Attachment_18-Final_USFWS_Winter-run_Chinook_Transition_Plan_v2.pdf

Reintroduction of

Winter-Run Chinook Salmon to Battle Creek

A plan to manage the Transition from the Jumpstart Project to the Winter-run Chinook Salmon Reintroduction Plan

Developed by:

U.S. Fish and Wildlife Service

Red Bluff Fish and Wildlife Office

Red Bluff, California

April 2020 ii

The U.S. Fish and Wildlife Service developed this document. The Battle Creek Winter-run

Chinook Salmon Reintroduction Technical Team (Technical Team) contributed to this document through discussions of the development of management options, consensus recommendations, and editorial review of a draft report.

Citation:

U.S. Fish and Wildlife Service. 2020. Reintroduction of Winter-Run Chinook Salmon to Battle

Creek: A plan to manage the Transition from the Jumpstart Project to the Winter-run Chinook

Salmon Reintroduction Plan. USFWS Report. Red Bluff Fish and Wildlife Office, Red Bluff, CA.

iii

Table of Contents

List of Tables ................................................................................................................................. iv

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

List of Appendices ......................................................................................................................... iv

Chapter 1. Background, Current Status, and a Need for a Transition Plan

1.1 Purpose and Content of This Transition Plan

1.2 Background

1.3 Essential Planning Documents

1.4 Recent Management Actions Affecting SRWCS Reintroduction

1.5 Initiation of the Formal Reintroduction Program

1.6 Need for a Transition Plan

Chapter 2. Management of Jumpstart Returns to Battle Creek

2.1 The Need for Flexibility and Adaptability

2.2 Management of Jumpstart SRWCS in 2019

2.3 Management Strategy Development

2.4 Management Strategies for Jumpstart SRWCS in 2020 and 2021

2.5 Evaluation of Potential Management Strategies

2.6 Recommended Strategy

Chapter 3. Strategy Implementation

3.1 Priorities

3.2 Implementation of Recommended Strategy

3.3. Monitoring

3.4 Staffing Plan and Funding

Chapter 4. Future Considerations and Adaptive Management

4.1 Adaptive Management

4.2 Adaptive Management Associated with Management of the Reintroduction of SRWCS to

Battle Creek

4.3 Uncertainties in Future Actions

4.4 Current Management Controls

4.5 Management Recommendation

References

Appendices iv

List of Tables

Table 2.1. Management Priorities and Implementation Constraints used for evaluating alternative management strategies

Table 2.2. Interpretation of color-coded rankings assigned to indicate the performance of each alternative Management Strategy relative to each of the five Implementation Constraints

Table 3.1. Summary of Jumpstart broodstock for Brood Years (BY) 2017–2019

Table 3.2. Spawning targets for feral SRWCS returns to Battle Creek and captive broodstock at

Livingston Stone National Fish Hatchery

Table 3.3. Tissue sample locations of Jumpstart Sacramento River winter-run Chinook Salmon based on planned disposition

Table 3.4. Semi-monthly targets for collecting Jumpstart Sacramento River winter-run Chinook

Salmon from Battle Creek for use as hatchery broodstock

Table 3.5. Resources of funds and staffing to implement hatchery operations, monitoring projects, and upgrade infrastructure associated with Management Strategy 7 for 2020 through

2024. A 3% increase was added to each year for actions or activities that include salary

List of Figures

Figure 2.1. Matrix of rankings for alternative management strategies considered for Jumpstart

Sacramento River winter-run Chinook Salmon returning to Battle Creek during the 2020 and

2021 spawning seasons

Figure 4.1. Diagram of the decision-making structure to support the coordinated implementation of the CNFH-AMP and BCRP-AMP (from Cramer Fish Sciences 2016)

List of Appendices

Appendix 1. All the monitoring and diagnostic studies that were incorporated into the Battle

Creek Salmon and Steelhead Restoration Adaptive Management Plan (BCRP-AMP) denoting the tasks that were acknowledged in the Coleman National Fish Hatchery Adaptive Management

Plan (CNFH-AMP) or the Battle Creek Winter-Run Reintroduction Plan (BC Reintro Plan).

Additional studies that were suggested in either the CNFH-AMP or BC Reintro Plan that were not included in the BCRP-AMP are also listed

Appendix 2. List of participants and their affiliation, for the Battle Creek winter-run

Reintroduction Technical Team

Appendix 3. Description of 2019 adult collection efforts at Coleman National Fish Hatchery.. 78

Chapter 1

Background, Current Status, and Need for a Transition Plan

1.1 Purpose and Content of This Transition Plan

The primary purpose of this document is to describe a plan to manage Sacramento River Winter-run Chinook Salmon (SRWCS) Oncorhynchus tshawytscha in Battle Creek during the transition from the “Jumpstart Project” to the multi-phased reintroduction process, formally described in the Battle Creek Winter-Run Chinook Salmon Reintroduction Plan (hereafter referred as the

“Reintroduction Plan”; ICF International 2016). This Transition Plan includes the background information considered in developing the plan, describes and evaluates alternative management strategies considered in selecting a preferred strategy, describes an approach and the resources needed to implement the selected strategy, and recommends initiation of the adaptive management processes described in the essential planning documents that were developed in conjunction with the Battle Creek Salmon and Steelhead Restoration Project (BCRP).

