C06__Attachment_3_Winter_Chinook_Supplementation_HGMP.pdf

HATCHERY AND GENETIC MANAGEMENT PLAN

Hatchery Program:

Species or

Hatchery Stock:

Agency/Operator:

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Livingston Stone National Fish Hatchery -

Integrated-Recovery Supplementation

Program

Sacramento River Winter Chinook Salmon

(Oncorhynchus tshawytscha)

U.S. Fish and Wildlife Service

Sacramento River

January 20, 2016

Initial Submission

SECTION 1. GENERAL PROGRAM DESCRIPTION

1.1) Name of hatchery or program The Livingston Stone National Fish Hatchery (NFH) houses the Winter Chinook Conservation

Hatchery, which consists of an integrated-recovery supplementation program and a captive broodstock program. The Livingston Stone NFH, together with the Coleman NFH, comprise the

Coleman NFH Complex.

1.2) Species and population (or stock) under propagation, and ESA status The Evolutionary Significant Unit (ESU) of Sacramento River Winter-run Chinook salmon

(Oncorhynchus tshawytscha) are listed as endangered under the Endangered Species Act (ESA) of 1973. Winter Chinook were first listed as threatened (August 4, 1989, 54 FR 32085), reclassified as endangered (January 4, 1994, 59 FR 440), reaffirmed as endangered (June 28, 2005, 70 FR 37160 and August 15, 2011, 76 FR 50447)

1.3) Responsible organization and individuals Indicate lead contact and on-site operations staff lead.

Primary Contact

Mr. Brett Galyean, Acting Project Leader

U.S. Fish and Wildlife Service

Coleman National Fish Hatchery

24411 Coleman Fish Hatchery Road

Anderson, CA 96007

Tel: (530) 365 - 8781

FAX: (530) 365 – 0193

e-mail: brett_galyean@fws.gov

Operations Staff Lead

Mr. John Rueth, Assistant Hatchery Manager

U.S. Fish and Wildlife Service

Livingston Stone National Fish Hatchery

16349 Shasta Dam Blvd

Shasta Lake, CA 96019

Tel: (530) 275 - 0549

FAX: (530) 275 – 4138

e-mail: john_rueth@fws.gov

Hatchery Evaluation and Permitting Contact

Mr. James G. Smith, Project Leader

U.S. Fish and Wildlife Service

Red Bluff Fish and Wildlife Office

10950 Tyler Road

Red Bluff, CA 96080

Tel: (530) 527 – 3043

FAX: (530) 529 – 0292

e-mail: jim_smith@fws.gov

Additional responsible agencies:

Coleman and Livingston Stone NFH are mitigation features to partially offset habitat and fish losses resulting from the construction of Shasta and Keswick dams, part of the Central Valley

Project (CVP). Both facilities are operated by the U.S. Fish and Wildlife Service (Service) and funded by the U.S. Bureau of Reclamation (Reclamation).

Reclamation Contact

Mr. Federico Barajas, Area Manager

U.S. Bureau of Reclamation

16349 Shasta Dam Blvd.

Shasta Lake, California 96019

(530) 275-1554

1.4) Funding source, staffing level, and annual hatchery program operational costs Reclamation provides to the Service an annual budget of approximately $5.6 million for operations and maintenance of the Coleman National Fish Hatchery Complex. Additional dedicated funding, such as for construction, facility rehabilitation, research and monitoring, or other projects, may be secured from other sources (e.g., CVPIA [CVPIA] and State funding).

The Coleman NFH has approximately 20 employees, including seasonal staff. A portion

(approx. $250,000) of the budget provided to the Service is allocated to the Livingston Stone

NFH for the winter Chinook propagation program. Total staff for the Livingston Stone NFH is four and occasionally, during periods of increased workload, additional staff are temporarily transferred from the Coleman NFH. The Livingston Stone NFH is also used to house a refugial population of delta smelt. Delta smelt reared at the Livingston Stone NFH are a genetically redundant secondary population of the primary delta smelt refugial population housed at Byron, California. Funding for the delta smelt refugial hatchery program is provided through the

Service’s Fisheries Program.

A portion of the annual funding provided by Reclamation for operations and maintenance of the

Coleman NFH Complex are used to fund programs that support hatchery operations.

Approximately $700,000 annually is transferred to the Red Bluff Fish and Wildlife Office

(RBFWO) to conduct evaluations, monitoring, research, and permitting related to hatchery operations. The Hatchery Evaluation Program at the RBFWO consists of eight to ten employees.

Another portion of the total annual funding from the Reclamation is transferred to the California-

Nevada Fish Health Center (CA-NV FHC) for technical expertise associated with fish health, including the prevention, diagnosis, and treatment of disease.

1.5) Location(s) of hatchery and associated facilities Livingston Stone NFH is located in the upper Sacramento River basin in the northern Central

Valley of northern California. The hatchery is located at the base of Shasta Dam (Keswick

Reservoir) on the west side of the Sacramento River approximately 12 river miles (RM) upstream of the limit of anadromy at Keswick Dam. The stock location code recognized by the

Pacific States Marine Fisheries Commission (PSMFC) Regional Mark Processing Center for

Livingston Stone NFH is 6FCSASAF LVNH. The Coleman NFH, which combines with the

Livingston Stone NFH to form the Coleman NFH Complex, is located on Battle Creek, an east-side tributary that enters the Sacramento River 32.5 river miles (RM) downstream of the

Keswick Dam.

