C06__Attachment_2_Captive_Broodstock_HGMP.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 –

Winter Chinook Captive Broodstock 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 Evolutionarily Significant Unit (ESU) of Sacramento River Winter-run Chinook salmon (Oncorhynchus tshawytscha) is 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), and 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:

The Coleman NFH Complex is a mitigation feature to partially offset losses of anadromous salmonids resulting from habitat losses caused by the construction and operation of Shasta and

Keswick dams, which are key components 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 NFH 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. 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 to conduct evaluations, monitoring, research, and permitting related to hatchery operations. The

Hatchery Evaluation Program at the Red Bluff Fish and Wildlife Office 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 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 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. Thus, winter Chinook captive broodstock are sourced from a program that is operated with an integrated-recovery strategy.

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.

Winter Chinook captive broodstock and their progeny may potentially be available to fulfill multiple purposes to advance the preservation and conservation of the winter Chinook ESU, including: 1) to provide a refugial population of winter Chinook in a safe and secure environment to be available for use as hatchery broodstock in the event of a catastrophic decline in the abundance of winter Chinook spawners in the Sacramento River; 2) to be a source of winter Chinook to contribute to multi-agency efforts to introduce winter Chinook upstream of

Shasta Dam; 3) to be a source of winter Chinook for multi-agency efforts to introduce winter

Chinook into restored habitats of Battle Creek; and 4) to be a source of winter Chinook to fulfill the needs of research projects approved by the Service, the National Marine Fisheries Service

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

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, as long as it is needed and operated as a conservation program

(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).

A captive broodstock program for Sacramento River winter Chinook was previously conducted from 1991 to 2007. That program was discontinued in 2007, based on the increased and sustained abundance of the natural spawning population. The Winter Chinook Captive

Broodstock Program was reinitiated in 2015, as a result of a mutual decision by the Service, National Marine Fisheries Service (NMFS), and the California Department of Fish and Wildlife

(CDFW). The decision to reinitiate the program was made, in part, to respond to threats to the winter Chinook population caused by the continuation of extreme drought and as a potential source of winter Chinook to be used for planned range expansion projects. Together with the integrated-hatchery program, the Winter Chinook Captive Broodstock Program is expected to increase the security of the winter Chinook ESU by rearing a captive population in a safe and secure environment, to be available for multiple potential uses, as mentioned above. Operated to achieve these purposes, the winter Chinook Captive Broodstock Program may be used to achieve two Priority 1 Recovery Actions, as identified I the Central Valley Salmon and Steelhead

Recovery Plan (NMFS 2014)

1) “Develop and implement a program to reintroduce winter-run Chinook salmon, spring-run Chinook salmon, and steelhead to historic habitats upstream of Shasta

Dam. The program should include feasibility studies, habitat evaluations, fish passage design studies, and pilot reintroduction phase prior to implementation of the long-term reintroduction program.”

2) “Develop and implement a winter-run Chinook salmon reintroduction plan to re-colonize historic habitats made accessible by the Battle Creek Salmon and Steelhead

Restoration Project.”

With the potential to benefit multiple projects, it will be necessary to determine how winter

Chinook captive broodstock and their progeny will be allocated amongst projects. Decisions regarding the apportioning of captive broodstock and their progeny towards each of these efforts has not yet been determined, but will be determined jointly by the Service, NMFS, and CDFW based on the merit of each competing need.

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

Winter Chinook Captive Broodstock Program.

Number Standard / Guideline

1. Provide winter Chinook captive broodstock and their progeny to be available, if necessary, to supplement broodstock for the integrated-recovery supplementation program, introduction to Battle Creek and upstream of Shasta Dam, and approved research projects

Preventing extinction, restoration, and recovery of native fish and aquatic ecosystems are priorities for the National Fish Hatchery System. One of the objectives of the Winter

Chinook Captive Broodstock Program is to propagate winter Chinook in a safe and secure environment so they are available to be used as broodstock in the Winter Chinook

Integrated-Recovery Supplementation Program, if necessary, due to a catastrophic decline in abundance of the natural spawning population. Additional objectives of the

Captive Broodstock Program are to produce winter Chinook to be available for efforts to introduce winter Chinook to Battle Creek and upstream of Shasta Dam, if necessary, and to provide winter Chinook for approved research projects. In providing fish for these purposes, winter Chinook from the Livingston Stone NFH advances efforts to conserve the species. Details of pilot studies and introduction strategies have yet to be developed.