1.2 Background

Sacramento River winter-run Chinook Salmon are listed as endangered under state and federal endangered species acts. Lack of spatial structure and diversity are principal threats to this

Evolutionary Significant Unit (ESU). Currently, SRWCS exist as a single population, which is restricted to spawn in the Sacramento River downstream of Shasta Dam – an area completely outside of the species’ geographical range of historic spawning. The persistence of SRWCS in the Sacramento River is completely dependent on receiving managed supplies of cold water from

Shasta Lake, leaving it extremely vulnerable to impacts from catastrophic events and climate change. A population of SRWCS that historically spawned in Battle Creek is extirpated; at least partially as a result of blocked access to spawning habitats and habitat alterations caused by hydropower development in Battle Creek dating back to the early 1900s. The recovery strategy developed by the National Marine Fisheries Service (NMFS) for Central Valley (CV) Chinook

Salmon and steelhead Oncorhynchus mykiss is “to secure all extant populations and to reintroduce populations into historic habitat such that each salmonid diversity group in the

Central Valley supports viable populations” (NMFS 2014). Thus, reintroduction of SRWCS to

Battle Creek is an important step to reducing the risk of extinction of the species.

A hydroelectric power generating system of dams, diversions, canals, and powerhouses, currently owned by Pacific Gas and Electric Company (PG&E), has operated in the Battle Creek watershed since approximately 1911. Operation of the Battle Creek Hydroelectric Project

(FERC Project No. 1121) has altered salmonid habitats because of blocked access, reduced instream flows, increased water temperature, and trans-basin water diversions. Restoration of anadromous fish habitats in Battle Creek is important to the conservation and recovery of three species of anadromous salmonids federally listed as threatened or endangered under the

Endangered Species Act (ESA), including SRWCS, CV spring-run Chinook Salmon (spring

Chinook), and CV steelhead.

Restoration actions and projects, planned or underway in Battle Creek, focus on restoring suitable habitats for these federally listed species. In 1999, a Memorandum of Understanding

(MOU) was established between the principle parties, including the National Marine Fisheries

Service, California Department of Fish and Wildlife (CDFW) (previously California Department

Fish and Game; CDFG), U.S. Fish and Wildlife Service (USFWS), United States Bureau of

Reclamation (USBR) and the Pacific Gas and Electric Company, herein referred to as MOU partners (NMFS et al. 1999). The MOU declared support in the restoration of Battle Creek through the development and implementation of the Battle Creek Salmon and Steelhead

Restoration Project; Ward and Kier 1999). The goal of the BCRP is to restore and enhance 42 miles of anadromous fish habitat in Battle Creek and six miles of habitat in its tributaries, while minimizing the loss of renewable energy. This goal will be achieved by implementing changes to the infrastructure and operations at PG&E hydropower facilities in Battle Creek, including the removal of five dams, constructing new fish ladders and screens at three dams, and increasing instream flows. Implementation of the BCRP will also eliminate or substantially reduce the release of water from North Fork Battle Creek into South Fork Battle Creek (i.e., trans-basin diversions), which affects the homing of anadromous fishes to preferred spawning habitats. The need for modifications to natural barriers, which restrict the migrations of anadromous fishes in

Battle Creek, was also recognized at the time the MOU was enacted; however, remediation of natural barriers was considered to be outside of the scope of the BCRP. Mitigation of passage impediments at natural barriers was subsequently included in the Adaptive Management Plan for the Battle Creek Salmon and Steelhead Restoration Project (BCRP-AMP; Terraqua 2004).

Habitat restoration actions identified in the BCRP were initially projected to be completed in

2004, but delays in the planning, designing, permitting, and construction have prolonged its completion. In an effort to start the construction portions of the project, the BCRP was implemented in three phases: Phase 1A, 1B, and 2. Phase 1A focused on the North Fork, and included an area considered optimal habitat for SRWCS (Ward and Kier 2001). Construction activities in Phase 1A included the removal of Wildcat Diversion Dam and its associated pipeline, installation of new fish screens and ladders at the North Fork Feeder Diversion Dam and Eagle Canyon Diversion Dam, and construction of a fish barrier on Baldwin Creek, a tributary to Battle Creek. Phase 1A construction activities were completed in 2013; however, the ladders and screens remain closed because additional work and testing were required to show the facilities were fail-safe before PG&E acceptance. Completion and acceptance by PG&E of

Phase 1A is anticipated in 2020. Phase 1B of the BCRP entails construction activities associated with the Inskip Powerhouse penstock bypass and tailrace connector, which directs mixed North

Fork and South Fork water directly into the Coleman Canal. Construction of the penstock bypass and tailrace connector has been completed and accepted. Currently the Inskip

Powerhouse is down indefinitely, so PG&E is only using the penstock bypass. The final phase of the BCRP construction activities, Phase 2, focus on the South Fork and its tributaries, including: installation of a fish screen and ladder at the Inskip Diversion Dam and removal of

Lower Ripley Creek Feeder Dam, Coleman Diversion Dam, Soap Creek Feeder Dam, and South

Diversion Dam. The most-recent revision of the BCRP schedule estimates a completion date of

January 2023 for Phase 2 construction actions (USBR 2019).

