Attachment_15-Hatchery_Genetic_Mgmt_Plan_2013.pdf

HATCHERY AND GENETIC MANAGEMENT PLAN

Hatchery Program:

Species or Hatchery Stock:

Agency/Operator:

Watershed and Region:

Date Submitted:

Date Last Updated:

Livingston Stone National Fish Hatchery

Sacramento River Winter Chinook Salmon (Oncorhynchus tshawytscha)

U.S. Fish and Wildlife Service

Sacramento River

July 03, 2013

Initial Submission

SECTION 1. GENERAL PROGRAM DESCRIPTION

1.1) Name of hatchery or program.

Winter Chinook are propagated at the Livingston Stone National Fish Hatchery (NFH).

Together with the Coleman NFH, these two facilities comprise the Coleman NFH Complex

1.2) Species and population (or stock) under propagation, and ESA status.

Sacramento River Winter Chinook Salmon (Oncorhynchus tshawytscha) are listed as endangered under the Endangered Species Act of 1973.

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

Primary Contact Mr. Scott Hamelberg, 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: scott_hamelberg@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. Brian Person, 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 $4.75 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., Central Valley Project Improvement Act [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. The delta smelt conservation program is operated by staff of the Livingston Stone NFH and funding for the delta smelt conservation 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 (FWO) 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. The stock location code recognized by the Pacific States Marine Fisheries Commission (PSMFC) Regional Mark Processing Center for Livingston Stone NFH is 6FCSASAF LVNH.

1.6) Type of program.

The winter Chinook salmon propagation program is an integrated-recovery program. That is, 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 rebuilding and recovery of that population. Hatchery-origin winter Chinook 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.

1.7) Purpose (Goal) of program.

The primary goal of the Service’s propagation program at Livingston Stone NFH is to provide a demographic enhancement to the natural spawning component of the winter Chinook population in the upper Sacramento River, assisting in the recovery of that population. Additionally, the program provides a source of marked and tagged winter Chinook that are used to monitor and assess impacts resulting from the commercial and sport ocean salmon fishery.

1.8) Justification for the program.

Livingston Stone NFH, a substation of Coleman NFH, was constructed by Reclamation in 1997.

The facility was constructed for the explicit purpose of propagating ESA-listed winter Chinook salmon to supplement natural production and assist in the recovery of that population. All or nearly all of the historic spawning and rearing habitat of Sacramento River Winter Chinook salmon is blocked by Shasta Dam. The winter Chinook supplementation program is supported in NMFS’s draft Recovery Plan for winter Chinook salmon.

1.9) List of program “Performance Standards”.

The following performance standards have been designed to evaluate the benefits and risks of fish propagation 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 harvest, restoration, conservation/preservation, and/or research). Performance standards categorized as “risks” measure the possible risks the artificial propagation program may pose to the naturally reproducing component of the populations. Performance standards designed to assess benefits

(B) are listed first, with performance standards designed to assess risks (R) following.

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

Performance Standards to Evaluate Risks

Risk Number Standard / Guideline

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

R2. Do not introduce, spread, or amplify pathogens

R3. Reduce the potential for negative genetic effects to natural stocks

R4. Conduct research to evaluate potential effects on natural stocks and adaptively manage hatchery operations and activities

R5. Minimize harmful effects of program operations on the ESA-listed population

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 winter Chinook propagation at the Livingston Stone NFH. Performance indicators have been separated into two categories: benefits (B) that the hatchery program will provide to the listed population by meeting program objectives; and risks (R) that the hatchery program may be pose to the listed 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. Artificial propagation of winter Chinook salmon at Livingston Stone NFH is conducted to supplement the natural population in the Sacramento River. The basis for the winter Chinook supplementation program is that hatchery production can provide a higher survival from egg-to-smolt life stages than occurs 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 parentage type analysis to confirm 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, only natural-origin adults are used as hatchery broodstock.

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 divergence between hatchery and natural stocks.

Relevant fish culture practices:

· 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

· 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 phenotype and mark status to effectively identify and spawn only winter Chinook

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

· Use genetic techniques to effectively identify target broodstock

Performance Indicators:

· 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 from fish propagation programs at the Livingston Stone NFH 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.