Figure 1.5.1. Locations of the Coleman and Livingston Stone National Fish Hatcheries

1.6) Type of program The Winter Chinook Conservation Hatchery consists of two interrelated programs; 1) the Winter

Chinook Integrated-Recovery Supplementation Program and the Winter Chinook Captive

Broodstock Program. In the Winter Chinook Integrated-Recovery Supplementation Program, hatchery propagated winter Chinook are managed to be integrated with the natural population of winter Chinook in the upper Sacramento River and are intended to supplement natural production, thereby providing a demographic enhancement to aid in the rebuilding and recovery of that population. Winter Chinook produced at the Livingston Stone NFH are intended to return as adults to the upper Sacramento River, spawn in the wild, and become reproductively and genetically assimilated into the natural spawning population. The Winter Chinook Captive

Broodstock Program is conducted by withholding from release a portion of the juveniles produced annually in the integrated-recovery supplementation program and rearing them to maturity at the Livingston Stone NFH.

1.7) Purpose (Goal) of program The overarching goal of the Service’s Winter Chinook Conservation Hatchery is preservation/Conservation of the winter Chinook ESU. Winter Chinook are propagated at the

Livingston Stone NFH to conserve genetic resources of a single fish population at low abundance and endangered of extinction. A potential complementary goal of the winter Chinook salmon program is restoration. When the need arises, this goal will be achieved by providing a source of winter-run Chinook salmon to re-establish naturally spawning populations in historical habitats. Reintroductions contribute to preservation and conservation by improving spatial structure, productivity, diversity, and abundance of the Sacramento River winter-run Chinook salmon ESU, thereby reducing the likelihood of extinction.

1.8) Justification for the program

Livingston Stone NFH was constructed by Reclamation in 1997 for the explicit purpose of propagating ESA-listed winter Chinook salmon. Hatchery propagated winter Chinook are managed to be integrated with the natural population of winter Chinook in the upper Sacramento

River and are intended to provide a demographic enhancement to aid in the resilience, rebuilding and recovery of that population. The Winter Chinook Integrated-recovery supplementation program is supported in NMFS’ Final Recovery Plan for Central Valley Chinook Salmon and

Steelhead (NMFS 2014). The Final Recovery Plan states that the program “…is expected to play a continuing role as a conservation hatchery to help recover winter-run Chinook salmon (NMFS

2014).

1.9) List of program “Performance Standards” The following performance standards have been designed to evaluate the benefits and risks of the

Winter Chinook Integrated-recovery supplementation program conducted at the Livingston

Stone NFH. Performance standards have been classified as either “benefits” or “risks.”

Performance standards categorized as “benefits” measure the benefits resulting from an artificial propagation program (e.g., contribution to recovery, restoration, conservation/preservation, and/or research). Performance standards categorized as “benefits” (B) indicate possible benefits to winter Chinook. Performance standards categorized as “risks” (R) indicate possible risks the artificial propagation program may pose to winter Chinook.

Performance Standards to Evaluate Benefits

Benefit

Number Standard / Guideline

B1. Provide a demographic benefit to the abundance of winter Chinook

B2. Maintain stock integrity and conserve genetic and life history diversity

B3. Provide fish for experimental purposes

B4. Conduct research to monitor and evaluate hatchery operations and practices

B5. Improve survival using appropriate incubation, rearing, and release strategies

B6. Improve survival by preventing disease introduction, spread, or amplification

B7. Provide a source of winter Chinook to be coded-wire tagged for purpose of informing decisions related to harvest management

B8. Provide a source of fish for the winter Chinook Captive Broodstock Program, which can be used to prevent extinction and support reintroduction efforts

Performance Standards to Evaluate Risks

Risk

Number Standard / Guideline

R1. Reduce potentially harmful genetic and ecological interactions between hatchery-and natural-origin fish

R2. Do not introduce, spread, or amplify pathogens

R3. Minimize harmful effects of program operations on winter Chinook

1.10) List of program “Performance Indicators”, designated by "benefits" and "risks" The following performance indicators can be used to monitor and evaluate the aforementioned benefits and risks of the Winter Chinook Integrated-recovery supplementation program at the

Livingston Stone NFH. Performance indicators have been separated into two categories:

benefits (B) that the hatchery program will provide to the population by meeting program objectives; and risks (R) that the hatchery program may be pose to the population.

1.10.1) “Performance Indicators” addressing benefits

Performance Standard B1: Provide a demographic benefit to the abundance of winter

Chinook

Restoration and recovery of native fish and aquatic ecosystems are priorities for the National

Fish Hatchery System. Hatchery propagation of winter Chinook salmon at Livingston Stone

NFH is conducted primarily to supplement the natural population in the Sacramento River. The basis for the winter Chinook Integrated-recovery supplementation program is that hatchery production can provide higher rates of survival from egg-to-smolt life stages than can be achieved in the natural environment.