Around the time the MOU was enacted, it was recognized that the benefits envisioned to result from the BCRP would take some time to be fully realized, and that extant populations of ESA-listed spring Chinook and steelhead in Battle Creek were at immediate risk of extirpation due to insufficient stream flows downstream of hydropower diversions. Preservation of these native populations of ESA-listed salmonids was a high priority of the MOU partners. Through the

Central Valley Project Improvement Act Water Acquisition Program, water acquisitions were made from 1995–2001 to provide immediate benefits to fishes downstream of Eagle Canyon

Diversion Dam (North Fork Battle Creek) and Coleman Diversion Dam (South Fork Battle

Creek). Increased stream flows in Battle Creek were subsequently extended through an Interim

Flow Agreement between USBR and PG&E, which have been beneficial to sustaining extant populations of spring Chinook and steelhead in Battle Creek. However, natural colonization of

SRWCS has not occurred, and it was recognized that human intervention would be required to initiate a self-sustaining population. A formal plan for reintroducing SRWCS to Battle Creek

(ICF International 2016) has been developed but awaits funding and the completion of restoration actions for implementation.

1.3 Essential Planning Documents

Several key documents exist to guide management and restoration actions within the Battle

Creek watershed and provide the basis for managing the reintroduction of SRWCS with on-going and future actions within the watershed. This section provides a brief summary of the key documents and describes the interrelationship between these processes.

Battle Creek Salmon and Steelhead Restoration Plan The Battle Creek Salmon and Steelhead Restoration Plan (Restoration Plan; Ward and Kier

1999) developed prescriptions to restore self-sustaining populations of anadromous fishes upstream of Coleman National Fish Hatchery (CNFH) Barrier Weir, focusing on ESA listed populations of Chinook Salmon and steelhead. This plan synthesized results from a comprehensive study conducted for CDFW in the 1980s. The Restoration Plan indicates priority stream reaches for specific species, identifies factors of greatest concern for each specie in those reaches, and recommends streamflow and temperatures parameters required for success. The

Restoration Plan provided essential biological information, which is the foundation of the BCRP and the MOU. It was noted in the Restoration Plan that adaptive management would be a critical component in evaluating the success of the BCRP.

1999 Memorandum of Understanding The 1999 MOU (NMFS et al. 1999) is a legal document that memorializes the agreement between NMFS, USBR, USFWS, CDFW, and PG&E to implement the BCRP, as described in the Restoration Plan. This document outlines the roles and responsibilities of the signatories, describes the restoration actions of the BCRP, explains the required monitoring and reporting, establishes a dispute resolution process, and identifies the cost and implementation commitments. This document also provides the framework for adaptive management, which will monitor the effectiveness of restoration actions and, if required, make recommendations for further adjustments to the hydroelectric project facilities or operations.

The Battle Creek Salmon and Steelhead Restoration Project Adaptive

Management Plan The Battle Creek Salmon and Steelhead Restoration Project Adaptive Management Plan

(Terraqua 2004) guides the implementation of adaptive management provisions identified in the

MOU. The BCRP-AMP recognizes that uncertainties exist about the ecological responses of fish populations to the restoration actions prescribed in the BCRP, and ensures that a mechanism of monitoring and adaptation is established to modify those actions, as necessary to achieve long-term fish population goals in Battle Creek. Implementation of the BCRP-AMP will involve learning more about the system under management (i.e., address uncertainties) and making adjustments toward achieving the goals of the program (ICF International 2016). Several studies identified in the BCRP-AMP have been completed, including: a threshold flow assessment

(Newton and Brown 2008); a study of the Battle Creek fish community (Whitton et al. 2010);

North Fork Battle Creek geomorphic monitoring of the Wildcat Diversion Dam removal

(Graham Matthews & Associates 2012); and, thermal infrared and coldwater refugia studies

(Watershed Sciences 2011; QSI Environmental 2015).

The adaptive management objectives outlined in the BCRP-AMP focus on management of hydroelectric operations to facilitate habitat changes beneficial to salmon and steelhead. The

BCRP-AMP developed 11 objectives that are broken out by: (1) improvements to population dynamics, (2) improvements to the habitats, and, (3) improvements on passage for adult and juvenile salmonids. To determine if the objectives are met, the adaptive management approach follows a stepwise scientific process in which the objective is restated as a testable hypothesis.

A monitoring and data assessment approach is described to test these hypotheses, consistent with contemporary standard methods and reporting practices that are adopted by CALFED and

CDFW, NMFS, and USFWS (herein referred to as the Resource Agencies). Trigger events are described, indicating when an adaptive response should be taken; and end points are described, indicating when an objective has been attained. The BCRP-AMP acknowledges that not all events are predictable and unforeseen circumstances will arise. The plan includes several focused studies to address some uncertainties and provide learning opportunities; however, it is inherent within adaptive management that additional studies may be required.

As defined in the BCRP-AMP, the term of the plan was to begin when the FERC license amendment for the BCRP was granted, coincide with the implementation of restoration actions, and continue through the FERC license. This includes additional studies and monitoring

(Appendix 1). Until that time, restoration and monitoring activities currently underway or planned for Battle Creek are guided by the goals, objectives, and strategies developed by the

Anadromous Fish Restoration Plan (USFWS 2001). Monitoring activities for both juvenile and adult salmonids are conducted, including: monitoring of upstream passage at the CNFH Barrier

Weir; surveys of spawning success and adult distribution downstream of Eagle Canyon and

Coleman Diversions Dams; and, monitoring of juvenile emigration using a rotary screw trap located upstream of CNFH Barrier Weir (Bottaro and Earley 2019; Schraml and Earley 2019).