1.10) List of program “Performance Indicators” The following performance indicators can be used to monitor and evaluate the winter Chinook

Captive Broodstock Program at the Livingston Stone NFH.

1.10.1) “Performance Indicators”

Performance Standard 1: Provide winter Chinook captive broodstock and their progeny to be available, if necessary, to supplement broodstock for the integrated-recovery supplementation program, introduction to Battle Creek and upstream of

Shasta Dam, and approved research projects

Performance Indicators:

· Estimated number of winter Chinook captive broodstock and their progeny available to satisfy the multiple program objectives

· Employed genetically-conscientious broodstock pairing and spawning protocols to promote retention of genetic diversity in captive broodstock progeny

· Selected juveniles for inclusion to the captive broodstock program in a manner that promotes retention of genetic variability

1.11) Expected size of program Production levels for the Winter Chinook Captive Broodstock Program are dictated by the number of juveniles that are retained from releases from the Integrated-Recovery

Supplementation Program. Beginning in the year 2015 (brood year 2014), 1035 winter Chinook juveniles were withheld from the Integrated-Recovery Supplementation Program release group.

These fish will be reared to maturity at the Livingston Stone NFH as captive broodstock.

Currently, we expect that approximately 1,000 fish will be withheld from future brood years;

however, the number of juveniles entered into the captive broodstock program will be re-considered on an annual basis by the Service, NMFS, and CDFW. Considerations in determining the actual number of juveniles to enter into the captive broodstock program annually are the ability of the Captive Broodstock Program to achieve the multiple program objectives while balancing the negative effects that result from removing winter Chinook from the integrated-recovery release groups. Based on previous performance of the Winter Chinook

Captive Broodstock Program, we anticipate at least 50% of the fishes retained as captive broodstock survive to sexual maturity, thereby producing approximately 500 mature winter

Chinook adults per brood year.

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

The Winter Chinook Captive Broodstock Program will instead utilize a portion of the juvenile winter Chinook salmon produced as part of the Winter Chinook Integrated-Recovery

Supplementation Program and will not require additional collection of broodstock.

Approximately 1,035 fish were withheld from releases in 2015 and approximately 1,000 winter

Chinook juveniles are planned to be withheld from future annual releases of the Integrated-

Recovery Supplementation Program; however, the actual number of juveniles withheld as captive broodstock in future years may be re-considered on an annual basis by the Service, NMFS, and CDFW.

1.11.2) Proposed annual fish release levels (maximum number) by life stage and location The Winter Chinook Captive Broodstock Program does not have annual targets for the release of winter Chinook captive broodstock or their progeny. Instead, the program goal is to maximize survival of fish retained as captive broodstock and to make available the maximum number of winter Chinook to satisfy the potential multiple objectives of the program. The numbers of winter Chinook of various life stages needed for each of these multiple objectives will be determined jointly by the Service, NMFS, and CDFW, and will require separate processes of planning and permitting.

1.12) Current program performance, including estimated smolt-to-adult survival rates, adult production levels, and escapement levels. Indicate the source of these data The goals of the captive broodstock program goals do not necessarily include release of captive broodstock or their progeny. However, the program aims to produce fish that could be made available to satisfy the multiple potential purposes, including augmenting broodstock for propagating supplementation releases and reintroducing winter Chinook to native habitats.

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 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

In 2015, one thousand thirty-five juvenile winter Chinook were withheld from the release of brood year 2014 winter Chinook to initiate the captive broodstock program.

A captive broodstock component of the winter Chinook propagation program was previously conducted from 1991 to 2007. The winter Chinook Captive Broodstock Program was discontinued in 2007 because the increased abundance of the natural spawning winter Chinook satisfied NMFS’ criteria for terminating the program. Previous guidance from NMFS had recommended the Captive Broodstock Program be considered for termination when the size of the wild population reached 1,000 per year on a sustained basis. Although the captive broodstock program was discontinued in 2007, the facilities and expertise for the operating the program continued to exist at the Livingston Stone NFH and these resources are again being used to reinstate the program.