Relevant fish culture practices:

· Rear fish using the water where the fish are intended to imprint to enhance homing abilities and promote integration with naturally produced winter Chinook in the upper Sacramento

River

· Developed a hatchery facility designed specifically for supplementing Sacramento River winter Chinook salmon

· Constrain the collection of broodstock (maximum of 15% of estimated total run) to lower the demographic and genetic risks to the naturally spawning population

· Use only natural-origin winter Chinook as broodstock to lower the degree of fitness reduction caused by domestication

· Implement strategies to effectively identify and spawn only target broodstock

· Use factorial-type mating strategy to avoid decreasing the effective population size

· Mark and tag 100% of hatchery production

Performance Indicators:

· Continue to conduct field surveys to generate adult run-size estimates and evaluate survival, spawning success, and integration of hatchery propagated winter Chinook salmon with the natural population

· Continue to monitor and evaluate genetic risks of the winter Chinook propagation program to measure potential genetic effects on the natural population

· Conducted a genetic grand parentage analysis to verify reproductive success of the winter

Chinook salmon from the propagation program at Livingston Stone NFH

Performance Standard B2: Maintain stock integrity and conserve genetic and life history diversity

Fish culture practices at the Livingston Stone NFH are designed to maintain stock integrity, conserve genetic and life history diversity, and reduce divergence from naturally reproducing stocks. Adult broodstock are collected across a range of phenotypic characteristics, including run timing and age. In addition, under typical conditions the hatchery uses only natural-origin winter Chinook as broodstock. However, under extreme circumstances, such as prolonged drought, the inclusion of adult hatchery-origin winter-run Chinook salmon in the broodstock may be warranted. These practices of broodstock selection are believed to help maintain the fitness of the hatchery stock by reducing the risks of domestication selection and decreasing the potential for divergence between hatchery and natural stocks.

· Use locally-collected, natural-origin adults for broodstock

· Conduct spawning in a manner that minimizes genetic drift and conserves genetic variability of the stock

· Collect adults throughout the duration of run timing, modeling the collection schedule upon historic run timing of naturally produced winter Chinook past the Red Bluff Diversion Dam

(RBDD)

· Employ a factorial type mating strategy, using at least two males (if possible) to fertilize a separate portion of eggs from each female. Spawn each male with preferably two but no more than four females

· Use phenotypic and genetic techniques to effectively identify and spawn only winter

Chinook

· Use mark status to identify hatchery-origin winter Chinook

· Use natal stream water at the hatchery to reinforce genetic compatibility with local environments and promote homing

· Monitor population trends in fecundity, return rates, return timing, spawn timing, adult size and age composition, survival for different life stages, effective population size, and other parameters

Performance Standard B3: Provide fish for approved experiments

Investigators from government agencies, academic institutions, and the private sector request fish or fish tissues to study a variety of issues. In these investigations, fishes propagated at

Coleman and Livingston Stone NFHs can be used as surrogates for natural-origin fish, which may not be available for research purposes. Additionally, some research projects involving winter Chinook may seek to improve the performance and cost-effectiveness of artificial production and provide a means for improving the program through adaptive management. All winter Chinook provided for experimental purposes must be approved by the National Marine

Fisheries Service (NMFS) and the California Department of Fish and Wildlife (CDFW).

· Spawn and rear fish in a manner that will support the needs of NMFS-CDFW approved research projects

· Mark and CWT experimental fish prior to release

· As appropriate for specific experimental design

Constraints:

· The size and configuration of rearing units limits total hatchery production and flexibility of lot sizes

· The endangered status of Sacramento River winter Chinook and the potential for reduced survival in some experiments constrains the use of ESA-listed fish for experimental purposes

Performance Standard B4: Conduct research, monitoring and evaluations of hatchery operations and practices

Standard and proven fish culture practices are used at the Livingston Stone NFH to produce fish necessary to accomplish program goals, while reducing the potential for negative effects resulting from the program. Research and monitoring are conducted on- and off-site.

Knowledge gained through experimentation and research is used to modify fish culture practices, when appropriate, to better accomplish program goals.

· All existing fish culture practices at the Livingston Stone NFH

· The existing Monitoring and Evaluation Program conducted from the Red Bluff FWO

· Marking and tagging of 100% hatchery-origin winter Chinook

· Periodically review and summarize ocean harvest data

· Analyze and summarize information collected during mainstem Sacramento River carcass surveys to evaluate program operations

· Livingston Stone NFH has served as the source of winter Chinook for acoustic tracking studies to assess survival during emigration

· Broodstock trapping efforts at the Keswick Dam Fish Trap (KDFT) have been the source of studies to assess survival of adult winter Chinook released back into the Sacramento River

(i.e., not used as broodstock at the Livingston Stone NFH).

· The endangered status of Sacramento River winter Chinook and the potential for reduced survival in some studies constrains the use of ESA-listed fish for experimental purposes

Performance Standard B5: Improve survival of propagated species/stock using appropriate incubation, rearing, and release strategies

The Service will continue to work to achieve a high level of survival of fish produced at the

Livingston Stone NFH, to ensure that the program is producing a demographic benefit to increase escapement and supplement natural production, while reducing the risks to naturally produced salmonids

· Release fish at a time and size that attempts to achieve a balance between high rates of survival and a low level of risk to naturally produced salmonids

· Incubate eggs and rear fish at densities favorable for reducing stress, disease, and mortality

· Use proper disease prevention and control techniques to achieve a high level of survival

· Conduct studies to investigate effects of fish culture practices, such as: food types; rearing densities; ponding strategies; natural-type rearing elements; and size, time, and location of release. Apply knowledge gained through investigations to modify hatchery practices, when appropriate, to achieve a balance between high rates of survival and low potential for detrimental impacts

· Analyze trends in survival for different life stages at the hatchery

· Analyze trends in rates of ocean harvest, freshwater harvest, and escapement

Performance Standard B6: Improve survival by preventing disease introduction, spread, or amplification

The primary goal of fish health management programs at the Livingston Stone NFH is to produce healthy fish that will contribute to program’s conservation goals. This goal is accomplished, with assistance and technical guidance from the Service’s CA-NV FHC, using state-of-the art technologies in disease prevention and treatment. Fish culture practices at the

Livingston Stone NFH are designed to produce healthy smolts. Propagation of healthy juveniles will maximize survival and contribution of hatchery fish, both before and after release, and reduce the potential to negatively impact naturally produced salmonids. The following list details specific projects or activities undertaken at the Livingston Stone NFH to prevent the introduction, spread, or amplification of fish pathogens.