Relevant fish culture practices:

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

· Mark and CWT experimental fish prior to release

Performance Indicators:

· As appropriate for specific experimental design

Constraints:

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

· The potential for reduced survival of experimental groups limits 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 (supplementation), 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.

Relevant fish culture practices:

· All existing fish culture practices at the Livingston Stone NFH

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

Performance Indicators:

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

· Mark screening and tag recovery efforts of adults collected on the Sacramento River Winter

Chinook Carcass Survey

· Periodically review and summarize ocean harvest data

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

Constraints:

· ESA-status as endangered limits the extent that winter Chinook can be used in research

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

Relevant fish culture practices:

· 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

Performance Indicators:

· 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 advice 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.

Relevant fish culture practices:

· 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 minimize occurrence of disease in hatchery and natural fish

· 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)

Performance Indicators:

· Analyze survival trends for different life stages at the hatcheries

Constraints:

· Difficult to control all pathways of disease transmission

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 intended to avoid or minimize their harvest in ocean and freshwater commercial or recreational fisheries.

To accomplish this, harvest constraints are developed in the Fishery Management Plan that reduce impacts to winter Chinook by implementing harvest restrictions. Winter Chinook originating at the Livingston Stone NFH are the only source of coded-wire-tagged winter Chinook. Data associated with harvest of tagged hatchery winter Chinook are used to inform the development of fishery regulations and provide feedback to evaluate their success.

Relevant fish culture practices:

· 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

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 to achieve the primary program goal of supplementing the abundance of winter Chinook while reducing the potential for negative effects resulting from the propagation program.

Relevant fish culture practices:

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

River

· Use only natural-origin fish as hatchery broodstock

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

Performance Indicators:

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

Constraints:

· Environmental conditions limit field monitoring capabilities

Performance Standard R2: Do not introduce, spread, or amplify pathogens of natural stocks The primary goal of fish health management programs at the Livingston Stone NFH is to produce healthy fish that will contribute to program goals of supplementation, conservation, and preservation, while minimizing the potential for negative effects on natural stocks. This goal is accomplished using state-of-the art technologies in disease prevention along with assistance and technical advice from the CA-NV FHC.

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. 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.

Relevant fish culture practices:

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

· Develop and conduct a disease control protocol for marking and tagging Chinook salmon

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

· Routinely monitor on-station mortality of Chinook salmon and conduct examinations when mortality levels exceed normal levels

Constraints:

· It is often difficult to determine the mode of disease transmittance

Performance Standard R3: Reduce the potential for negative genetic effects to natural stocks Fish propagation practices at the Livingston Stone NFH are conducted so that hatchery fish remain genetically similar to naturally produced winter Chinook in the upper Sacramento River.

Maintaining a high level of genetic similarity between fish of hatchery- and natural-origins decreases the possibility of hatchery-origin fish having deleterious genetic effects. Hatchery broodstocks are screened using phenotypic and genetic criteria to reduce chances of interbreeding between different stocks (e.g., winter and spring or fall and late-fall). Some of the fish culture practices employed at the Livingston Stone NFHs to accomplish this Performance Standard are listed below.

Relevant fish culture practices:

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

· Use only native, 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.

Performance Indicators:

· Monitor and analyze trends in fecundity, survival for different life stages, return rates, return timing, spawn timing, adult size and age composition, and other parameters to indicate potentially deleterious changes occurring in the hatchery stock

· Calculate estimates of effective population size associated with releases of juvenile hatchery-origin winter Chinook salmon

Other Indicators and Achievements

· Developed genetic techniques to effectively identify winter Chinook broodstock

Performance Standard R4: Conduct monitoring, evaluations, and research to investigate potential effects on natural stocks and adaptively manage hatchery operations

Monitoring and evaluation are conducted to evaluate potential negative effects to resulting from the winter Chinook propagation program at the Livingston Stone NFH. Knowledge gained through experimentation and research is used to modify fish culture practices, when appropriate, to maximize program benefits and reduce negative effects.