1.14) Expected duration of program The Winter Chinook Captive Broodstock Program at the Livingston Stone NFH is a temporary measure, intended to safeguard the existence of the winter Chinook ESU and bolster the production of winter Chinook salmon to contribute to the program’s multiple objectives. A termination date for the captive broodstock program has not been determined, but it is expected to terminate when the objectives have been achieved, as determined jointly by the Service, NMFS, and CDFW.

1.15) Watersheds targeted by program Watersheds targeted by the Winter Chinook Captive Broodstock Program at Livingston Stone

NFH include the Sacramento River downstream of Keswick Dam, historic winter Chinook spawning habitats upstream of Shasta Dam, and Battle Creek. The Captive Broodstock Program benefits the Sacramento River downstream of Keswick Dam by providing additional winter

Chinook broodstock to supplement hatchery production during years when wild broodstock are unavailable or very limited in abundance. Historic winter Chinook habitats upstream of Shasta

Dam and Battle Creek are potentially benefitted by providing a source for winter Chinook for pilot studies and reintroduction efforts.

1.16) Indicate alternative actions considered for attaining program goals, and reasons why those actions are not being proposed Alternative actions considered for attaining program goals include 1) using surrogate species for pilot introduction efforts, and 2) using winter Chinook from the Integrated-Recovery Program in pilot reintroduction efforts; 3) waiting until sufficient fish numbers are present. Surrogate species are not a preferred option for pilot reintroduction efforts because it is unknown to what extent study results will be affected by the use of surrogate species; differences in morphology, behaviors, and the timing of life history events may result in erroneous interpretations and conclusions. Waiting until the population increases naturally is not a preferred option because the entire ESU of Sacramento River winter Chinook currently exists as only a single population, which, without redundancy, faces an elevated risk of extinction. The Winter Chinook Captive

Broodstock Program is a preferred source of providing fish for pilot reintroduction efforts because it can provide a source winter Chinook for multiple purposes while reducing the effects of removing individuals from the winter Chinook population. Because survival of winter

Chinook captive broodstock is substantially higher than that of fish living in the wild, introduction efforts benefit by utilizing the captive broodstock program fish to contribute to the goals of multiple projects while limiting the numbers of fish that are removed from the endangered population.

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 program and a separate one for Captive

Broodstock Program, 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 the Winter

Chinook Captive Broodstock Program at the Livingston Stone NFH. Winter Chinook retained as captive broodstock will be unavailable to be released into the Sacramento River as juveniles and contribute directly to natural spawning.

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 artificial propagation programs, including the captive broodstock program, 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 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 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 was decreased after 2012 when dam gates were raised for a longer portion of the migration season and passage-based estimates were ended after 2012 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 mid-1990s until 2006 the winter Chinook salmon population steadily increased in abundance, reaching a high of 17,296. From 2006 to 2011 the abundance of winter Chinook spawners declined to an estimate of only 827, and rebounded somewhat to approximately 2600, 6000, and

3,000 in 2012, 2013, and 2014, respectively. The cohort replacement rate for winter Chinook salmon was less than one for six consecutive years between 2007 and 2012, indicating a sustained period of declining abundance. Cohort replacement rates for winter Chinook returns of

2013 and 2014 were greater than one.

Recovery criteria for winter-run Chinook salmon have been developed and are included in the

Final Recovery Plan for ESA-listed Central Valley Salmon and Steelhead (NMFS 2014). The recovery criteria incorporate four parameters into the assessments of population viability, including: diversity, spatial structure, productivity, and abundance. In order for winter Chinook salmon to achieve the recovery criteria, three viable populations must exist at low risk of extinction (NMFS 2014).