In addition to salmonid population monitoring, habitat assessments including, temperature and discharge measurements (Bottaro and Earley 2019), barrier passage assessments (Earley 2014), and sediment monitoring (Bottaro and Earley 2019) have occurred. These efforts are planned to continue until the BCRP-AMP is implemented, although the stream surveys are only funded through September 2020.

Coleman National Fish Hatchery Adaptive Management Plan To facilitate restoration of natural salmonid populations in Battle Creek, operations at the CNFH must be compatible with the BCRP; the Coleman National Fish Hatchery Adaptive Management

Plan (CNFH-AMP) was developed for this purpose. The CNFH-AMP provides an adaptive management framework to acknowledge, identify, study, and evaluate uncertainties regarding the operation of a large-scale fish hatchery located in a watershed that is also being restored for natural salmonid populations. The purpose of the CNFH-AMP is to provide the framework to develop solutions and processes to support the optimization of CNFH programs, operations, and infrastructure so that CNFH goals and objectives are achieved while maximizing the capability with the BCRP (Cramer Fish Sciences 2016). Implementation of the CNFH-AMP will be closely coordinated with the BCRP-AMP to share findings on key uncertainties, coordinate study designs and preliminary findings, and provide assistance to achieve mutual benefits. In addition, the CNFH-AMP provides an integrated monitoring plan and quantitative life-cycle model to support the assessment of CNFH and BCRP, and identifies diagnostic studies to address key areas of uncertainty (Appendix 1). Through the development of this plan, it was recognized that there was a need for an improved trapping and fish sorting capabilities at CNFH for fish returning to Battle Creek. This has led to the development of the CNFH Trapping and Sorting

Facility project, which is currently in the design phase (USFWS, memorandum, 2019).

Battle Creek Winter-run Chinook Salmon Reintroduction Plan The Reintroduction Plan (ICF International 2016) was developed to describe the issues, considerations, and necessary steps to reestablish a population of SRWCS in Battle Creek.

These efforts will contribute to the recovery of SRWCS ESU and are essential to NMFS recovery plan for California’s CV salmon and steelhead (NMFS 2014). The document describes a multi-phased process for reintroducing SRWCS to Battle Creek, under the assumption of successful implementation of the BCRP. The vision of the plan is to “establish a viable, self-sustaining and locally adapted population of winter-run Chinook Salmon (winter Chinook) in

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

Chinook Salmon ESU”. In order to achieve this goal, the plan identifies a need for artificial production to establish a founding population in Battle Creek. To increase imprinting of

SRWCS to optimal habitats within the watershed, rearing of juvenile SRWCS were to take place at a fish culture facility located in North Fork Battle Creek. The use of artificial propagation in establishing a self-sustaining population will decrease through the phases of recolonization and establishment of a self-sustaining population. It is recognized that Battle Creek, however, has a relatively small expanse of habitat suitable for SRWCS, which will limit the distribution, capacity, and maximum abundance of the Battle Creek population. These characteristics make the population vulnerable to demographic constraints and catastrophic events, reinforcing the need for continual monitoring and management efforts and highlight a continued role for artificial propagation in the long-term management of Battle Creek.

The Reintroduction Plan describes a three-phased process of reintroducing SRWCS to Battle

Creek. Phase 1 was to establish a return of SRWCS into Battle Creek with sufficient abundance to overcome founder effects and provide the basis for development of a self-sustaining, genetically diverse, and locally adapted population. Phase 1 was to use a mix of artificial production and translocation of wild juveniles to establish a population. Recognizing the vulnerability of SRWCS, the Reintroduction Plan aimed to establish a return of SRWCS as soon as feasibly possible. To accomplish this, Phase 1 was broken out into two phases: Phase 1-Initial and Phase 1-Late. The focus of Phase 1-Initial was to establish a return of hatchery-origin fish to

Battle Creek and allow them to colonize suitable areas for natural spawning. Phase 1-Late was to occur once it has been documented that the restored habitats are functioning sufficiently to support SRWCS populations, as evidenced by the observation of natural reproduction. Phase 1-

Late was designed to increase the genetic diversity of fish returning to Battle Creek by incorporating the translocation of wild-caught fry from the Sacramento River. Phase 2 of the

Reintroduction Plan was to develop a viable, self-sustaining, and locally adapted population of

SRWCS in Battle Creek by reducing transfers from the donor 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.

The Reintroduction Plan calls attention to the fact that the BCRP-AMP does not account for scientific uncertainties associated with using a supplementation program to accelerate recolonization efforts. To integrate these processes, the Reintroduction Plan identifies additional monitoring that would need to occur, under the assumption that these additional efforts will be integrated with monitoring and decision-making framework described in the BCRP-AMP

(Appendix 1). In addition, the Reintroduction Plan describes annual hatchery production and performance monitoring actions needed to evaluate the effectiveness of the reintroduction program.

