Attachment_3-Battle_Creek_winter-run_Chinook_Salmon_reintroduction_plan.pdf

Battle Creek Winter-Run Chinook Salmon Reintroduction Plan

P R E P A R E D F O R :

California Department of Fish and Wildlife

830 S Street

Sacramento, CA 95811

P R E P A R E D B Y :

ICF International

615 SW Alder, Suite 200

Portland, OR 97205

Willis E. (Chip) McConnaha, Ph.D.

Lead Scientist

(503) 525-6141

Greg Blair

Fisheries Biologist

(206) 801-2862

Jim Lecky

Project Manager

(206) 801-2805

August 2016

ICF International. 2016. Battle Creek Winter-Run Chinook Salmon Reintroduction Plan. (ICF

00148.15.) August. Sacramento, CA. Prepared for California Department of Fish and Wildlife.

Sacramento, CA.

Battle Creek Winter-Run Chinook Salmon Reintroduction Plan i

ICF 00148.15

Contents

Page

List of Tables .......................................................................................................................................... iii

List of Figures ......................................................................................................................................... iv

List of Acronyms and Abbreviations ....................................................................................................... v

Chapter 1 Introduction and Goals .................................................................................................... 1-1

1.1 Introduction .................................................................................................................................. 1-1

1.2 Purpose and Content of This Reintroduction Plan ....................................................................... 1-1

1.3 Historical and Present Status ........................................................................................................ 1-2

1.4 Battle Creek Restoration Program – History, Current Status, and Future Direction .................... 1-5

1.5 Reintroduction Goals .................................................................................................................... 1-6

1.5.1 Assumptions ...................................................................................................................... 1-6

1.5.2 Vision and Goals for Reintroduction ................................................................................. 1-7

Chapter 2 Background ..................................................................................................................... 2-1

2.1 Biological Setting ........................................................................................................................... 2-1

2.1.1 Overview of Fish Species in Battle Creek .......................................................................... 2-1

2.1.2 Battle Creek ....................................................................................................................... 2-2

2.1.3 Climate Change .................................................................................................................. 2-5

2.2 Regulatory Setting ......................................................................................................................... 2-6

2.3 Scientific Knowledge and Synthesis of Experiences: .................................................................... 2-7

2.3.1 Considerations for Reintroduction .................................................................................... 2-8

2.3.2 Review of Salmonid Reintroduction Programs................................................................ 2-10

2.3.3 Framework for Planning and Implementing Reintroduction .......................................... 2-14

Chapter 3 Planned Program Implementation ................................................................................... 3-1

3.1 Reintroduction Considerations ..................................................................................................... 3-1

3.1.1 Sources of Fish for Reintroduction .................................................................................... 3-1

3.1.2 Transfer and Release Strategies ........................................................................................ 3-6

3.1.3 Physical Components and Hatchery Facility Needs........................................................... 3-7

3.2 Marking Strategies ........................................................................................................................ 3-8

3.2.1 Genetic Testing ................................................................................................................ 3-10

3.2.2 PIT Tags and Coded Wire Tags......................................................................................... 3-10

3.2.3 Secondary Marks ............................................................................................................. 3-11

3.3 Reintroduction Phases ................................................................................................................ 3-13

3.3.1 Phase 1 – Recolonization ................................................................................................. 3-13

California Department of Fish and Wildlife ii

3.3.2 Phase 2 – Local Adaptation ............................................................................................. 3-20

3.3.3 Phase 3 – Long-Term Management................................................................................. 3-23

3.4 Implementation Schedule ........................................................................................................... 3-23

Chapter 4 Program Evaluation – Adaptive Management ................................................................... 4-1

4.1 Introduction .................................................................................................................................. 4-1

4.2 Adaptive Management Framework .............................................................................................. 4-1

4.2.1 Related Adaptive Management Programs ........................................................................ 4-3

4.3 Information Needs for Winter-Run Chinook Reintroduction Plan ............................................... 4-8

4.3.1 Monitoring to Evaluate Reintroduction Strategies ........................................................... 4-9

4.3.2 Monitoring Natural Production to Evaluate Progress ..................................................... 4-16

4.3.3 Phase Monitoring ............................................................................................................ 4-23

4.4 Oversight and Decision Making .................................................................................................. 4-26

Chapter 5 Facility Needs and Program Costs ..................................................................................... 5-1

5.1 Overview of Facility Needs to Implement the Reintroduction Plan ............................................. 5-1

5.1.1 Broodstock Facility Details ................................................................................................ 5-2

5.1.2 Fish Culture Facility Details................................................................................................ 5-2

5.1.3 Transplant Fry Facility Details ............................................................................................ 5-4

5.2 Approximate Costs to Implement the Reintroduction Plan ......................................................... 5-4

5.2.1 Cost Estimate for Facility Planning, Design, and Environmental Compliance ................... 5-4

5.2.2 Cost Estimate for Facility Construction ............................................................................. 5-5

5.2.3 Cost Estimate for Fish Culture ........................................................................................... 5-5

5.2.4 Cost Estimate for Additional Facilities ............................................................................... 5-6

5.2.5 Cost Estimate for Monitoring Reintroduction Strategies .................................................. 5-6

5.2.6 Combined Cost Estimate ................................................................................................... 5-6