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, based on run-timing, averaged 11,155 over the last 13 years, but yearly estimates ranged widely from just over 3,000 spawners to over 31,000. There are only a few isolated, naturally-spawning populations remaining and these generally exist at relatively low levels of abundance (typically

<1000) (NMFS 2014). The National Marine Fisheries Service (2014) classifies watersheds based on their known ability or potential to support viable populations of Spring Chinook. Core

1 watersheds have the highest potential to support viable populations (low risk of extinction) of spring Chinook. Core 2 populations have the potential to support populations at a moderate risk of extinction, and likely increase diversity within the ESU and provide a buffering effect against local catastrophic occurrences to Core 1 populations. Core 3 populations are present on an intermittent basis and require straying from nearby populations. Recovery Criteria for spring

Chinook include (NMFS 2014) core 1 populations in Battle Creek, Clear Creek, Deer Creek, Mill Creek, and Butte Creek along with reintroduction into Core 1 populations in historic habitat above Shasta Dam, in the upper Yuba River, and the San Joaquin River. Hybridization with fall

Chinook salmon is a primary concern for naturally-spawning spring Chinook salmon in the mainstem Sacramento River, Feather 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 the Central Valley steelhead DPS prior to the construction of Shasta Dam. Early salvage investigations associated with the construction of

Shasta Dam documented steelhead runs to the upper Sacramento River to be of “negligible” size

(Hanson et al. 1940), and it is likely that steelhead populations in the upper Sacramento River had already been depleted considerably at that time. Following construction of Shasta Dam, steelhead abundance in the upper Sacramento River was believed to initially increase appreciably

(Azevedo and Parkhurst 1958, Moffett 1949). Between 1953 and 1959, steelhead run-size estimates for the Sacramento River system (above Feather River) ranged from over 14,000 to over 28,000 (Hallock et al. 1961). Hallock et al. (1961) estimated a total run size of 40,000 in the Sacramento River system in the early 1960s. From 1966 through 1993 estimates of steelhead abundance in the upper Sacramento River were conducted by counting passage through the fish ladders at RBDD. Abundance of steelhead in the upper Sacramento River declined from the

1980s through 1993, when fish ladder counts at the RBDD were discontinued in mid-September.

Average escapement past RBDD for the years 1966 - 1977 (15,000) is more than eight times higher than the average return for the years 1989 - 1993 (1,855), a decline of about 9% per year.

Since 1998 all hatchery-origin steelhead in the Central Valley have been marked with an adipose fin-clip. The number of non-clipped (wild) steelhead has declined since 1998 in the Chipps

Island Trawl and CVP/SWP salvage data while the number of adipose fin-clipped steelhead has remained the same, further supporting conclusions of the trend of declining abundance of naturally spawned Central Valley steelhead.

The NMFS (2014) uses a similar system of classifying steelhead habitats as Core 1, Core 2, and

Core 3, based on their suitability of supporting viable populations. Core 1 watersheds have the highest potential to support viable populations of steelhead. Core 2 populations have a lower potential to support viable populations, and likely increase diversity within the DPS and provide a buffering effect against local catastrophic occurrences to Core 1 populations. Core 3 populations are present on an intermittent basis and require straying from nearby populations.

Based on this classification system, NMFS (2014) has identified the following populations as belonging to the Core 1 Classification: Battle Creek, Clear Creek, Deer Creek, Mill Creek, Antelope Creek, and the Calaveras River, as well as reintroductions upstream of Shasta Dam, and the upper Yuba River.

Southern DPS of North American Green Sturgeon

Green sturgeon are known to range from Baja California to the Bering Sea along the North

American continental shelf. In North America, spawning populations of green sturgeon are currently found in only three river systems: the Sacramento and Klamath rivers in California and the Rogue River in southern Oregon. Data from commercial trawl fisheries and tagging studies indicate that the green sturgeon occupy waters within the 110 meter contour (Erickson and

Hightower 2007). During the late summer and early fall, sub-adults and non-spawning adult green sturgeon frequently can be found aggregating in estuaries along the Pacific Coast (Emmett et al. 1991, Moser and Lindley 2007). Particularly large concentrations of green sturgeon from both the northern and southern populations occur in the Columbia River estuary, Willapa Bay, Grays Harbor and Winchester Bay, with smaller aggregations in Humboldt Bay, Tillamook Bay, Nehalem Bay, and San Francisco and San Pablo bays (Emmett et al 1991, Moyle et al. 1992, and