Assessment and Recommendation for Using the Progeny of Captive Broodstock to Benefit the Conservation of Sacramento River Winter-run Chinook Salmon This document was developed to assess the recommendation to use the progeny of SRWCS captive broodstock at the Livingston Stone National Fish Hatchery (LSNFH) to hasten the planned reintroduction of SRWCS to Battle Creek as a means to mitigate for the effects of extreme drought on the SRWCS ESU (USFWS 2017). Two potential conservation uses of

SRWCS captive broodstock progeny are considered: (1) increasing the size and scope of the existing SRWCS supplementation program in the Sacramento River, and (2) “jump-starting” the process of reintroducing SRWCS to Battle Creek. Based on the assessment, it was recommended that the progeny of captive broodstock matings in 2017 be dedicated to jump-starting the SRWCS reintroduction efforts in Battle Creek. This document also provided suggestions on how to implement this action, including, transfer and release strategies and marking and tagging of the juvenile fish.

1.4 Recent Management Actions Affecting SRWCS Reintroduction

In 2017 the Resource Agencies, collectively made the decision to spawn SRWCS captive broodstock at the LSNFH and release their offspring into Battle Creek (USFWS 2017; USFWS

2018), thereby accelerating and modifying the planned process of reintroducing SRWCS to that watershed. This decision was prompted by a severe multi-year drought in California’s Central

Valley, which significantly decreased natural reproduction of SRWCS in the Sacramento River for two consecutive years. The near complete failure of SRWCS natural reproduction during

2014 and 2015 highlighted the potential for extinction of the SRWCS ESU. Lack of diversity and spatial structure are the principal vulnerabilities of the SRWCS ESU, which are represented by only a single population that is entirely dependent on managed releases of cold water from

Shasta Dam. Establishment of a second population of SRWCS in Battle Creek has the potential to decrease the risk of extinction by increasing diversity and spatial structure of the ESU.

Although restoration actions were not yet complete (e.g., fish ladders were not open and rock barrier modifications had not been completed in North Fork Battle Creek), the Interim Flow

Agreement provides the potential for adequate spawning temperature for SRWCS downstream of

Eagle Canyon Diversion Dam. In hindsight, the 2018 and 2019 water years provided an excellent opportunity to release juvenile SRWCS into Battle Creek, as high flows in both Battle

Creek and the Sacramento River likely contributed to increased survival during emigration.

Sacramento River Winter Chinook captive broodstock were spawned at the LSNFH during the

2017–2018 spawning seasons. Offspring of captive broodstock matings were transferred as eyed-eggs or button-up fry to CNFH, where they were reared until their release as pre-smolts.

Prior to their liberation, juvenile salmon were coded-wire tagged and marked with a unique combination of fin clips (adipose and left pelvic fin) to provide life-long identification of their origin. Captive broodstock progeny were first released into Battle Creek during the spring of

2018 (brood year 2017). This action initiated the reintroduction of SRWCS to historic spawning and rearing habitats in the watershed. The ‘Jumpstart Project’ moniker has become the commonly accepted name for referring to this fast-tracked approach to the reintroduction process.

Benefits of Jump-starting Reintroduction Efforts The decision to jump-start the reintroduction of SRWCS to Battle Creek was made with the expectation that this action would benefit the reestablishment of a viable population in that tributary and add to the resilience of the SRWCS ESU (USFWS 2017). The abundance of

SRWCS is expected to increase in both Battle Creek and for the ESU as a whole. Increased spawner abundance provides increased population resiliency to environmental and anthropogenic perturbations and helps to maintain genetic diversity. It is likely that SRWCS juveniles released into Battle Creek will imprint to that tributary and return there to spawn. Therefore, the introduction and establishment of a viable population of SRWCS to Battle Creek is expected to directly increase the spatial structure of the SRWCS ESU as translocated fish exploit newly accessible spawning and rearing habitats. Increasing the spatial structure of the SRWCS ESU is a high priority goal in the NMFS recovery plan. Because we expect a high degree of fidelity for jump-start fish to return to the Battle Creek watershed, this project poses minimal risk of negative effects to the productivity of SRWCS in the Sacramento River.

Uncertainties with Jump-starting Reintroduction Efforts There were some uncertainties regarding the decision to use the progeny of captive broodstock to jump-start the reintroduction of SRWCS to Battle Creek. If captive broodstock progeny have reduced productivity compared to the existing population in the Sacramento River, then releasing these fish into Battle Creek has the potential to carryover and negatively affect the initial success of the formal reintroduction plan. This possibility was recognized during the development of the

Battle Creek Winter Chinook Reintroduction Plan, which focused on using naturally-produced

SRWCS to avoid the possibility of this impact. However, if this effect exists, it will be transitory, and is likely to be ameliorated as the introduced population adapts to new habitats through the process of natural selection.

The effects of this conservation action on diversity are largely dependent on the success of founding a population of SRWCS in Battle Creek. In the short-term, diversity within the

SRWCS ESU is expected to benefit as a direct result of the release of increased numbers of juvenile SRWCS that were produced from a large number of parental combinations. Captive broodstock from brood years 2014 and 2015 are the best available representation the genetic diversity within the SRWCS ESU that existed prior to the recent severe drought, which severely impacted natural spawning success. Therefore, releasing a representative portion of the captive broodstock progeny into the Sacramento River could help to ameliorate the effects of two catastrophic year class failures by maintaining available diversity within the SRWCS ESU. In the long-term, diversity is expected to increase if habitats in Battle Creek are suitable for

SRWCS and if the jump-start efforts are successful at promoting natural spawning within those habitats. In this situation, benefits to diversity are expected to be realized as a secondary population of SRWCS adapt to a different set of selective forces in Battle Creek as compared to the Sacramento River. If habitats in Battle Creek, however, are not suitable for SRWCS or if the efforts to jump-start a new population in that tributary otherwise fail, then diversity within the

SRWCS ESU would not benefit from the jump-start efforts and the opportunity to use the progeny of captive broodstock to bolster diversity within the existing population would be lost.