· Maintain sanitary conditions for fish rearing

· Monitor fish behaviors and mortality during incubation and rearing for issues potentially related to fish heath

· Use fencing and/or bird netting to reduce predation and disease transmission into or out of the hatchery

· Prescribe appropriate treatments (prophylactics, therapeutics, or modified fish culture practices) to alleviate disease-contributing factors using approved methods and chemicals

· Conduct applied research leading to improved control of disease epizootics

· Develop and conduct propagation strategies to reduce opportunities for transferring disease from the hatchery to natural fish (e.g., water filtration for embryos and emergent fry)

· Routinely perform examinations of live fish to assess health status and detect problems before they progress into clinical disease or mortality

· Remove dead and moribund fish from rearing containers. In cases of increased mortality, perform necropsies of diseased and dead fish to diagnose the cause of death

· Examine hatchery broodstock for disease organisms (viral, bacterial and parasites)

· Analyze survival trends for different life stages at the hatcheries

· It is difficult to control all pathways of disease transmission

· Fish health can be compromised by poor water quality

Performance Standard B7: Provide a source of winter Chinook salmon to be coded-wire tagged for purpose of informing decisions related to harvest management

Because winter Chinook are protected as an endangered species, harvest regulations are implemented to avoid or minimize their harvest in ocean and freshwater commercial or recreational fisheries. Harvest constraints may be implemented, if necessary, to reduce impacts to winter Chinook. Winter Chinook originating at the Livingston Stone NFH are the only source of coded-wire-tagged winter Chinook, which are used to gauge the success of harvest regulations.

· All hatchery produced winter Chinook salmon are marked and coded-wire tagged prior to release. Releases and recoveries of CWT winter Chinook are reported to the coast-wide

CWT database (RMIS; maintained by the PSMFC), where the data are available to evaluate impacts of harvest.

· Report coded-wire tag releases and recoveries

· Coded-wire tag 100% of the winter Chinook produced at the Livingston Stone NFH

Performance Standard B8: Provide a source of fish for the winter Chinook Captive

Broodstock Program, which can be used to prevent extinction and support reintroduction efforts

The abundance of winter Chinook is low, and the fact that there is only one population places the species at a high risk of extinction. The Winter Chinook Captive Broodstock Program was reinstituted in 2014 to increase the security of the winter Chinook ESU by rearing a captive population in a safe and secure environment, to be available for use as hatchery brood stock in the event of a catastrophic decline in the abundance of winter Chinook spawners in the

Sacramento River. Furthermore, the Captive Broodstock Program will potentially will be used to re-establish winter Chinook to native habitats upstream of Shasta Dam and to Battle Creek.

· Developed a hatchery facility designed specifically for propagating Sacramento River winter

Chinook salmon

· Select captive broodstock in a manner that represents the genetic diversity of the parent stock

· Implement proactive strategies of fish health monitoring and treatment achieve high rates of survival

· Implement proactive strategies of fish health monitoring and treatment to achieve high rates of survival

· Report survival across all life-stages of captive broodstock

· Report reproductive success of winter Chinook captive broodstock

· The size and configuration of rearing units at the Livingston Stone NFH limits flexibility of lot sizes and necessitates trade-offs between the size of the winter Chinook Integrated-recovery supplementation program and the Captive Broodstock Program

1.10.2) “Performance Indicators” addressing risks

Performance Standard R1: Reduce potentially harmful genetic and ecological interactions between hatchery- and natural-origin stocks

Hatchery propagation of winter Chinook at the Livingston Stone NFH is designed primarily to aid in the recovery, conservation and/or reintroduction of the natural winter-run Chinook salmon population, and fish produced are intended to spawn in the wild or be genetically integrated with the targeted natural population while reducing the potential for negative effects resulting from the propagation program.

· Propagate only genetically-identified winter Chinook collected from the upper Sacramento

River

· Release fish at the area intended for supplementation to promote imprinting and reduce straying

· Use natal stream water to reinforce genetic compatibility with local environments

· Use primarily natural-origin winter Chinook from the upper Sacramento River as hatchery broodstock

· Spawn numbers of adults necessary to minimize genetic drift and to conserve genetic variability

· Collect and spawn adults throughout the duration of run timing

· Use a factorial-type mating (e.g., 1 male to fertilize half eggs from two females) to increase effective population size relative to single pair matings

· Select and pair broodstock randomly from collected broodstock

· Incorporate jacks into the spawning plan.

· Monitor and assess characteristics of hatchery-origin winter Chinook in comparison to naturally produced winter Chinook

· Limited funding and endangered status limit field monitoring capabilities

Performance Standard R2: Do not introduce, spread, or amplify pathogens

The primary goal of fish health management programs at the Livingston Stone NFH is to produce healthy fish that will contribute to program goals conservation, and preservation, while minimizing the potential for negatively impacting natural stocks. Propagation of healthy juveniles will maximize survival and contribution of hatchery fish, both before and after release.

This goal is accomplished using state-of-the art technologies in disease prevention along with assistance and technical advice from the CA-NV FHC. It is equally important to reduce potential negative effects that releasing diseased fish may have on natural salmonid populations. The following list identifies specific projects or activities undertaken at the Livingston Stone NFH to prevent the introduction, spread, or amplification of fish pathogens from hatchery stocks into natural populations.