Beamesderfer et al. 2007). Data indicate that North American green sturgeon migrate from the

Sacramento-San Joaquin Estuary considerable distances up the Pacific Coast and sometimes migrate into other estuaries, particularly the Columbia River estuary. Green sturgeon tagging studies (CDFG 2002) confirm this life-history characteristic; the CDFG tagged a total of 233 green sturgeon in the San Pablo Bay estuary between 1954 and 2001. A total of 17 tagged fish were recovered: 3 in the Sacramento-San Joaquin Estuary, 2 in the Pacific Ocean off of

California, and 12 from commercial fisheries off of the Oregon and Washington coasts. Eight of the 12 recoveries in the commercial fishery occurred in the estuary of the Columbia River

(CDFG 2002). Interestingly, Lindley et al (2011) found that green sturgeon of the northern and southern DPS’s do not appear to enter the freshwater of each other’s natal rivers.

Abundance of the Southern DPS of green sturgeon is described in the NMFS status reviews

(http://www.nmfs.noaa.gov/pr/listing/reviews.htm). Israel (2006) estimated the abundance of green sturgeon spawners using sibling-based genetics, which indicated spawning populations upstream of the RBDD of 32 spawner pairs in 2002, 64 in 2003, 44 in 2004, 92 in 2005, and 124 in 2006. Limited information of population abundance comes from incidental captures of North

American green sturgeon while monitoring white sturgeon during the CDFG’s sturgeon tagging program (CDFG 2002). By comparing ratios of white sturgeon to green sturgeon captures, CDFG provides estimates of adult and sub-adult North American green sturgeon abundance.

Estimated abundance between 1954 and 2001 ranged from 175 fish in 1993 to more than 8,421 in 2001, and averaged 1,509 fish per year. Unfortunately, there are many biases and errors associated with these estimates, and CDFG does not consider these estimates reliable because they are based on small sample sizes, intermittent reporting, and are drawn from inferences made from incidental catches while monitoring catch of white sturgeon.

Collections of juvenile green sturgeon at the John E. Skinner Fish Collection Facility between

1968 and 2006 can also be used to make inferences on the abundance of the Southern DPS of green sturgeon. The average number of Southern DPS of green sturgeon entrained per year at the State Facility prior to 1986 was 732. From 1986 to 2006, the average per year was 47 (April

5, 2005, 70 FR 17386). For the Harvey O. Banks Pumping Plant, the average number prior to

1986 was 889; from 1986 to 2001 the average was 32 (April 5, 2005, 70 FR 17386). However, because these incidental catches at the State and Federal pumping plants are likely to be highly influenced by pumping volumes, these data have uncertain reliability for making inferences about green sturgeon abundance.

The Southern DPS of green sturgeon spawn in the Sacramento, Feather, and possibly the Yuba rivers. Most spawning occurs in the upper Sacramento River in deep pools between Dry Creek and just downstream of the Glen-Colusa Irrigation District (GCID) diversion (Antelope Creek).

Larval and juvenile green sturgeon have been caught in traps at two sites in the upper

Sacramento River: the RBDD (RM 342; Poytress 2011, 2013) and the GCID pumping plant

(RM 205; CDFG 2002). Salmonid monitoring efforts at RBDD and GCID on the upper

Sacramento River have captured between 0 and 2,068 larvae and juvenile green sturgeon per year (Adams et al. 2002). Larvae captured at the RBDD site are typically only a few days to a few weeks old, with lengths ranging from 24 to 31 mm. This body length is equivalent to 15 to

28 days post hatch as determined by Deng et al. (2002). Recent data indicate that very little production took place in 2007 and 2008 (13 and 3 larval green sturgeon captured in the RST monitoring sites at RBDD, respectively; Poytress 2008, Poytress et al. 2009).