Chapter 6 References ...................................................................................................................... 6-1

6.1 Printed References ........................................................................................................................ 6-1

6.2 Personal Communications ............................................................................................................ 6-8

Appendix A Battle Creek Winter-Run Chinook Salmon Reintroduction Plan Interagency

Technical Advisory Committee Participants

Appendix B Habitat Suitability of Battle Creek for Winter-Run Chinook Salmon

Appendix C Battle Creek Winter-Run Chinook Salmon Reintroduction Plan Scenarios iii

List of Tables

Table 1. Estimated Maximum Number of Winter-Run Chinook Salmon Spawners That

Could Be Supported in Battle Creek ....................................................................................... 2-5

Table 2. Planned Program Broodstock Collection and Juvenile Release – Phase 1 ........................... 3-16

Table 3. Observed Post-Release Survival Rates for LSNFH Winter-Run Chinook Salmon ................. 3-17

Table 4. Sacramento River Winter-Run Chinook Salmon Estimated Run Size by Origin and

Number of Adults Counted at Keswick Dam Fish Trap ........................................................ 3-18

Table 5. Planned Program Broodstock Collection and Juvenile Release – Phase 2 ........................... 3-22

Table 6. Adaptive Management Objectives in the Battle Creek Restoration Project

Adaptive Management Plan ................................................................................................... 4-5

Table 7. Hypothesis Testing for Population Objectives in the Battle Creek Restoration

Project Adaptive Management Plan ...................................................................................... 4-6

Table 8. Expected Average Outcomes for Each Phase of Reintroduction and Run Triggers for Phase Transitions ............................................................................................................ 4-10

Table 9. Key Hatchery Production and Translocation Monitoring Elements ..................................... 4-11

Table 10. Key Hatchery Production Performance Indicators ............................................................... 4-14

Table 11. Key Natural Production Monitoring Elements ..................................................................... 4-19

Table 12. Key Natural Production Performance Indicators ................................................................. 4-22

Table 13. Summary of Facilities ............................................................................................................. 5-2

Table 14. Conceptual Requirements for NF Battle Creek Fish Culture Facility ...................................... 5-3

Table 15. Combined Estimated Costs for Implementing the Reintroduction Plan ................................ 5-7 iv

List of Figures

Figure 1. Geographic Area and Relevant Facilities ........................................................... follows page 1-2

Figure 2. Estimated Escapement of Winter-Run Chinook Salmon in the Sacramento River ................ 1-3

Figure 3. Phases of the Battle Creek Winter-Run Chinook Salmon Reintroduction Plan...................... 1-9

Figure 4. Framework for Consideration of Contingent Actions ..................................... follows page 2-14

Figure 5. Natural-Origin Triggers ...................................................................................... follows page 3-4

Figure 6. Reintroduction: Phase 1 Initial Actions ........................................................... follows page 3-14

Figure 7. Reintroduction: Phase 1 Late Actions ............................................................ follows page 3-14

Figure 8. Reintroduction: Phase 2 Actions ..................................................................... follows page 3-20

Figure 9. Reintroduction: Phase 3 Actions ..................................................................... follows page 3-24

Figure 10. Adaptive Management Process.............................................................................................. 4-2 v

List of Acronyms and Abbreviations

Advisory Committee interagency technical advisory committee

ACID Anderson-Cottonwood Irrigation Dam

AMP Adaptive Management Plan

AMPT Adaptive Management Policy Team

AMTT Adaptive Management Technical Team

BCRP Battle Creek Salmon and Steelhead Restoration Project

BCRP AMP Battle Creek Salmon and Steelhead Restoration Project Adaptive Management Plan

CDFW

CESA

California Department of Fish and Wildlife

California Endangered Species Act

CFR Code of Federal Regulations

CNFH Coleman National Fish Hatchery

CNFH AMP Coleman National Fish Hatchery Adaptive Management Plan

Coleman weir barrier weir at Coleman National Fish Hatchery

CTWS Confederated Tribes of the Warm Spring Reservation of Oregon

CWT coded wire tag

Delta Sacramento-San Joaquin River Delta

ESA federal Endangered Species Act

ESU evolutionarily significant unit

FGP full genetic parentage

HGMP Hatchery and Genetics Management Plan

ICF ICF International

LSNFH Livingston Stone National Fish Hatchery

LSNFH HGMP Livingston Stone National Fish Hatchery – Hatchery and Genetics Management Plan

MOU memorandum of understanding

Ne Effective population size: defined as an ideal population that would have the same rate of genetic change as a natural population under consideration

NF Battle Creek North Fork Battle Creek

NMFS National Marine Fisheries Service vi

NMFS Recovery Plan Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter-Run Chinook Salmon and Central Valley Spring-Run Chinook Salmon, and the Distinct Population Segment of California Central Valley Steelhead

ODFW Oregon Department of Fish and Wildlife

PG&E Pacific Gas and Electric Company pHOS contribution of hatchery spawners in nature