· Employ strategies of propagation, rearing, tagging, and release that minimize occurrence of disease in hatchery fish and decrease the potential for transmission of diseases to natural fish

· Maintain sanitary conditions for fish rearing including: 1) disinfecting all equipment (e.g., nets, tanks, rain gear, boots, brooms) with iodophor between uses with different fish/egg lots,

2) disinfecting (with iodophor) the surface of all eggs spawned at the facility and 3) when practicable, disinfect outside rearing units between use with a portable ozone sprayer

· Prescribe appropriate treatments (prophylactics, therapeutics, or modified fish culture practices) to alleviate disease-contributing factors using approved methods and chemicals

· Conduct applied research through the U. S. Food and Drug Administration Investigational

New Animal Drug process to control disease epizootics

· Routinely remove dead and moribund fish from rearing containers. Perform necropsies of diseased and dead fish to diagnose the cause of death

· Perform examinations of collected broodstock for disease organisms (bacterial, viral and parasitic)

· Routinely observe juveniles to assess for abnormal appearance and behaviors that could indicate health problems before they progress into clinical disease or mortality o Routinely monitor on-station mortality of Chinook salmon and conduct examinations when dictated by abnormal appearance, behaviors, or mortality levels

Performance Standard R3: Minimize harmful effects of program operations on the ESA-listed population

Hatchery propagation of winter Chinook could impose negative effects upon the winter Chinook population. For example, trapping of winter Chinook for use as hatchery broodstock could result in mortality, injury or behavioral effects, resulting in decreased natural spawning success.

Minimizing such effects is necessary to promote achievement of program objectives

Relevant fish culture practices:.

· Broodstock collection activities at the Livingston Stone NFH

· Conduct floy/dart tagging of fishes released from trapping activities to gain insights into the fate of released fish

· Conducted a study to monitor the movements of winter Chinook released during the course of broodstock collection activities. A final report of this study is being prepared and will be provided to NMFS upon completion.

1.11) Expected size of program Unlike typical production-oriented hatchery programs, the Winter Chinook Integrated-Recovery

Supplementation Program does not have a fixed annual target for juvenile production. Rather, production levels are dictated by the number of broodstock that are collected and spawned annually, which is dependent upon the estimated upriver escapement. The broodstock collection target is limited to a maximum of 15% of the estimated upriver escapement, with an upper limit of 120 broodstock per brood year (i.e., when run sizes >800). To maintain genetic diversity in the event of very low abundance, no less than 20 winter Chinook adults will be collected for broodstock regardless of run size (i.e., when run sizes <135).

In emergency situations, such as the extreme drought that was experienced during the summer of

2014 and 2015, production of winter Chinook may be increased above the standard production levels indicated above to partially mitigate for extremely poor conditions faced by naturally spawning winter Chinook in the Sacramento River. This temporary expansion of winter

Chinook propagation activities is intended to partially mitigate for the effects of drought, and is based on the anticipation of temperatures unfavorable for successful natural spawning of winter

Chinook in the Sacramento River. In these situations, potential expansion of program goals will be determined collaboratively by the Service, NMFS, and CDFW.

1.11.1) Proposed annual broodstock collection level (maximum number of adult fish)

The standard collection target for winter Chinook is 15% of the estimated upriver escapement, with a minimum of 20 and a maximum of 120. These collection targets include any mortality to potential broodstock while being held captive. In some years, these numbers may be increased to address drought emergencies by mitigating for high levels of in-river mortality due to low flows and lethal water temperatures. In these situations, potential expansion of broodstock collection targets will be determined collaboratively by the Service, NMFS, and CDFW.

1.11.2) Proposed annual fish release levels (maximum number) by life stage and location Annual targets for the Winter Chinook Integrated-Recovery Supplementation Program are not fixed in terms of numbers of juveniles produced, but rather, the program goal is to maximize production from the adults collected and used as hatchery broodstock (as explained above). The typical annual production level anticipated when operating under normal broodstock collection limits (i.e., n=120 spawners comprised of 60 females and 60 males) is approximately 250,000 smolts. During years when the program is expanded to mitigate for poor in-river conditions, hatchery production may increase, perhaps substantially. For example, during the drought-related expansion of 2014 total hatchery releases exceeded 600,000 juvenile winter Chinook.

Table 1.11.2 Proposed release location and maximum release level of winter Chinook from the Livingston Stone National Fish Hatchery

Life Stage Release Location Annual Release Level

Eyed Eggs N/A 0

Unfed Fry N/A 0

Fry N/A 0

Fingerling (Smolt) Sacramento River – RM 298.5

Maximum annual production at standard program level is approx. 250,000

Maximum annual production during a drought-related program expansion may exceed 700,000

Yearling N/A 0

1 Release levels, life stages, and locations may vary with approval by NMFS and CDFW, depending on drought contingencies, reintroduction efforts, recovery goals, etc.

1.12) Current program performance, including estimated smolt-to-adult survival rates, adult production levels, and escapement levels. Indicate the source of these data

For brood years 2000 through 2011, the average estimated rate of total contribution (i.e., ocean harvest plus spawning escapement) for winter Chinook salmon from the Livingston Stone NFH was approximately 0.62% (95% CI, 0.23% - 1.01%) of the total number of juveniles released per brood year. The total contribution includes an average of approximately 759 (95% CI, 309 –

1,210) adults returning to the upper Sacramento River.