Hydropower Relicensing

Pacific Gas & Electric announced in the summer of 2018 that the company will not seek to relicense the Battle Creek Hydroelectric Project. This announcement has created substantial uncertainty about the timing and completion of habitat restoration actions in Battle Creek. Given this recent decision, the MOU partners agreed in 2019 to continue implementing select portions of the BCRP on South Fork Battle Creek, including the removal of four dams. Restoration actions requiring new construction, however, are suspended, including completion of the tailrace connector at South Powerhouse, which is needed to reduce or eliminate inter-basin transfers.

The potential also exists that the hydropower project is altered or decommissioned, and there is no timeline for a final decision. Given the uncertainties surrounding the future operations of the hydroelectric project, it is difficult to predict which actions will occur, and the effects that project revisions will have on potential SRWCS habitat.

Remediation of Natural Barriers in Battle Creek

Two rock barriers that impede upstream migrations have been identified in the North Fork Battle

Creek (North Fork river mile [RM] 5.06 and 5.41). These barriers block salmonids from accessing a substantial portion of the habitat identified as being optimal for SRWCS.

Modification of these barriers will be required to make these areas accessible to anadromous salmonids (Thomas R. Payne and Associates 1998; Earley 2014). Plans are underway to modify these barriers; funding has been secured, and USFWS is pursuing the project with an anticipated start date of June 2020, pending landowner approval. Construction activities associated with the modification of these rock barriers are likely to coincide with, at minimum, the 2020 and 2021

SRWCS spawning seasons. The barrier removal project is expected to be finished prior to the completion of the BCRP.

2019 Grant Agreement In June 2019, USFWS and CDFW entered into a $14 million agreement that will be used to fund several actions in the Battle Creek watershed to benefit the establishment of a population of

SRWCS. The agreement provides funding for several critical needs, including elements of construction, operations, planning, and permitting. The North Fork Battle Creek Barrier

Modification and Fish Passage Improvement Project will benefit all the target salmonid species in Battle Creek, including SRWCS. Establishment of a short-term rearing facility in North Fork

Battle Creek will provide USFWS the opportunity to gain valuable knowledge of rearing these fish on the North Fork Battle Creek and assessing their imprinting response. An alternative analysis will be developed to determine the best location for a permanent fish culture facility at the North Fork Battle Creek, as called for in the Reintroduction Plan. Funds are also available for construction of the hatchery facilities. Funds for the acquisition of equipment and infrastructure necessary for monitoring (e.g., fish marking, tagging, and genetic analyses) has also been provided. Lastly, the agreement provides funding for the preparation of the environmental documents and permits for the CNFH Fish Trapping and Sorting Facility. All these efforts will benefit the reintroduction and establishment of a self-sustaining population of

SRWCS in the Battle Creek watershed.

1.5 Initiation of the Formal Reintroduction Program

The Battle Creek Winter-run Reintroduction Technical Team (Technical Team; Appendix 2), has recommended that the release of SRWCS juveniles as part of the Jumpstart Project be continued until the Reintroduction Plan is initiated. Specific criteria, which are necessary to transition to the formal Reintroduction Plan, include the following:

1) Implementation of BCRP instream flow requirements (MOU flows) in North Fork Battle

Creek;

2) Modification of natural barriers in North Fork Battle Creek;

3) Elimination or reduction of mixing and releasing water from North Fork Battle Creek into South Fork Battle Creek; and,

4) Establishing and operating a SRWCS rearing facility on the North Fork Battle Creek.

When the aforementioned criteria are in place, the Jumpstart Project will transition to the reintroduction process described in the Reintroduction Plan. It is apparent that natural-origin fish may return to Battle Creek prior to the initiation of the Formal Reintroduction Program, and management of adult jumpstart SRWCS returning to Battle Creek is the focus of current planning efforts.

1.6 Need for a Transition Plan

With the release of juvenile Jumpstart SRWCS into Battle Creek beginning in 2018 (brood year

2017), it was anticipated that maturing SRWCS would begin returning to Battle Creek for spawning in the winter of 2019. This timeline of Jumpstart SRWCS returns to Battle Creek precedes the completion of habitat restoration actions through the BCRP. Specifically, none of the four criteria necessary to implement the Reintroduction Plan had been completed. In addition, the monitoring associated with the BCRP-AMP has not begun. Thus, SRWCS adults would be returning to Battle Creek prior to enacting the full suite of adaptive management processes that were designed to promote their successful colonization of newly available habitats. This “Transition Plan” will guide the management of returning Jumpstart SRWCS in

Battle Creek prior to implementation of the Reintroduction Plan, address the monitoring needs that are not currently being met, and identify essential research questions that will aid in the future implementation of the Reintroduction Plan.

Chapter 2

Management of the Jumpstart Returns to Battle Creek

2.1 The Need for Flexibility and Adaptability

The strategy for managing the return of adult Jumpstart SRWCS in Battle Creek must be flexible and capable of responding to rapidly changing circumstances associated with the composition of

SRWCS in Battle Creek and the uncertain timeline of implementing restoration actions. For example, Jumpstart SRWCS returning to Battle Creek in 2019 were expected to consist largely or completely of early-maturing, age-2 males, or “Jacks”, which turned out to be the case.