PIT tag passive integrated transponder tag

PNI proportionate natural influence

RBDD Red Bluff Diversion Dam

Reintroduction Plan Battle Creek Winter-Run Chinook Salmon Reintroduction Plan

RM river mile

RM&E research, monitoring, and evaluation

SAR smolt-to-adult return

SCARF San Joaquin Conservation and Research Facility

SF Battle Creek South Fork Battle Creek

SJRRP San Joaquin River Restoration Program

TCD temperature control device

TRT Central Valley Technical Recovery Team

USBR U.S. Bureau of Reclamation

USFWS U.S. Fish and Wildlife Service

VSP Viable Salmonid Population

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Chapter 1 Introduction and Goals

1.1 Introduction

Expanding the spatial structure of the winter-run Chinook Salmon (Oncorhynchus tshawytscha)

Evolutionarily Significant Unit (ESU) into vacant but historically occupied habitat is a high-priority action identified by the National Marine Fisheries Service (NMFS) in its recovery plan for threatened and endangered salmonids in the California Central Valley (NMFS 2014a). The restoration of Battle

Creek pursuant to a memorandum of understanding (MOU) between several federal and state agencies and Pacific Gas & Electric Company (PG&E) presents an opportunity to implement an important recovery action for winter-run Chinook Salmon in Battle Creek.

The California Department of Fish and Wildlife (CDFW) contracted with ICF International (ICF) to work with an interagency technical advisory committee (Advisory Committee, Appendix A) to develop a Battle Creek Winter-Run Chinook Salmon Reintroduction Plan (Reintroduction Plan). The

Advisory Committee comprised representation from CDFW, U.S. Fish and Wildlife Service (USFWS), U.S. Bureau of Reclamation (USBR), NMFS, PG&E, and the Battle Creek Watershed Conservancy. This group, along with the ICF team, is referred to in this plan as the “workgroup.”

The workgroup built upon the considerable work of a prior interagency effort involving the same entities. The prior team developed much of the background information and analyzed several options for reintroduction, but did not have the time or resources to finish a plan. The workgroup is thankful for their contribution to this effort.

At the time of drafting this plan, an implementing agency had not been identified to carry out the plan. Consequently, some of the content is less precise than it otherwise might have been. For example, we were unable to specify a location and precise design for alternative collection sites or facilities for producing and growing winter-run Chinook Salmon in Battle Creek.

The geographic areas referred to in this plan and the existing facilities important to implementation of the plan are shown in Figure 1.

1.2 Purpose and Content of This Reintroduction Plan

The purpose of the Reintroduction Plan is to describe the issues, considerations, and steps necessary to reestablish a population of Sacramento River winter-run Chinook Salmon in North Fork Battle

Creek (NF Battle Creek), which will contribute to the recovery of the Sacramento River winter-run

Chinook Salmon (NMFS 2014a).

The NMFS recovery strategy for California’s Central Valley salmon and steelhead is to secure existing populations and reintroduce salmon to historically occupied or suitable habitats (NMFS

2014a). Specifically for winter-run Chinook Salmon, the strategy calls for the establishment of three populations at low risk of extinction. Battle Creek presents a reasonable option for reestablishment of an independent population because the Battle Creek Salmon and Steelhead Restoration Project

(BCRP) (USBR 2008) is expected to restore unencumbered access to quality spring-fed spawning

1-2 habitat in NF Battle Creek by 2017.1 This document describes the process for reintroducing winter-run Chinook Salmon to its historical spawning and rearing habitat in NF Battle Creek, assuming successful implementation of the BCRP.

1.3 Historical and Present Status

The winter-run Chinook Salmon ESU is uniquely adapted to the basalt and porous lava geology of the upper Sacramento River Basin (Lindley et al. 2004). It is the only Chinook Salmon ESU that exhibits aspects of both stream-type and ocean-type life histories (Healy 1991).2 Winter-run

Chinook Salmon begin their migration from the ocean to their spawning grounds in late fall and winter. They leave the ocean in an immature condition (i.e., gametes are not sufficiently ripe for spawning) and migrate to coldwater habitats where they hold while their eggs mature (a stream-type strategy). Spawning occurs during late spring and summer months when air temperatures usually approach their yearly maxima. Juveniles rear in the river and Sacramento-San Joaquin River

Delta (Delta) from summer into fall and winter, and migrate to sea in late winter and spring (ocean-type strategy) before water temperatures in the mainstem Sacramento River become too warm.

Historically, these spawning and rearing habitats were found in the Little Sacramento, McCloud, and

Pit Rivers and in Battle Creek (Yoshiyama et al. 1998), which are fed by glacial and snow melt from the flanks of Mt. Shasta and Mt. Lassen.

Winter-run Chinook Salmon are the only salmon ESU on the West Coast that has been entirely dislocated from its historical spawning and rearing habitat (Myers et al. 1998). Winter-run Chinook

Salmon were excluded from their spawning and rearing habitat in Battle Creek in the early 1900s, in large part by hydroelectric development, and they were excluded from the remainder of their spawning and rearing habitat in the upper Sacramento River Basin by construction of Shasta and

Keswick Dams in the 1940s (Reynolds et al. 1993).

Winter-run Chinook Salmon persist in the Sacramento River as a single population in habitat artificially maintained by the release of cold water from Shasta Dam on the upper Sacramento

River.3 This persistence is precarious, however, because limited supplies of cold water in Shasta

Reservoir are sometimes insufficient to meet the needs of winter-run Chinook Salmon in critically dry or consecutively dry years (Reynolds et al. 1993; NMFS 2014a).