Table 1.12. Estimated number and proportion of juvenile winter Chinook salmon produced at the Livingston Stone NFH from 2000 through 2011 contributing to fisheries and returning to spawning areas of the upper Sacramento River. Data presented include progeny produced from cryopreserved semen, which is a standard back-up propagation strategy occasionally used at Livingston Stone NFH. Captive broodstock progeny were excluded from tabulated information as these releases may not be representative of general performance of the Integrated-recovery supplementation program. Data are complete only through 2014.

Brood Year Release No. Return No.

% Return

2000 166,206 558 0.336

2001 190,732 390 0.204

2002 164,806 3,326 2.018

2003 152,011 2,226 1.465

2004 148,385 126 0.085

2005 160,273 166 0.104

2006 161,212 481 0.299

2007 71,883 196 0.272

2008 146,211 34 0.023

2009 198,582 1,116 0.562

2010 123,859 411 0.332

2011 194,264 738 0.380

1. Return data for hatchery origin winter Chinook from the Service’s Hatchery Evaluation Program, Red

Bluff, California and the RMPC database (http://www.rmpc.org).

1.13) Date program started (years in operation), or is expected to start

The Service initially propagated winter Chinook salmon at Coleman NFH in 1955. This initial attempt, as well as several subsequent efforts from 1958 through 1967, was generally unsuccessful. Similarly, from 1978 through 1985, several additional attempts to propagate winter Chinook salmon at Coleman NFH were met with limited success as high water temperatures at the Coleman NFH on Battle Creek resulted in substantial mortality of broodstock, eggs, and juveniles.

With a decline in the natural-origin winter Chinook salmon population and a pending petition to list winter Chinook salmon under the ESA, the Service re-committed to developing a successful propagation program for winter Chinook in 1988. The goal of the resurrected Winter Chinook

Integrated-Recovery Supplementation Program would be to supplement natural production and assist in recovery of winter Chinook salmon in the upper Sacramento River. Winter Chinook salmon were propagated at the Coleman NFH, located on Battle Creek, from 1989 through 1995.

However, despite attempts to imprint juveniles to the Sacramento River, hatchery-origin adults instead returned to the site of the hatchery on Battle Creek, where suitable spawning habitats were not available. Because of this failure to imprint juveniles to the Sacramento River and additional concerns about possible hybridization with spring Chinook, the Service temporarily discontinued collecting winter Chinook broodstock during 1996 and 1997. During these years, hatchery spawning of winter Chinook was limited to very low numbers of fish from a Captive

Broodstock Program that was conducted cooperatively with the Bodega Marine Laboratory of the University of California at Davis and the Steinhart Aquarium of the California Academy of

Sciences, San Francisco, California. The collection of winter Chinook broodstock from the

Sacramento River was re-initiated in 1998 after refined broodstock selection methods and a new rearing facility on the Sacramento River (Livingston Stone NFH) alleviated concerns of hybridization and imprinting. Since that time the winter Chinook propagation program has operated continuously, including the annual collection and spawning of broodstock from the upper Sacramento River.

1.14) Expected duration of program The Winter Chinook Integrated-Recovery Supplementation Program is a temporary measure to assist in the recovery of the winter-run Chinook ESU, which currently includes only one population in the upper Sacramento River. Hatchery propagation of winter Chinook is expected to cease when the ESU has been recovered and the program is no longer needed to support reintroduction efforts. The Final Recovery Plan calls for the development of criteria and a process for phasing out the Livingston Stone winter-run Chinook salmon hatchery program as recovery criteria are reached.

1.15) Watersheds targeted by program The Winter Chinook salmon Integrated-Recovery Supplementation Program at Livingston Stone

NFH is operated to supplement natural production in the upper Sacramento River. All natural spawning of Sacramento River Winter Chinook Salmon occurs in the Sacramento River upstream of the city of Red Bluff, California (Pacific States Marine Fisheries Commission

[PSMFC] Recovery Location code: 6FCSASAF ABRB). This same recovery location code is used in CalFish to identify spawning locations for winter Chinook, which are primarily within the city limits of Redding, California.

1.16) Indicate alternative actions considered for attaining program goals, and reasons why those actions are not being proposed Several alternative/complementary actions have been implemented to improve environmental conditions and population status of winter Chinook salmon, including habitat restoration activities (including a large-scale restoration project on Battle Creek), establishment of criteria for managing flow and water temperature in the upper Sacramento River, harvest restrictions, removal of migration impediments, and a myriad of actions to improve survival through the

Delta.

Processes are underway to introduce winter Chinook to areas where they have been extirpated, such as upstream of Shasta Dam and Battle Creek; these actions could be considered either alternative or complementary actions to the conservation hatchery program. Both of these actions have been proposed and are in process of being implemented through separate (but linked) planning processes, and will likely involve participation by the Winter Chinook

Conservation Hatchery.