Beginning in 2020, multiple year-classes of Jumpstart SRWCS are expected to return to Battle

Creek annually, consisting of both males and females. Furthermore, natural-origin (i.e., unmarked) SRWCS are expected to return to Battle Creek as early as two years following the commencement of natural spawning in that tributary. Naturally produced SRWCS will be unmarked and untagged, and may require different processes for identification. These differences in run composition through time necessitate that management strategies have the flexibility to respond accordingly.

The uncertain timeline of habitat restoration actions in Battle Creek also points to the need for flexibility of management actions. For example, the timeline for providing MOU flows and access upstream of hydropower facilities in Battle Creek are closely tied to the completion and acceptance of construction projects associated with fish ladders and screens at PG&E facilities.

These timelines are uncertain and must be negotiated between the BCRP MOU partners.

Potential delays associated with landowner access add further uncertainty to the timeline of the planned projects to modify natural barriers in North Fork Battle Creek. As currently configured, these natural barriers will likely prevent naturally migrating fish from accessing a portion of the best SRWCS spawning habitats. Although preventive measures will be taken during the natural barrier modification project, once implementation begins, there must be some flexibility of strategies for managing natural spawning SRWCS in Battle Creek to reduce the potential for fish to be impacted by construction activities.

Based on the knowledge that the circumstances affecting the management of adult SRWCS in

Battle Creek are likely to change, perhaps rapidly and in ways that merit reconsideration of management plans, we have limited the management recommendation and the detailed plan described in this document to the upcoming two return years - 2020 and 2021. A similar management approach may also be appropriate for 2022 and beyond, up to the commencement of strategies described in the Reintroduction Plan. Since much uncertainty surrounding the completion of restoration actions in Battle Creek and the response of Jumpstart SRWCS to newly available habitats, we recommend that management strategies for 2022 and beyond be revisited annually, in order to assess up-to-date changes to the Battle Creek watershed and to apply information that has been learned over the years. This includes knowledge gained as a result of monitoring, the updated status of habitat restoration actions in Battle Creek, consideration of

PG&E hydropower operations, and the expectation that naturally produced (i.e., unmarked)

SRWCS could potentially return to Battle Creek two or three years after natural spawning.

2.2 Management of Jumpstart SRWCS in 2019

Based on the expectation that returns of Jumpstart SRWCS to Battle Creek in 2019 would consist mostly of all of males, the recommendation of the Technical Team was to intercept all returning Jumpstart fish and transport them to LSNFH for spawning with female captive broodstock (Appendix 3). These returning SRWCS would be intercepted either during CNFH broodstock collection (October through February) or Battle Creek adult monitoring (March through July). The recommendation to capture all Jumpstart fish returning to Battle Creek in

2019 was based on the desire to incorporate the genetics of these “successful” fish into the

LSNFH spawning plan and the knowledge that natural reproduction in Battle Creek would be unlikely due to the absence or paucity of female returns in 2019. This recommendation was subsequently approved by the Resource Agencies and implemented in the spring of 2019.

Consistent with expectations, only age-2 male “Jacks” Jumpstart SRWCS returned to Battle

Creek during the spring of 2019. A total of 95 SRWCS Jacks were observed attempting to migrate past the CNFH Barrier Weir from May 1, through July 31, 2019, after hatchery spawning had terminated for the year. With the exception of 21 fish observed migrating upstream of the CNFH Barrier Weir through the fish ladder while entrance to the hatchery was closed, the remaining 74 fish were diverted into the hatchery where they were captured. All genetically confirmed Jumpstart SRWCS captured at the CNFH during the spring of 2019 were transported to the LSNFH. A portion of the Jumpstart SRWCS jacks died prior to spawning at the LSNFH, some were kept alive until they were spawned with female captive broodstock, and others were used as a source of semen for cryopreservation. Cryopreserved semen samples collected from Jumpstart jacks were subsequently used to fertilize captive broodstock females, which reach sexual maturation substantially later than SRWCS in the wild. The brood year 2019 juvenile SRWCS produced from Jumpstart jacks collected in 2019 will contribute to the initial release of second-generation SRWCS in Battle Creek during early 2020.

2.3 Management Strategy Development

The process to develop a recommended strategy to manage the adult return of Jumpstart SRWCS to Battle Creek was initiated with a meeting of the Technical Team on November 14, 2018.

Discussions were guided by the following information and assumptions:

1) Restoration of Battle Creek will not be completed by the time Jumpstart SRWCS return to spawn. Consequentially, flow agreements per the BCRP may not be implemented, trans-basin water conveyances will continue, and the remaining dams on

South Fork and its’ tributaries will not be removed. Additionally, the fish ladders and fish screens associated with PG&E’s hydropower facilities may not be fully operational.

Considered together, these factors raised concerns regarding the certainty of Battle Creek for providing high quality habitats, and access to these habitats to support a viable, independent, and self-sustaining population of SRWCS.

2) A rearing facility for SRWCS on North Fork Battle Creek, which was recommended in the Reintroduction Plan to promote imprinting to optimal spawning habitats, has not been developed. Jumpstart SRWCS returning to Battle

Creek in 2019 were reared at the CNFH, located approximately 6 river miles upstream from the confluence with the Sacramento River and 12 river miles downstream of areas of Battle Creek that are likely to provide suitable temperatures for SRWCS spawning and egg incubation. In an attempt to promote imprinting to areas with suitable spawning habitat, Jumpstart SRWCS juveniles were released in North Fork Battle Creek, in locations thought to provide the best spawning habitats. The effect that releasing

Jumpstart SRWCS upstream of the CNFH will have on their imprinting is unknown.