Releases of cold water from Shasta Reservoir created cold-water habitat downstream of Keswick

Dam in a portion of the river that previously would have warmed to lethal temperatures (CDWR

1988) for incubating salmon eggs and fry during summer and early fall. For a period of time in the mid-1960s, prior to the construction of Red Bluff Diversion Dam (RBDD), winter-run Chinook

Salmon thrived in this modified habitat.

1 Available at: http://www.usbr.gov/mp/battlecreek/status.html.

2 Spring run-Chinook adults also enter the Sacrament River in an immature condition and hold in cool springs and pools until spawning in late summer and fall. Some juveniles, particularly those spawned in lower elevation streams such as Butte Creek, outmigrate as young of the year (ocean type). Others remain and outmigrate as yearlings (stream type) (CDFG 2004).

3 For purposes of this document, the upper Sacramento River is defined as the reach between RBDD and Shasta Dam.

http://www.usbr.gov/mp/battlecreek/status.html

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Following construction of RBDD, the population began to decline. Although RBDD was constructed with fish passage facilities, the dam impeded passage and contributed to adults spawning downstream of the structure (Hallock et al. 1982). Spawning downstream of RBDD tends to be unsuccessful because that reach of the river is beyond the influence of the cold water released from

Shasta Reservoir, and water temperatures above 56°F result in increased egg mortality (Gains and

Martin 2002). RBDD also was a source of mortality for downstream migrant juveniles that were spawned above the dam. Turbulence created when the dam’s gates were lowered into the river disoriented juvenile outmigrants, making them easy prey for predatory fish such as the Sacramento pikeminnow (Ptychocheilus grandis) that concentrated below the dam (Vogel and Marine 1991).

Following closure of the dam gates in 1966, the year classes that were at sea returned strong, and then the population began a steady decline (Figure 2) attributable to the cumulative effects of habitat loss, fishing pressures, entrainment, and the added effects of the new barrier. (Myers et al.

1998). This decline ultimately led to their listing under the California Endangered Species Act

(CESA) and federal Endangered Species Acts (ESA) in 1989 (NMFS 1989).

Figure 2 Estimated Escapement of Winter-Run Chinook Salmon in the Sacramento River

(Source: CDFW GrandTab 2015)

20,000

40,000

60,000

80,000

100,000

120,000

140,000

A d u lt

S p aw n er s

Year

Winter-Run Chinook Escapement 1967–2014

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In 1989, USFWS initiated a hatchery supplementation program at Coleman National Fish Hatchery

(CNFH) on Battle Creek to supplement the declining winter-run Chinook Salmon population in the

Sacramento River. The program captured natural-origin spawners, spawned them in the hatchery, and reared them to pre-smolt stage for release on the spawning grounds in the Sacramento River.

The expectation of the program was that adult returns from these releases would return to spawn in the Sacramento River; however, many of the adults returned instead to Battle Creek (Hedrick et al.

2000). In 1998, the supplementation program was transferred to the Livingston Stone National Fish

Hatchery (LSNFH), a new hatchery facility at the foot of Shasta Dam on the Sacramento River. The program in this new location has been successful in returning spawners to the Sacramento River and contributing to the persistence of the population (NMFS 2014a).

In 1992, a captive broodstock program was initiated at Bodega Bay Marine Laboratory, University of

California, and at Steinhart Aquarium, California Academy of Sciences, out of concern for the continued existence of the stock following the sever decline in 1989. This program was worked collaboratively with the winter-run Chinook Salmon supplementation program at CNFH and then at

LSNFH by providing gametes for fertilization with wild winter-run Chinook Salmon collected for the supplementation program (Arkush et al. 1996). The captive broodstock program ended in 2004 based on signs that the population was recovering (Figure 2). In 2014, the captive broodstock program was revived at LSHFH due to concerns about low population levels and adverse temperature effects related to persistent drought conditions (Interagency Fish Passage Steering

Committee 2015).

USBR also has contributed to the conservation of winter-run Chinook by enhancing its ability to manage and provide cold water to maintain spawning and rearing habitat below Keswick Dam. It installed a temperature control device (TCD) at Shasta Dam in 1997, with a low-level intake structure and a series of gates to access cold water from various depths, and it sequentially modified operations at RBDD to improve passage, culminating in construction of a new diversion facility and permanent suspension of the dam gate operations in 2012.4 These actions, in combination with other conservation measures (e.g., reduction in ocean harvest, installation of fish screens at water diversions, constraints on Delta operations, and a supplementation program), led to a period of higher returns between 2001 and 2006 (NMFS 2010). In 2007, however, returns faltered, likely due to poor ocean conditions (NMFS 2010), and have remained low to date (Figure 2).

Even with a TCD to assist in management of the coldwater pool in Shasta Reservoir, the ability to influence temperatures in the Sacramento River is limited by water supply and ambient air temperature. In years of abundant snow pack and cool weather conditions, spawning habitat may be available as far downstream as RBDD. In low water years or years with hotter ambient air temperatures, spawning habitat may be extremely limited, as evidenced by the near reproductive failure of the 1976 and 1977 brood years (Nehlsen et al. 1991).