Relevant fish culture practices:

· Existing fish culture practices at the Livingston Stone NFH

· The existing Hatchery Evaluation program conducted from the Red Bluff FWO

Performance Indicators:

· Investigated mode(s) and potential for IHNV transmission between hatchery- and natural-origin Chinook salmon (inferences gained from research using fall Chinook at Coleman

NFH)

· Conducted a survey for IHNV in natural-origin fall Chinook salmon from Battle Creek and the upper Sacramento River (inferences gained from research using fall Chinook)

· Conducted a post-release evaluation of hatchery-origin smolts to examine disease progression during emigration (inferences gained from research using fall Chinook)

· Conducted a grand-parentage analysis to document successful reproduction of hatchery-origin winter Chinook

· Conducting an acoustic tracking study to evaluate effects of broodstock collection and to evaluate the accuracy of existing methods to estimate abundance

Constraints:

· Environmental conditions (e.g., flows, turbidity) may limit field monitoring capabilities

· ESA-status as endangered limits the extent that winter Chinook can be used in research

Performance Standard R5: Minimize harmful effects of program operations on the ESA-listed population The act of conducting propagation activities for 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 ensure that the program achieves the intended demographic benefits

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

· Planned a study to monitor the movements of winter Chinook released during the course of broodstock collection activities

1.11) Expected size of program.

Unlike typical production-oriented hatchery programs, the winter Chinook program does not have an annual target for juvenile production. Rather, production levels for the winter Chinook propagation program 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). No hatchery-origin winter Chinook are used as broodstock to reduce the potential for negative effects resulting from domestication selection.

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

The broodstock 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.

1.11.2) Proposed annual fish release levels (maximum number) by life stage and location.

Annual targets for the winter Chinook production are not defined 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 annual production level anticipated when broodstock collections are maximized (i.e., n=120 spawners comprised of 60 females and 60 males) is approximately 250,000 smolts.

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 Approx. 250,000 (maximum)

Yearling N/A 0

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 2008, 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 0.41% (95% CI, 0.06% - 0.77%) of the total number of juveniles released per brood year. The total contribution includes an average of approximately 854 (95% CI, 11 - 1697) adults returning to the upper Sacramento River.

Table 1.12 Estimated proportion of juvenile winter Chinook salmon produced at the Livingston Stone NFH from 2000 through 2008 returning to spawning areas of the upper Sacramento River. Data presented include progeny produced from cryopreserved semen, which is a standard production strategy at Livingston Stone NFH. Captive broodstock progeny were excluded from tabulated information as these releases were experimental (i.e., a study to evaluate the captive rearing program) and have been discontinued, and may not be representative of general performance of the supplementation program.

Brood Year Release No. Return Year Return No. % Return

2000 166,206 2003 474 0.285 2001 190,732 2004 633 0.332 2002 165,015 2005 3,092 1.874 2003 152,011 2006 2,382 1.567 2004 148,385 2007 189 0.127 2005 160,274 2008 170 0.106 2006 196,288 2009 467 0.238 2007 71,883 2010 199 0.277 2008 146,211 2011 80 0.055

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

The Service initially attempted to propagate winter Chinook salmon at Coleman NFH in 1955.

This 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. High water temperatures at the hatchery on Battle Creek resulted in substantial mortality of broodstock, eggs, and juveniles.

The Service re-committed to developing a successful propagation program for winter Chinook in 1988, with a decline in the natural winter Chinook salmon population and a pending petition to list winter Chinook salmon under the Endangered Species Act. The goal of the resurrected winter Chinook propagation 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. 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.

Supplementation of winter Chinook salmon using the propagation program at the Livingston Stone NFH is a temporary measure to assist in the recovery of winter Chinook salmon in the upper Sacramento River. Winter Chinook propagation is expected to cease when the population has been recovered, as described in the NMFS’ Draft Recovery Plan.

A captive broodstock component of the winter Chinook propagation program was conducted from 1991 to 2007. The winter Chinook captive broodstock program was discontinued in 2007 based on the increased abundance of the natural spawning population. Previous guidance from NMFS had recommended the captive broodstock program be terminated when the size of the wild population reaches 1,000 per year on a sustained basis. If the abundance level of winter Chinook salmon again falls to critically low levels, the captive broodstock element of this program could be reconsidered.

