excessively embedded and armored substrate, making redd construction more challenging for adults and reducing permeability in constructed redds. Agricultural practices, channelization and diking, roads, and timber harvest are the biggest threats to this population.

2.4.4 Factors Affecting SONCC Coho Salmon Population Units and Critical Habitat in the

Action Area.

There are a variety of factors affecting SONCC Coho Salmon in the action area, most of which have a negative effect on SONCC Coho Salmon and their critical habitat (Table 2-2). The

California drought, combined with the warm water “Blob” in the northeast Pacific Ocean had a toll on SONCC Coho Salmon in the action area, contributing to low returns of adult Coho

Salmon. Limited and poor quality freshwater habitat, disease, and lack of forage in the ocean environment for multiple years in a row appears to have pushed adult returns to their lowest levels throughout the region. Restoration activities in the Trinity River basin and the lower

Klamath River will likely benefit Coho Salmon populations by reducing several stressors in the action area like sedimentation or loss of LWD.

Table 2-2. Factors affecting Coho Salmon in the action area.

Factors affecting Coho

Salmon in the Action Area Effects Stressors

Forestry Activities Negative

Sedimentation of spawning gravels, increased water temp, loss of LWD, poor water quality, reduced pool frequency and depth

Roads Negative

Sedimentation, habitat blockage, reduced pool frequency and depth

Hatchery Activities

Negative and positive

Negative: Genetic and ecological interactions.

Positive: Demographic support at low run sizes, marine derived nutrients.

Climate Change Negative

Warming water temperatures, reductions in summer and fall streamflow

Agriculture Negative

Sedimentation, decrease in water quality, decrease in summer base flows, riparian habitat loss

Urban, residential, and industrial development Negative

Urban non-point pollution runoff, increased water utilization, channelization, riparian habitat loss

Water Diversions Negative

Loss or reduction of summer baseflow (tributaries other than mainstem Trinity River), habitat reduction, increase in water temperatures, hydrologic alteration, habitat reductions.

Restoration Positive

Addition of LWD, increase in habitat quantity and quality

Fisheries Negative Mortality of returning adults and jacks

Effects from timber harvest including sedimentation, riparian habitat loss, reduced LWD recruitment, and water temperature impacts, are expected to continue through the action period.

Impacts from roads are expected to remain similar or slightly decrease throughout the Proposed

Action as more roads are decommissioned. Road decommissioning and culvert replacement will help to reduce sedimentation in the future. Boutique wineries, organic farms, and residential development exacerbate late summer and fall water shortages, which impacts summer rearing areas for Coho Salmon. Marijuana cultivation and associated water utilization and unchecked grading and deforestation poses a significant threat to Coho Salmon in some locales, such as areas on the South Fork Trinity River. Residential growth in the Trinity basin and Lower

Klamath River is expected to continue at a moderate pace, and its effects are negative due to increasing runoff and water use. Mortality of marked and unmarked Trinity River Coho Salmon averaged 6.2% (range 3.0% to 12.1%) in ocean fisheries and 3.8% (range 0.9% to 10.2%) in tribal fisheries in the lower Klamath and Trinity Rivers.

2.4.5 Climate Change in the Action Area

Figure 2-3 shows downscaled projections for representative climate pathway 4.5 (RCP4. 5) developed by the International Panel on Climate Change for 32 climate models for the region near Lewiston, CA, the location of TRH. Assuming emissions peak around 2040 and then decline, the modeled annual mean maximum and minimum air temperatures are expected to increase approximately 3°F from the historical period (1961-1990) to the modeled future period

(2020-2050). Average annual mean precipitation is expected to increase approximately

2.3 inches from 35.9 inches to 38.2 inches from the historical period to modeled future period.

There has already been a significant loss of snowpack in northern California, particularly at low elevations (Mote et al. 2018), and warming caused by climate change will continue to exacerbate future snowpack loss, regardless of any potential increases in precipitation (Zhu et al. 2005, Vicuna et al. 2007). A transition to a warmer climate state and sea surface warming may be accompanied by reductions in ocean productivity which affect fisheries (Ware and Thomson

2005; Behrenfeld et al. 2006). Due to the corresponding increase in water temperatures, decrease in summer and fall stream flows and potential declines in ocean productivity, the amount of habitat available to all life stages of SONCC Coho Salmon in the action area is expected to shrink and/or become less suitable. This is expected to reduce the number of successful offspring produced per adult spawner, and challenge the resiliency of SONCC Coho Salmon in the action area.

Figure 2-3. Panel figure showing predicted A) maximum temperature, B) minimum temperatures, and C) precipitation through 2050 for the region near Lewiston, CA. Data are from www. cal-adapt.org.

A

B

C

2.5 Effects of the Action

Under the ESA, “effects of the action” means the direct and indirect effects of an action on the species or critical habitat, together with the effects of other activities that are interrelated or interdependent with that action, that will be added to the environmental baseline (50 CFR

402.02). Indirect effects are those that are caused by the proposed action and are later in time, but still are reasonably certain to occur.

The Proposed Action would affect SONCC Coho Salmon by creating the following ecological interactions between TRH Steelhead and Chinook Salmon and SONCC Coho Salmon:

competition; predation; redd superimposition; and disease transmission. In addition, the proposed action is expected to increase marine derived nutrients. For our analysis, we relied on information provided in Reclamation (2018), peer-reviewed journal publications, and reports from local state, federal, and tribal entities. Reclamation used the PCDRISK-1 model (Pearsons and Busack 2012) to quantify the effects of predation and competition from TRH Steelhead and

Chinook Salmon on Coho Salmon. PCDRISK-1 is a flexible computer model designed to assist in assessment and reduction of ecological risks to natural origin fish from hatchery fish releases.

PCDRISK-1 simulates predation, competition, and disease impacts on naturally produced salmonids caused by hatchery smolts in fresh water as they move downstream or residualize after release (Pearsons and Busack 2012). Individual-based, the model relies upon user specified inputs of up to 45 variables, such as number and size of hatchery and wild fish, and water temperature (Pearsons and Busack 2012). The model generates hatchery and natural fish of specified size distributions, then randomly pairs them for interactions for a specified number of days and encounters (Pearsons and Busack 2012).

For the purposes of modeling, Reclamation (2018) assumed that 1 million SONCC Coho Salmon fry would be present at the time that Steelhead and Chinook Salmon are released from TRH.

PCDRISK-1 is a relatively new model that has not been rigorously tested (Pearsons and Busack

2012). Like other models of biological and ecological processes, the accuracy and quality of the model inputs help determine the accuracy and quality of the model results. NMFS is not aware of other peer reviewed studies or models that are readily available and that could be used to quantify the ecological effects of the TRH Steelhead and Chinook Salmon releases on Coho

Salmon. Therefore, NMFS believe the analysis provided in Reclamation (2018) is the best available information regarding the ecological effects of the TRH Steelhead and Chinook

Salmon programs on Coho Salmon.

2.5.1…