The winter-run Chinook Salmon ESU remains a single population, persisting in a high-risk, artificially maintained environment entirely, dependent on the availability of cold water in Shasta

Reservoir and USBR’s ability to manage and deliver it. This makes the ESU extremely vulnerable to catastrophic events (i.e., drought) and climate change (NMFS 2014a). The ongoing drought (2010–

2016) has depleted reservoir storage, and the USBR is again challenged with lack of coldwater

4 The Fish Passage Improvement Project at the Red Bluff Diversion Dam: http://www.tccanal.com/RBDD-Bro- Sept2012-NoCrop.pdf.

http://www.tccanal.com/RBDD-Bro-Sept2012-NoCrop.pdf http://www.tccanal.com/RBDD-Bro-Sept2012-NoCrop.pdf

1-5 reserves. In 2014, the winter-run Chinook Salmon egg-to-fry survival was exceptionally low as a result of depletion of cold water reserves that increased water temperatures in the spawning areas

(USBR 2015). In 2015, the California State Water Resources Control Board (SWRCB 2015) approved a change in operations to retain water in Shasta Reservoir for summer temperature control. This situation is consistent with climate change models, which predict more frequent and prolonged droughts creating increasing challenges for management of the coldwater pool in Shasta Reservoir and adverse effects—particularly for winter and spring-runs of Chinook Salmon—as average atmospheric temperatures warm by 2°C or more (Yates et al. 2008). These conditions also emphasize the importance of increasing the spatial distribution of the winter-run ESU for long-term viability by establishing additional populations in secure locations within its historical range

(e.g., NF Battle Creek).

1.4 Battle Creek Restoration Program – History, Current Status, and Future Direction

Reestablishing winter-run Chinook Salmon in Battle Creek has been under consideration for some time (see timeline in USBR 2008).The U.S. Bureau of Sportfish and Wildlife (1962, as cited in Kier

Associates 1999) recognized the unique environmental conditions in Battle Creek and proposed that natural streamflow be restored to meet the needs of winter- and spring-run Chinook Salmon.

However, the hydropower system within Battle Creek was an impediment to restoration due to blockages, depletion of flows, and conveyance of water from NF Battle Creek to South Fork Battle

Creek (SF Battle Creek). In 1999, PG&E, the owner and operator of the hydropower facilities in

Battle Creek; NMFS; USBR; USFWS; and the California Department of Fish and Game (now the

California Department of Fish and Wildlife ) entered into an MOU to facilitate development of the

BCRP.

Following signing of the MOU, the signatories formed the Greater Battle Creek Watershed Working

Group and, in cooperation with the Battle Creek Watershed Conservancy, undertook a period of investigation, project design, and environmental review. In 2008, USBR published a record of decision, identifying the preferred alternative for the restoration program to be implemented cooperatively by the signatories to the MOU and other interested parties. When completed, the

BCRP will provide passage either by removing facilities or providing passage over manmade and natural barriers in the system, augmenting flows within the North and South Forks of Battle Creek, and disconnecting the conveyance of water from the North Fork to the South Fork of Battle Creek.

Upon completion of the project, access to approximately 48 miles of spawning and rearing habitat is expected to be restored in the Battle Creek watershed for the assemblage of salmonids5 that inhabited Battle Creek historically. Twenty-five miles of this habitat will be in the North Fork, of which 10 to 12 miles is expected to be suitable for winter-run Chinook Salmon spawning and incubation of winter-run Chinook Salmon eggs.6

Implementation of the BCRP was divided into three phases. Phase 1A, focuses on actions in NF Battle

Creek, where cold spring-fed habitat most suitable for winter-run likely exists year round. Phases 1B

5 Historically, four runs of salmon (fall, late-fall, winter, and spring-runs) and steelhead trout occurred in Battle Creek.

6 See Normandeau Associates report (Appendix B).

1-6 and 2 focus on SF Battle Creek, where spring-run and steelhead are likely to be the beneficiaries.

Phase 1A is nearing completion, and final construction is expected to be completed by the end of

2017 (USBR, http://www.usbr.gov/mp/battlecreek/status.html). Completion of Phase 1A is essential to ensuring that winter-run Chinook Salmon have access to the quality spawning and rearing habitat expected to exist in the reaches above Eagle Canyon and North Battle Creek Feeder

Diversion Dams.

The Reintroduction Plan described in this document is an outgrowth of the BCRP and is a key action in the NMFS Recovery Plan for the Evolutionarily Significant Units of Sacrament River Winter-Run

Chinook Salmon and Central Valley Spring-Run Chinook Salmon, and the Distinct Population Segment of California Central Valley Steelhead (NMFS Recovery Plan) (NMFS 2014a). Reintroduction of winter-run Chinook Salmon into NF Battle Creek is part of a larger strategy in the NMFS Recovery

Plan to restore some of the spatial structure of the ESU by reintroducing populations to habitats from which they have been extirpated.