1.15) Watersheds targeted by program.

The winter Chinook salmon propagation 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 upstream of the city of Red Bluff, California (PSMFC Recovery Location code: 6FCSASAF ABRB), primarily within the city limits of Redding, California.

Planning is underway to introduce winter Chinook to restored habitats of Battle Creek. The Service is collaborating with the California Department of Fish and Wildlife, NMFS, and others to develop a strategy to introduce winter Chinook to that tributary. The role that the Livingston Stone NFH propagation program has in this effort, if any, has not yet been determined.

1.16) Indicate alternative actions considered for attaining program goals, and reasons why those actions are not being proposed.

Several alternative and 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), flow and water temperature regulation, harvest restrictions, removal of migration impediments, and a myriad of actions to improve survival through the Delta.

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 steelhead Current Permit: Section 7 Biological Opinion covering propagation of non-listed salmonids at Coleman NFH Issue Date: February 18, 1999 Expiration Date: December 31, 1999, the Service is currently operating under an extension of this permit

In July, 2011, the Service submitted an updated Biological Assessment and is currently awaiting NMFS’ issuance of a Biological Opinion.

Section 10 Permitting History:

Program: Artificial propagation of ESA-listed winter Chinook salmon Current Permit: Section 10 Enhancement Permit (No. 1,027) authorizing the winter

Chinook salmon propagation and captive broodstock programs, and associated monitoring projects

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. 1,415) authorizing the take of winter Chinook salmon for various monitoring projects Issue Date: Permit Application originally submitted 2002 and resubmitted 2005 Expiration Date: Permit is currently being processed by NMFS

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.

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 supplementation program at the Livingston Stone NFH. General information is presented on geographic distribution and life history characteristics.

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 Red Bluff Diversion Dam (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. Migrating 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 Keswick Dam fish trap. Adult males ranged between 240 and 1,151 millimeter (mm) fork length (FL), and females ranged between 500 and 980 mm FL. Average male-to-female sex ratio was approximately 1:1. 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 in September. 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 1998-20008a,b.

Males Females

Return Year

Fork Length (mm)

Fork Length (mm)

Sex

Ratio Number Min Max Mean Number Min Max Mean (♂ to ♀)

1998 42 621 833 724 63 523 781 674 0.7 to 1 1999 14 492 772 578 10 610 782 678 1.4 to 1 2000 48 391 958 678 57 673 886 768 0.8 to 1 2001 116 445 1,151 688 89 584 845 737 1.3 to 1 2002 90 450 1,000 693 104 665 828 750 0.9 to 1 2003 114 412 1,000 674 123 538 880 750 0.9 to 1 2004 255 420 935 587 65 640 881 757 3.9 to 1 2005 164 475 1,000 786 212 620 910 779 0.8 to 1 2006 160 490 1,000 829 149 620 900 776 1.1 to 1 2007 79 430 1,000 819 75 680 960 789 1.1 to 1 2008 96 450 930 763 98 500 890 778 1.0 to 1 2009 105 550 990 852 163 520 930 776 0.6 to 1 2010 191 240 1010 819 228 560 980 737 0.8 to 1 2011 185 480 1000 641 193 500 980 655 1.0 to 1

Overall 1,659 240 1,151 724 1,629 500 980 743 1.0 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 2008 were conducted by the Abernathy Fish Technology Center, Service, Longview, Washington.

Central Valley Spring Chinook Salmon Current spawning habitats for spring Chinook salmon are restricted to the upper Sacramento River (below Keswick Dam), a few larger east-side tributaries (including Mill, Deer, and Butte creeks), Clear Creek, Battle Creek, and a remnant population in Beegum Creek. 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 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 pass 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 (Service 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, Service 2002).

- 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 the propagation program at the Livingston Stone NFH. 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 Distinct Population Segment (DPS) of North American Green Sturgeon, and Southern Resident Killer Whale may be incidentally affected by artificial propagation programs at the Livingston Stone NFH.

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 (see definitions in “Attachment 1").