SECTION 2. PROGRAM EFFECTS ON NMFS ESA-LISTED SALMONID

POPULATIONS

2.1) List all ESA permits or authorizations in hand for the hatchery program

Section 7 Permitting History:

Programs: Artificial propagation of non-listed hatchery-origin fall and late-fall

Chinook salmon and ESA-listed steelhead

Current Permit: Section 7 Biological Opinion covering propagation of non-listed Chinook salmon and ESA-listed steelhead at Coleman NFH

Issue Date: February 06, 2014

Section 10 Permitting History:

Program: Artificial propagation of ESA-listed winter Chinook salmon

Current Permit: Section 10 Enhancement Permit (No. 1027) authorizing the winter

Chinook salmon propagation and Captive Broodstock Programs, and associated monitoring projects. Application for renewal of Permit 1027

(Permit 16477) was submitted July 2013 and is currently being processed by NMFS

Issue Date: January 31, 1997

Expiration Date: July 31, 2001

Program: Monitoring projects targeting winter Chinook salmon conducted from the

Red Bluff Fish and Wildlife Office

Current Permit: Section 10 Permit (No. 1415) authorizing the take of winter Chinook salmon for various monitoring projects

Issue Date: February 6, 2014

Expiration Date: December 31, 2018

2.2) Provide descriptions, status, and projected take actions and levels for NMFS ESA-listed natural populations in the target area

2.2.1) Description of NMFS ESA-listed salmonid population(s) affected by the program Both hatchery and naturally produced winter Chinook salmon are included in the ESU of

Sacramento River winter Chinook salmon and are provided protections under section 9 of the

Endangered Species Act. Information presented below briefly summarizes biological information and life history characteristics of Sacramento River Winter Chinook Salmon and

Central Valley Spring Chinook Salmon and Central Valley Steelhead, which could be affected by the Winter Chinook Integrated-Recovery Conservation Hatchery Program at the Livingston

Stone NFH. Below, general information is presented on geographic distribution and life history characteristics of ESA-listed salmonids potentially affected by the integrated hatchery program.

Sacramento River Winter Chinook Salmon

Spawning habitat for winter Chinook salmon is restricted to downstream of the Keswick Dam, primarily within the city limits of Redding, California. Prior to 2012 spawning migrations of winter Chinook were partially blocked or delayed by the RBDD and limited spawning occurred downstream as far as the city of Red Bluff, California. The RBDD was deactivated in 2012, and is no longer a migration impediment. Winter Chinook salmon generally migrate past the RBDD between mid-December and early August, with most fish passing that point between January and

May and numbers peaking in March. Winter Chinook spawning occurs from mid-April through mid-August, with most spawning activity occurring in May and June. Based on data collected in the Sacramento River carcass survey from 2001 through 2010, age structure of hatchery-origin winter Chinook salmon was 6.2% age-2, 91.4% age-3, and 2.4% age-4, with a rare age-5 fish returning. Detailed information on the age structure of natural-origin winter Chinook salmon is not readily available, but proportion of jacks (age-2) and adults (age 3+) from 2001 to 2010 were

5.1% and 94.9%, respectively based on length-frequency distributions. Fisher (1994) reported that most winter Chinook females mature at age-3 (1% age-2, 91% age-3, and 8% age-4).

Size and sex ratio data for spawning winter Chinook salmon are available for adults captured during 1998 through 2011 at the Battle Creek barrier weir, RBDD fish trap, and KDFT. Adult males ranged between 240 and 1,151 millimeter (mm) fork length (FL), and females ranged between 500 and 1,000 mm FL. Average male-to-female sex ratio was approximately 0.9:1.

Winter Chinook eggs incubate and hatch in about two months, depending on water temperatures.

Juveniles emerge between the end of June and mid-October. Juvenile winter Chinook salmon generally emigrate between August and April, with peak emigration rates at RBDD in September to early October. Studies involving acoustic tagging of juvenile hatchery-origin winter Chinook provide information on survival and travel speeds during their emigration to the Delta. In studies conducted in 2013 and 2014, survival and travel speeds of acoustically tagged hatchery-origin winter Chinook was shown to be highly variable and largely dependent on environmental conditions in the Sacramento River. Acoustic tagged winter Chinook emigrating coincident with precipitation events, associated with increased river flow and turbidity, travel downstream faster and survive at higher rates as compared to winter Chinook emigrating during conditions of low flow and clear water. For example, survival of acoustic tagged winter Chinook in 2014 (0.42), which were associated with a rainfall event in the upper Sacramento River Basin, exceeded nearly three-fold those conducted in 2013 (0.16), which was not associated with a precipitation event (A. Amman, NMFS, personal communication). Juvenile winter Chinook salmon enter saltwater at approximately 120 mm FL.

Table 2.2.1 Size ranges, means, and sex ratios of winter Chinook salmon captured during broodstock collection activities at the Coleman NFH barrier weir, Red Bluff Diversion

Dam, and Keswick Dam Fish Trap for years 1998-2014 a,b

Males Females

Return

Year

Fork Length (mm)

Fork Length (mm)

Sex

Ratio

Number Min Max Mean Number Min Max Mean (♂ to

38 621 833 735

76 523 815 675

0.5 to 1

14 488 818 569

10 617 718 672

1.4 to 1

50 391 958 674

59 673 886 767

0.8 to 1

117 445 1,151 686

89 584 845 737

1.3 to 1

87 450 1,000 693

101 665 828 750

0.9 to 1

106 412 1,000 671

121 538 880 749

252 420 935 586

68 600 881 755

3.7 to 1

163 475 1,000 785

211 620 910 779

151 490 1,000 829

163 620 1,000 780

56 430 1,000 836

98 680 990 787

0.6 to 1

96 450 930 763

98 500 890 778

1.0 to 1

107 550 990 852

162 520 900 775

0.7 to 1

191 240 1,010 819

228 560 980 737

185 480 1,000 641

193 500 980 655

1.0 to 1

313 520 930 804

490 580 880 731

0.6 to 1

132 440 1,000 733

182 550 820 733

178 440 1,041 701

247 540 1,000 760

Overall 2,236 240 1,151 728 2,596 500 1,000 742 0.9 to 1

a. Source: U.S. Fish and Wildlife Service unpublished data.

b. Winter Chinook salmon were identified through genetic analyses. Genetic analyses for 1998 to 2003 were conducted by Bodega Marine Laboratory, University of California-Davis, Bodega, California. Genetic analyses for 2004 to present were conducted by the Abernathy Fish Technology Center, USFWS, Longview, Washington.