1.5 Reintroduction Goals

NMFS has determined that a primary threat to the continued existence of winter-run Chinook

Salmon is that the current naturally spawning component of the ESU consists of a single population in the mainstem Sacramento River, whose existence depends on the release of cold water from

Shasta Reservoir (NMFS 2014a). As noted, the ESU is extremely vulnerable to catastrophic events that could lead to its extinction. Establishment of a separate, independent population of winter-run

Chinook Salmon in Battle Creek is a goal of the BCRP and a key component of the NMFS Recovery

Plan for the Evolutionarily Significant Units of Sacramento River Winter-Run Chinook Salmon and

Central Valley Spring-Run Chinook Salmon and the Distinct Population Segment of California Central

Valley Steelhead (NMFS Recovery Plan) (NMFS 2014a). This Reintroduction Plan describes the process for establishing an independent population of winter-run Chinook Salmon in Battle Creek to address this threat by increasing the spatial diversity of the ESU and increasing its resiliency.

1.5.1 Assumptions

This Reintroduction Plan is confined to actions leading to establishment of a population of winter-run Chinook Salmon in NF Battle Creek. A first principle of the NMFS recovery strategy is that functioning, diverse, and interconnected habitats are necessary for species recovery (NMFS 2014a).

This Reintroduction Plan has been developed assuming that there is sufficient quantity and quality of habitat in NF Battle Creek to support a viable, independent, self-sustaining population of winter-run Chinook Salmon. It also assumes completion of the BCRP and implementation of its adaptive management plan (AMP) (Terraqua, Inc. 2004) to ensure that properly functioning habitat is available for a winter-run Chinook Salmon population.

The Reintroduction Plan assumes that supplementation will be necessary to speed the rate at which a population can be established in Battle Creek. The current rate of winter-run Chinook Salmon entering Battle Creek is small and variable (Brown and Newton 2002; Stafford and Newton 2010) and likely is insufficient to reestablish a natural run in a timely manner, given the vulnerability of the current population and ongoing environmental challenges. Consequently, natural straying is not included as a strategy in the plan for reestablishing a population of winter-run Chinook Salmon in

Battle Creek.

http://www.usbr.gov/mp/battlecreek/status.html

1-7

Successful reintroduction of winter-run Chinook Salmon in Battle Creek depends on conditions in the Sacramento River, the Delta, and the eastern Pacific Ocean. Actions to improve conditions in these areas are addressed in a myriad of biological opinions and permit actions and in a number of restoration programs, including the Central Valley Project Improvement Act – Anadromous Fish

Restoration Program, CDFW’s Ecosystem Restoration Program, and the NMFS Recovery Plan. This

Reintroduction Plan assumes that these actions will be successful in addressing limiting factors outside of Battle Creek so that winter-run Chinook Salmon spawned in NF Battle Creek can survive to live, grow, and return to NF Battle Creek as adults.

1.5.2 Vision and Goals for Reintroduction

The Reintroduction Plan is structured around a vision for the reintroduction program, a set of goals for each phase of the plan, and a number of measurable objectives that relate to specific decisions and steps in the reintroduction. The vision and goals for this plan were developed in consultation with the Advisory Committee. The vision describes the overall intent and desired endpoint for the plan with enough specificity to constrain the goals and objectives. It is a statement about the future that shapes actions in both the short and long term. Goals describe specific steps and strategies needed to achieve the vision. As discussed in subsequent chapters, the Reintroduction Plan is structured in three phases. Each phase has one or more goals that characterize strategies and conditions. Objectives provide specific, measurable conditions that are tied to key decisions in the

Reintroduction Plan. Objectives relate to decisions in the Reintroduction Plan and provide the criteria for moving from one phase of reintroduction to another. For example, a goal for the first phase of reintroduction is to establish a return of winter-run Chinook Salmon to NF Battle Creek from releases of juvenile fish in the stream. A set of objectives would define a return goal in terms of numbers of adult fish over a time period.

Thus, the Reintroduction Plan has one overall vision, several goals, and numerous objectives—with an increasing level of quantitative specificity moving from vision to goals to objectives. This section describes the overall vision and goals that characterize each phase of reintroduction. Additional goals and all objectives are described in Chapters 2 and 3.

1.5.2.1 Vision

The vision for the Reintroduction Plan is as follows.

Establish a viable, self-sustaining and locally adapted population of winter-run Chinook Salmon in

Battle Creek that adds to the spatial diversity and abundance of the Sacramento River winter-run

Chinook Salmon ESU.

A viable population of winter-run Chinook Salmon is defined by the criteria of the Viable Salmonid

Population (VSP) concept used by NMFS to evaluate populations under the ESA (McElhany et al.

2000). The VSP concept assesses the status of populations in terms of abundance, productivity, biological diversity, and spatial structure. McElhany et al. (2000) define a viable salmonid population to be one “with a low extinction risk in the wild over time.” The Central Valley Technical

Recovery Team (TRT)(Lindley et al. 2007) provided specific criteria for viability that are incorporated into the NMFS Recovery Plan (e.g., <5 percent chance of extinction within 100 years).

Lindley et al. (2007) also discuss guidelines for a minimum spawning population size for population viability based on demographic and genetic considerations.

1-8

A self-sustaining population is one that reproduces naturally in the environment with sufficient productivity and abundance to maintain a viable population without intervention from outside production, including hatcheries. However, this aspect of the vision does not preclude the use of artificial production, especially during the initial phases of reintroduction or as a future contingency measure. The Reintroduction Plan does envision a reduction in, and eventual elimination of, the use and influence of artificial production over time.