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. 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 mainstem 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. However, the ability to estimate winter Chinook passage at the RBDD ended after 2008 with the completion of construction of a pumping plant, which enabled year-round diversion of water without lowering the dam gates. Beginning in 1996, estimates of winter Chinook spawner abundance have been derived by employing daily surveys of winter Chinook spawning areas and a combination of carcass mark-and-recapture estimators, including the Peterson, Schaefer, Jolly-Seber, and Cormack Jolly-Seber.

Abundance of winter Chinook have fluctuated greatly, exhibiting multi-year trends of either increase or decrease. From 1967 through the early 1990s, the Sacramento River winter Chinook salmon population declined at an average rate of 18% per year, or roughly 50% per generation.

Based on passage estimates at RBDD, the Sacramento River winter Chinook salmon population reached a low abundance in 1994 when an estimated 189 adults passed above RBDD. From the early 1990s until 2006 the winter Chinook salmon population steadily increased in abundance, reaching a high of 17,296. Since 2006, the abundance of winter Chinook spawners has consistently declined to an estimate of only 825 in 2011. The cohort replacement rate for winter Chinook salmon returning in 2012 was less than one for the sixth consecutive year, indicating a trend of declining abundance. Estimated number of natural-origin winter Chinook juveniles emigrating past the RBDD from 2002 to 2006 averaged over 6.8 million, ranging between 3,758,790 and 8,941,241 (Standard Deviation [SD]=2,062,045; Service 2008a).

Newly developed recovery criteria for winter Chinook salmon have been proposed by NMFS (2009b) and included in the draft recovery plan for ESA-listed Central Valley salmonids. The new recovery criteria incorporate four parameters into the assessments of population viability, including: diversity, spatial structure, productivity, and abundance. Recovery scenarios have been developed based on ESU, population, and ecological considerations to identify combinations of populations and population and habitat status levels that meet biological and threat abatement recovery criteria for the species. Considerations for the viability of the winter Chinook ESU depends on the number of populations, their individual status, their spatial arrangement with respect to each other, sources of catastrophic disturbance, and diversity of the populations and their habitats. In general terms, viability of the winter Chinook ESU increases with the number of populations, the viability of those populations, the diversity of the populations, and the diversity of habitats they occupy (Lindley et al. 2007). In order for winter Chinook to achieve recovery, three viable populations must exist at low risk of extinction.

Central Valley Spring Chinook Salmon Spring Chinook salmon were once the predominant run in the Central Valley. Present day abundance of spring Chinook has declined dramatically from historical levels. Commercial harvest data comparing average catch from 1916 through 1949 and 1950 through 1957 showed a 90% reduction in spring Chinook salmon harvest over that time period (Skinner 1958). Dam construction and habitat degradation have eliminated spring Chinook populations from the entire San Joaquin River Basin and from many tributaries to the Sacramento River Basin. Estimated spawner escapement for the Sacramento River basin population of spring Chinook salmon averaged 11,155 over the last 13 years, but yearly estimates ranged widely from just over 3,000 spawners to over 31,000 (Table 2-2). There are only a few isolated, naturally-spawning populations remaining and these all exist at relatively low levels of abundance (typically <1000) (Yoshiyama et al. 1998). Streams that support wild, persistent, and long-term documented populations of spring Chinook salmon are Mill, Deer, and Butte Creeks (CDFG 1998). Other streams that may support weak or non-persistent populations include Battle, Antelope, Cottonwood, Clear, and Big Chico Creeks (CDFG 1998). Spring Chinook salmon may also be present in the Feather River, another tributary to the Sacramento River. The extent of natural spawning by spring Chinook in the mainstem Sacramento River is unknown. Juvenile emigration data collected at the RBDD do not show a discrete emigration of spring Chinook from the upper Sacramento River; rather, most juveniles within the spring Chinook size-class appear to fit better into the leading-tail of fall Chinook distribution (Service 2002).

Hybridization with fall Chinook salmon is a primary concern for naturally-spawning spring Chinook salmon in the mainstem Sacramento River and elsewhere, because of similar spawn timing and lack of spatial separation in limited geographic distribution.

Central Valley Steelhead Run size estimates are not available for…