Central Valley Spring Chinook Salmon

Current spawning habitats in the upper Sacramento River include the mainstem Sacramento

River downstream of Keswick Dam and Clear, Beegum, Battle, Antelope, Mill, Deer, and Butte creeks. Central Valley Spring Chinook also occur in Feather and Yuba Rivers, and spring

Chinook are currently being reintroduced as an experimental population into the San Joaquin

River. Migration of adult spring Chinook salmon in the upper Sacramento River begins in late-

March. Historical accounts suggest that spring Chinook salmon migration continued until

October, peaking July through September. However, recent data for spring Chinook populations in Mill and Deer creeks show adult migrations occurring primarily from March through June, peaking during the month of May. Changes in timing of migration apparently occurred after the construction of Shasta Dam, and indicate possible hybridization with fall Chinook salmon.

Spring Chinook spawning occurs from mid-August through October and peaks in late

September. Data on age and sex ratios of upper Sacramento River spring Chinook spawners are not currently available.

Age at emigration varies; spring Chinook salmon have been captured emigrating past the RBDD as fry, fingerlings, and yearlings. Newly-emerged spring Chinook fry begin migrating past

RBDD in November. Emigration continues through April, with the largest numbers of juveniles passing RBDD as fry in December and January. Spring Chinook salmon undergo physiological changes that enable transition to saltwater at about 80 mm FL.

Central Valley Steelhead

Life history characteristics for steelhead are highly variable. Adult steelhead migrate past RBDD throughout the year. Most of the migrating adults arrive between the end of August and the end of November, with peak numbers passing in late September and early October. Spawning occurs between late December and early May, peaking in February (Hallock 1989, Busby et al. 1996).

Hallock (1989) reports age structure of naturally-spawning steelhead as follows: 17% age-2, 41% age-3, 33% age-4, 6% age-5, and 2% age-6. Most steelhead spawn once then die, but repeat spawning does occur, mostly among females. Analysis of scale data indicated 83% were first-time spawners, 14% were second-time spawners, 2% were spawning for the third time, and

1% spawned for the fourth time (Hallock 1989). Sex ratios for naturally-spawning populations of steelhead in the Sacramento River are not available, but overall sex ratio of steelhead along the west coast of the US is thought to be 1 to 1 (Pauley et al. 1986).

Steelhead eggs generally hatch in four to seven weeks, and fry emerge one to two weeks after hatching (Pauley et al. 1986). Juvenile steelhead may emigrate soon after emergence, or spend one to two years in freshwater before their seaward migration. Hallock (1989) reported a small percentage of steelhead rear for three years in freshwater before smolting. Most steelhead fry disperse downstream past the RBDD shortly after emergence from the gravels (USFWS 2002).

Newly-emerged steelhead fry emigrate from the upper Sacramento River in two temporal peaks annually. Steelhead fry (≈50 mm) typically begin to pass RBDD in February and downstream movement continues through August. A second, distinct peak of steelhead fry typically begins to pass RBDD in early-July and continues through November (Johnson and Martin 1997, USFWS

2002).

Southern Distinct Population Segment (DPS) of North American Green Sturgeon, Southern

Resident Killer Whale, and Delta Smelt

The Southern DPS of North American Green Sturgeon, Southern Resident Killer Whale, and

Delta Smelt are ESA-listed species that overlap in time and space with a portion of the life cycle of winter Chinook salmon that are not expected to be negatively affected by the propagation program at the Livingston Stone NFH. Southern Resident Killer Whale could benefit slightly from hatchery production of winter Chinook due to increased forage base of salmon, which is their principle prey item.

Identify the NMFS ESA-listed population(s) that will be directly affected by the program

The Sacramento River winter Chinook salmon ESU will be directly affected by Winter Chinook

Integrated-Recovery Supplementation Program. Winter Chinook are trapped from the upper

Sacramento River for use as hatchery broodstock. Returning hatchery-origin adults are intended to spawn in the upper Sacramento River and integrate into the naturally spawning population.

Identify the NMFS ESA-listed population(s) that may be incidentally affected by the program

Central Valley Spring Chinook, Central Valley steelhead, the Southern DPS of North American

Green Sturgeon, and Southern Resident Killer Whale may be incidentally affected by the Winter

Chinook Integrated-Recovery Supplementation Program.

2.2.2) Status of NMFS ESA-listed salmonid population(s) affected by the program

Describe the status of the listed natural population(s) relative to “critical” and “viable” population thresholds Sacramento River Winter Chinook Salmon

Sacramento River Winter Chinook Salmon were historically abundant and comprised of populations in the McCloud, Pit, Little Sacramento, and Calaveras rivers. Evidence also indicates winter Chinook inhabited Battle Creek at least on an intermittent basis. Most of these populations have since been isolated from historic native spawning areas by the construction and operation of Shasta Dam. Currently available spawning habitats are restricted to the main stem

Sacramento River between the Keswick Dam and the city of Red Bluff.

Estimates of winter Chinook abundance have been derived using a combination of methods.

From 1967 to 2008, estimates for winter Chinook abundance were derived by counting passage through the fish ladders at the RBDD.