Considerable uncertainty exists as to whether Jumpstart SRWCS will seek out and locate suitable spawning habitats higher in the watershed.

3) The number of Jumpstart SRWCS anticipated to return to Battle Creek annually exceeds the capacity of available hatchery facilities, including facilities for holding adults at LSNFH and facilities for rearing juveniles at the CNFH. The estimated return of Jumpstart SRWCS to Battle Creek approaches 600 fish annually. This number of adults exceeds the capacity of adult holding at the LSNFH, which is largely occupied at that time for producing SRWCS to supplement the population in the main stem

Sacramento River. Furthermore, if we estimate that half of the expected return of 600

Jumpstart SRWCS are female, each with a fecundity of 5,000 eggs, then the reproductive capacity of returning adults is 1.5 million eggs. To rear this number of juveniles would greatly exceed the amount of available space at the LSNFH (for egg incubation and early rearing of fry) and CNFH (for egg incubation and rearing to release). Thus, hatchery propagation of all returning Jumpstart SRWCS according to existing program protocols will not be possible within the limitations of existing facilities.

Based on the aforementioned information and assumptions, the Technical Team brainstormed alternative strategies for managing the return of Jumpstart SRWCS to Battle Creek, prior to commencing the phases of the formal Reintroduction Plan. It was acknowledged that the selected strategy must attempt to reduce impacts to ESA threatened salmonids that will be encountered while managing for SRWCS, specifically spring Chinook. At the conclusion of discussions, the team developed consensus of recommendations for the strategies to manage future returns of Jumpstart SRWCS to Battle Creek. The USFWS was tasked with further developing these recommendations for consideration by the Resource Agencies.

2.4 Management Strategies for Jumpstart SRWCS in 2020 and 2021

Most of the strategies considered in this document were discussed during the Technical Team meeting in November 2018. However, the list of potential management strategies discussed in that forum has been expanded upon and further developed in this document. For example, two management strategies, strategies 5 and 6 listed below, were mentioned but not fully vetted during the November Technical Team meeting. These two strategies are included in this document to increase the breadth of management alternatives considered.

The following seven potential strategies to manage the return of Jumpstart SRWCS to Battle

Creek in 2020 and 2021 are considered in this document:

1) Collect and retain all Jumpstart SRWCS for spawning at the LSNFH;

2) Allow all Jumpstart SRWCS to migrate past the CNFH Barrier Weir and spawn naturally in Battle Creek;

3) Relocate all Jumpstart SRWCS to reaches within North Fork Battle Creek to spawn naturally;

4) Relocate all Jumpstart SRWCS to the Sacramento River to spawn naturally;

5) Block all Jumpstart SRWCS at the CNFH Barrier Weir;

6) Collect and cull all Jumpstart SRWCS collected at the CNFH Barrier Weir; and,

7) A multi-faceted strategy, including elements of more than one potential action previously listed.

The strategy selected for managing adult returns from the Jumpstart project during the 2020 and

2021 spawning seasons would apply to Jumpstart SRWCS throughout their entire period of migration into Battle Creek, including fish encountered at CNFH during broodstock collection activities and those attempting to migrate past the CNFH Barrier Weir after the cessation of hatchery spawning. During the period of broodstock collection, Jumpstart SRWCS may be encountered in the CNFH spawning building during the process of sorting fall-run Chinook

Salmon (fall Chinook) and late-fall run Chinook Salmon (late-fall Chinook) and steelhead broodstock. After hatchery spawning concludes in March, salmonids migrating in Battle Creek will be handled in a manner similar to 2019 (Appendix 3). Previous monitoring efforts at the

CNFH Barrier Weir ceased handling fish when water temperatures reached 60ºF. The Technical

Team discussed the likelihood of not being able to intercept fish if the previous temperature threshold remained. As per agreement by the Resource Agencies, the threshold was increased to

68ºF, at which handling of salmonids will be terminated. If the sorting of SRWCS is terminated due to high water temperature prior to the closing of the upstream fish ladder on July 31, the

Battle Creek Monitoring program will enumerate all salmonids, including Jumpstart SRWCS, migrating upstream of the CNFH Barrier Weir through video surveillance.

Management Priorities To objectively evaluate the list of alternative strategies for managing Jumpstart SRWCS in Battle

Creek, it was necessary to first develop a list of ‘Management Priorities’. Management Priorities are a mutually agreed upon list of key benefits to be advanced or accomplished by the selected management strategy. As such, Management Priorities can also be used as metrics to gauge the evaluation of alternative management actions. All else being equal, strategies that satisfy

Management Priorities to a greater extent would generally be considered favorable to strategies that are neutral or adverse to their achievement of those goals. Management Priorities for the return of Jumpstart SRWCS during the 2020-2021 spawning seasons are indicated below, in no particular order:

1) Conservation of genetic diversity

Genetic diversity provides the basis of variation of phenotypic traits, which enable organisms to survive and adapt to new and changing environments. Thus, maximizing genetic diversity is a priority for managing SRWCS reintroduced to restored habitats of

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