A locally adapted population is one that has been shaped by natural selection to be adapted to the characteristics of a specific environment—in this case, Battle Creek. Because selection operates at a genetic level, a locally adapted population will have some degree of reproductive isolation and genetic divergence from similar populations of the same species in other environments. Hence, a self-sustaining winter-run Chinook population in Battle Creek would be expected to diverge from the mainstem Sacramento River population due to selection and reproductive isolation of the Battle

Creek population. However, the proximity of the Sacramento River and Battle Creek populations creates the likelihood that the two populations will be part of a meta-population with some degree of genetic exchange as the two populations act as sources and sinks, depending on relative productivity and abundance.

Spatial diversity and abundance are metrics of the VSP concept that apply to the Sacramento River winter-run Chinook Salmon ESU as a whole. The TRT (Lindley et al. 2007) has developed extinction risk criteria for listed salmon populations that are incorporated into the NMFS Recovery Plan. The rationale behind establishing a new population of winter-run Chinook Salmon in Battle Creek is to contribute to the viability of the ESU by increasing abundance, diversity, and spatial structure, which reduces risk from local events (e.g., a toxic spill, or loss of a cold-water pool) (NMFS 2014a).

1.5.2.2 Goals

The Reintroduction Plan is structured around a sequence of three phases of actions that lead to achievement of the vision articulated above. The contribution from artificial production is reduced over time in each phase, ultimately resulting in a self-sustaining population of winter-run Chinook

Salmon. This section describes the goals that characterize the strategies and intent of each phase.

Additional goals for each phase may be developed during implementation of the plan.

The three phases of reintroduction describe an ideal temporal sequence of actions. However, it is important to stress that the delineation between phases is not stark. Instead, the phases describe a continuum of actions, which may be punctuated by dramatic changes. Nor is reintroduction expected to be uni-directional across the three phases. It is entirely possible that environmental conditions, climate change, or other factors may “re-set” the continuum and require the reintroduction process to revert back to strategies more characteristic of a past phase. For example, it is possible that at some point in the future, catastrophic events or novel conditions, such as a prolonged drought, may require artificial production using locally adapted wild broodstock to stave off loss of the population. Such emergency measures do not negate the intent of the Reintroduction

Plan to reduce the use of artificial production over time and achieve a self-sustaining population of winter-run Chinook Salmon in Battle Creek.

A general schematic of the three phases of reintroduction is shown in Figure 3. Phase 1 of reintroduction will establish a return of winter-run Chinook Salmon into Battle Creek with sufficient abundance to overcome founder effects and provide a basis for development of a self-sustaining, genetically diverse, and locally adapted population. Phase 1 will use a mix of artificial production

1-9 and translocation of wild juveniles to build up population abundance based on the donor population.

Phase 2 of reintroduction will develop a viable, self-sustaining and locally adapted population of winter-run Chinook Salmon in Battle Creek by reducing transfers from the donor population

(creating a self-contained Battle Creek population) and reducing the use of artificial production.

Hatchery production would be eliminated in Phase 3, and the focus would shift to management for long-term sustainability of the Battle Creek population, including monitoring to assess population productivity and health. Battle Creek has a relatively small expanse of habitat suitable for winter-run Chinook Salmon,7 which will limit the capacity and maximum abundance of the winter-run

Chinook Salmon population. This will make the population vulnerable to demographic constraints and catastrophic events, reinforcing the need for continual monitoring and management efforts.

Figure 3

Phases of the Battle Creek Winter-Run Chinook Salmon Reintroduction Plan

Goals describe the condition at the end of each phase; achievement of the goals marks the transition between phases.

Phase 1 Goal

Establish a population of winter-run Chinook Salmon in Battle Creek that meets abundance objectives, retains the genetic diversity of the Sacramento River population, and includes a substantial proportion of natural-origin fish.

The goal of Phase 1 is to establish a return of winter-run Chinook Salmon to Battle Creek that can serve as the basis for establishment of a Battle Creek population. The abundance objectives are intended to establish sufficient abundance to overcome founder effects and provide the basis for development of a genetically diverse, self-sustaining population in Phase 2. The “substantial

7 Ibid.

1-10 proportion of natural-origin fish” phrase reflects the need for natural-origin fish to begin the process of recolonization, including setting the stage for development of local adaptation in Phase 2. It is necessarily qualitative, recognizing that during Phase 1, the number of natural-spawning winter-run

Chinook Salmon in Battle Creek will range from zero to approximately 500 fish (Section 3.3.1). The

TRT (Lindley et al. 2007) and the NMFS Recovery Plan (NMFS 2014a) provide abundance objectives that are appropriate to this goal. The expectation is that artificial production to support the Battle

Creek winter-run Chinook Salmon reintroduction will be initiated from broodstock derived from the mainstem Sacramento River population and spawned at LSNFH. Artificial production to meet abundance objectives in Phase 1 will be based on contribution from the donor population.

Phase 2 Goal

Establish a self-sustaining, locally adapted population of winter-run Chinook Salmon in Battle

Creek by encouraging local adaptation of the Battle Creek population, phasing out the contribution of artificial production, and eliminating the genetic contribution from the Sacramento River population into the artificial production program.

The goal of Phase 2 is to promote development of a locally adapted population. Phase 2 is characterized by elimination of the contribution of brood stock from outside Battle Creek and development of a distinct, locally adapted population of winter-run Chinook Salmon in Battle Creek.