Southern Resident Killer Whales

The historical abundance of Southern Residents is estimated from 140 to 200 whales. The minimum estimate (≈140) is the number of whales killed or removed for public display in the

1960s and 1970s added to the remaining population at the time of the captures. The maximum estimate (≈200) is based on a recent genetic analysis of microsatellite DNA (May 29, 2003, 68

FR 31980). At present, the Southern Resident population has declined to essentially the same size that was estimated during the early 1960s, when it was likely depleted (figure 4-13 in

Olesiuk et al. 1990). Since censuses began in 1974, J and K pods steadily increased; however, the population suffered an almost 20 percent decline from 1996-2001, largely driven by lower survival rates in L pod. There were increases in the overall population from 2002-2007, however, the population declined in 2008 with 85 Southern Residents counted, 25 in J pod, 19 in

K pod and 41 in L pod. Two additional whales have been reported missing since the 2008 census count.

Provide the most recent 12 year (e.g. 1988-present) progeny-to-parent ratios, survival data by life-stage, or other measures of productivity for the listed population. Indicate the source of these data

For brood years 2000 through 2014, the median estimated cohort replacement rate (CRR) was

0.80 for Sacramento River Winter Chinook salmon. The winter Chinook CRR was less than one for seven of the recent twelve recent years.

Table 2.2.2.1 Estimated run sizes and cohort replacement rates for Sacramento

River winter Chinook salmon, 2000-2014

Return Year Estimated Run Size Cohort Replacement Rate

2000 1,352

2001 8,224 -

2002 7,441 -

2003 8,218 6.08

2004 7,869 0.96

2005 15,839 2.13

2006 17,296 2.10

2007 2,541 0.32

2008 2,830 0.18

2009 4,537 0.26

2010 1,596 0.63

2011 827 0.29

2012 2,674 0.59

2013 6,123 3.84

2014 3,015 3.65

Median

0.80

Estimated Run Size from CDFG GRANDTAB file dated April 22, 2014

(http://www.calfish.org/portals/0/Programs/AdditionalPrograms/CDFGFisheriesBranch

/tabid/104/Default.aspx).

Cohort Replacement Rate (CRR) calculated by dividing the run size in year "x+3" by the run size in year "x". The predominant age at return for winter Chinook salmon is three years.

Return Year Estimated Run Size

2000 1,352

2001 8,224

2002 7,441

2003 8,218

2004 7,869

2005 15,839

2006 17,296

2007 2,541

2008 2,830

2009 4,537

2010 1,596

2011 827

2012 2,674

2013 6,123

2014 3,015 Estimated Run Size from CDFG GRANDTAB file dated April 22, 2014

(http://www.calfish.org/portals/0/Programs/AdditionalPrograms/CDFGFisheriesBranch/ta bid/104/Default.aspx).

- Provide the most recent 12 year (e.g. 1988-1999) annual spawning abundance estimates, or any other abundance information. Indicate the source of these data

Table 2.2.2.2 Estimated run size of Sacramento River Winter Chinook, 2000-2014

- Provide the most recent 12 year (e.g. 1988-1999) estimates of annual proportions of direct hatchery-origin and listed natural-origin fish on natural spawning grounds, if known.

Table 2.2.2.3 Sacramento River winter Chinook salmon estimated run size, estimated number and percentage of hatchery-origin winter Chinook for return years 2000 – 2014.

Return Year

Total Estimated

Run-size

Hatchery Origin

Run-size

% of Run

Hatchery Origin

2000 1,352 Not available -

2001 8,224 513 6.2

2002 7,441 570 7.7

2003 8,218 423 5.1

2004 7,869 636 8.1

2005 15,839 3,056 19.3

2006 17,296 2,380 13.8

2007 2,541 140 5.5

2008 2,830 170 6.0

2009 4,537 467 10.3

2010 1,596 199 12.5

2011 827 80 9.7

2012 2,674 809 30.3

2013 6,123 400 6.5

2014 3,015 705 23.4

Median 4,537 490 8.9

1 Estimated Run Size for 2000-2010 from CDFW GRANDTAB file dated February 1, (http://www.calfish.org/portals/0/Programs/AdditionalPrograms/CDFGFisheriesBranc h/tabid/104/Default.aspx). Estimated run size from 2011 from Doug Killam, CDFG

Red Bluff (pers. com.).

2 Hatchery-origin run size…