The contribution of artificial production in general would be reduced throughout Phase 2, leading to development of a self-sustaining population of winter-run Chinook Salmon in Battle Creek.

Phase 3 Goal

Monitor the viability of the Battle Creek population and respond to concerns set by ESA recovery needs.

The focus of Phase 3 is the long-term management of the restored Battle Creek winter-run Chinook

Salmon population. In Phase 3, the vision of a viable, self-sustaining, and locally adapted population should be maintained through active management of the population and habitat, and monitoring of population abundance and productivity. As noted above, the limited extent of habitat in Battle Creek will likely result in a population with relatively low abundance and high vulnerability to catastrophic events or downturns in environmental conditions (e.g., more frequent and prolonged droughts). This vulnerability warrants continued monitoring and adaptive management to maintain the new population, which will contribute to meeting recovery criteria established under both the

ESA and CESA.

2-1

Chapter 2 Background

2.1 Biological Setting

2.1.1 Overview of Fish Species in Battle Creek

Seventeen resident and anadromous fish species are known to occur in Battle Creek, four of which are introduced species (USBR 2005). Limited studies indicate that each of the Chinook Salmon runs in Battle Creek exhibit life history patterns and run timing similar to those derived from the studies at RBDD (CH2M Hill 1999). The actual timing of runs throughout the Sacramento River and its tributaries varies slightly from year to year as a function of weather, streamflow, and water temperature (Vogel and Marine 1991).

The distribution and abundance of resident fish in Battle Creek were examined in detail in 1989

(Thomas R. Payne and Associates 1998). Unlike anadromous species, the resident species in Battle

Creek spend their entire lives in fresh water. Resident species include native and nonnative fishes.

The assemblage of resident native fish that evolved in streams like Battle Creek transitions from warmwater species that occupy warmer, low-velocity reaches of the lower to mid-elevations to coldwater species that use colder, higher velocity reaches of the mid- to high elevations (Moyle and

Cech 1988). Warmwater species such as non-native striped bass (Morone saxatilis), introduced centrachids (bass and sunfish), and native cyprinids (minnows) typically prefer slow-moving, low-velocity stream reaches in the low elevations of Battle Creek. Recreationally important coldwater resident species, such as Brown Trout (Salmo trutta) and Rainbow Trout (Oncorhynchus mykiss) trout, generally prefer colder water and higher velocity water than warmwater fish; however, their occurrences overlap to varying degrees. The upper portions of Battle Creek and the hydroelectric project’s canal system are both acknowledged to support a sport fishery for rainbow and brown trout (Kier Associates 1999).

Fall and late-fall runs of Chinook Salmon are relatively abundant in lower Battle Creek owing to their production at CNFH. There is also an isolated anadromous Steelhead Trout (steelhead) hatchery program at CNFH that mitigates steelhead production lost from the construction of Shasta and Keswick Dams (see Section 4.2.1.3 for a discussion of the CNFH Adaptive Management Plan).

Natural-origin steelhead and spring-run and winter-run Chinook Salmon also occur in Battle Creek, but at much lower levels. Monitoring of adult Chinook Salmon passed through the CNFH barrier weir fish ladder into upper Battle Creek documents the passage of a few tens to several hundred spring-run Chinook; and since the winter-run Chinook Salmon hatchery supplementation program was transferred to LSNFH in 1997, escapement of winter-run Chinook Salmon to Battle Creek has varied between 0 and 6 adults (CDFW GrandTab 2015). Reports from screw trap monitoring in Battle

Creek for the period from 1998 to 20101 also indicate regular production of a small number of spring-run Chinook Salmon and an occasional occurrence of a few winter-run Chinook Salmon in upper Battle Creek above the CNFH weir. The screw trap monitoring program has documented the

1 Available at: http://www.fws.gov/sacramento/fisheries/CAMP-Program/Documents-Reports/fisheries_camp-program_documents-reports.htm.

http://www.fws.gov/sacramento/fisheries/CAMP-Program/Documents-Reports/fisheries_camp-program_documents-reports.htm http://www.fws.gov/sacramento/fisheries/CAMP-Program/Documents-Reports/fisheries_camp-program_documents-reports.htm

2-2 use of lower Battle Creek by juvenile winter-run Chinook, which are likely juveniles from the

Sacramento River rearing in lower Battle Creek. While the current number of winter-run Chinook

Salmon in Battle Creek is unknown, available evidence indicates that at least a few occasional winter-run Chinook Salmon stray into and spawn in Battle Creek. Thus, the current populations of winter-run Chinook Salmon appear to be severely depressed when compared to scant historical evidence (Brown and Newton 2002) and in need of supplementation to facilitate reestablishment of a viable population.

2.1.2 Battle Creek

Battle Creek enters the Sacramento River at River Mile (RM) 272 upstream of Red Bluff, California, and 30 miles downstream of Keswick Dam. Battle Creek includes the North and South Forks, which join to form the main stream channel at RM 17. The Battle Creek watershed encompasses about

357 square miles. NF Battle Creek, which is the focus of this Reintroduction Plan, has a watershed of

213 square miles, or about 60 percent of the Battle Creek watershed.

Ba…