Attachment_17-Summary_of_Actions_to_Jumpstart_2018.pdf

Summary of Actions to Jumpstart the Reintroduction of Sacramento River Winter-run Chinook Salmon to Battle Creek, 2017 – 2018

Prepared By:

U.S. Fish and Wildlife Service

Red Bluff Fish and Wildlife Office

Red Bluff, California

August 2018

Photo Credits: (1) Robert Null, USFWS, Anderson, CA (2) Steve Martarano, USFWS, Sacramento, CA iii

TABLE OF CONTENTS

Document Overview

Background

Sacramento River Winter-run Chinook Salmon

Spawning Distribution

Status

Winter Chinook Salmon Conservation Hatchery

Severe Drought

Hatchery Role in Mitigating the Effects of Drought

Effects of Drought on Winter Chinook Abundance

Using captive broodstock to Improve Population Resiliency

Jumpstarting the Battle Creek SRWCS Reintroduction Process

Spawning

Incubation and Rearing

Marking and Tagging

Fish Health

Fine-scale Imprinting

Juvenile Releases

Next Steps

LITERATURE CITED

ATTACHMENT 1.Fish Health Inspection Report for captive winter Chinook Salmon broodstock, and their progeny, contributing to the brood year 2017 release group iv

TABLES

TABLE 1.Record of broodstock pairings and egg production for Sacramento River

Winter Chinook captive broodstock spawned at the Livingston Stone National

Fish Hatchery in 2017

TABLE 2.Relevant early life history dates and count summary of brood year 2017 winter Chinook Salmon captive broodstock progeny produced at the Livingston

Stone National Fish Hatchery and transferred for rearing to the Coleman National

Fish Hatchery (CNFH)

TABLE 3.Estimated rates of mark-tag retention and numbers (in parenthesis) of winter

Chinook released with various combinations of marks and tags, based on sampling conducted >21-days after marking and tagging

TABLE 4.Summary of release data for brood year 2017 winter Chinook Salmon captive broodstock progeny

FIGURES

FIGURE 1.Daily water temperature profile for the Coleman NFH from October 1 to

November 30, 2017

FIGURE 2.Measured rate of flow, cubic feet per second, on Battle Creek near the

Coleman National Fish Hatchery and on the Sacramento River at Bend Bridge from March 1 to May 2, 2018 (

FIGURE 3.Map of the North Fork Battle Creek section containing the three proposed winter Chinook Salmon captive progeny release sites

Document Overview This document describes actions taken during 2017 – 2018 to initiate the reintroduction of

Sacramento River winter-run Chinook Salmon Oncorhynchus tshawytscha (hereafter referred as

SRWCS or winter Chinook Salmon) to Battle Creek using the progeny of captive broodstock from the Livingston Stone National Fish Hatchery (LSNFH). Winter Chinook Salmon are listed as endangered under state and federal endangered species acts. Lack of spatial structure and diversity are principle threats to SRWCS. Currently, SRWCS exist as a single population, which is restricted to spawn in the Sacramento River downstream of Shasta Dam – an area completely outside of the species’ geographical range of historic spawning. The persistence of SRWCS is completely dependent on receiving managed supplies of cold water from Shasta Lake, leaving it extremely vulnerable to impacts from catastrophic events and climate change. The U.S. Fish and

Wildlife Service (USFWS) operate a conservation hatchery for SRWCS at the LSNFH, located at the base of Shasta Dam. The Winter Chinook Salmon Integrated-Recovery Conservation

Hatchery consists of two programs, a captive broodstock program and a supplementation program. Together, these two programs are intended to reduce the risk of extinction, increase abundance, preserve genetic diversity, and contribute to the recovery of the Sacramento River winter Chinook Salmon Evolutionarily Significant Unit (SRWCS ESU).

Battle Creek is an east-side tributary of the Sacramento River located in Shasta and Tehama

Counties, California. A population of SRWCS that historically spawned in Battle Creek was extirpated because of habitat changes resulting from hydropower development, dating back to the early 1900s. An ongoing, large-scale habitat restoration project aims to restore fish habitats in Battle Creek by providing conditions suitable to once again support a population of SRWCS.

In preparation for the completion of restoration actions, a comprehensive plan (Reintroduction

Plan) to reintroduce SRWCS to Battle Creek was collaboratively developed by a multi-stakeholder team. The USFWS has been identified as lead agency for implementing the

Reintroduction Plan, which is currently on hold pending receipt of funding.

As a result of a prolonged and severe drought in California’s Central Valley, natural production of SRWCS in the Sacramento River was severely diminished during 2014 and 2015, increasing the risk of imminent extinction. In response, a multi-agency decision was made to lessen the risk of extinction and improve population resiliency by spawning captively-reared SRWCS and releasing their progeny into Battle Creek, thereby accelerating the timeline of reintroducing

SRWCS to that tributary (USFWS 2017). This reintroduction strategy differs from that proposed in the Reintroduction Plan. This document describes the strategies that were used to “Jumpstart” the reintroduction of SRWCS to Battle Creek and describes the issues, considerations, and rationale for choosing specific reintroduction strategies.

Background

Sacramento River Winter-run Chinook Salmon

Spawning Distribution

Winter Chinook Salmon are unique amongst the four races of Chinook Salmon of California’s

Central Valley in that they spawn during the summer months, from mid-April to mid-August, when air temperatures typically reach their annual maxima. Historic spawning locations of

SRWCS included the cold headwater reaches of rivers and streams on the flanks of Mt. Shasta and Lassen Peak - areas where a reliable supply of cold water from snow melt and underground springs provided suitable temperatures throughout the summer months. Native SRWCS spawning areas on the slopes of Mt. Shasta include the watersheds of the Little Sacramento, McCloud, and Pit rivers; all of these areas have been inaccessible to SRWCS since the construction of Shasta and Keswick dams in the early 1940s. Historic SRWCS spawning areas on the slope of Lassen Peak were limited to the Battle Creek watershed. Naturally reproducing

SRWCS in Battle Creek were likely impacted and locally extirpated as a result of hydropower development dating back to the early 1900s, which degraded and blocked access to suitable spawning habitats. Currently, the SRWCS ESU is comprised of a single population that spawns in the Sacramento River downstream of Keswick Dam, an area that is completely outside of the historic range of SRWCS spawning. Nonetheless, winter Chinook Salmon have persisted downstream of Keswick Dam as a result of cold water releases from Shasta Dam, which are managed by the Bureau of Reclamation to provide temperatures suitable for spawning, egg incubation, and early rearing.

Battle Creek is an east-side tributary to the Sacramento River downstream of Shasta Dam. Battle

Creek is unique because its cold water springs and high year-round base flows provide the only historic spawning habitats for SRWCS downstream of Shasta Dam. In 1999 agencies and stakeholders struck an agreement to restore fish habitats in Battle Creek, which was formalized with the signing of a Memorandum of Understanding leading to implementation of the Battle

Creek Salmon and Steelhead Restoration Project (BCRP). Habitat improvement projects associated with the BCRP are currently underway and scheduled to be completed in 2023. When completed, the BCRP will restore and provide access to an additional 48 miles of habitat for salmon and steelhead, including the only potentially suitable historic habitat for SRWCS spawning within the range of anadromy.

Status

Sacramento River winter Chinook Salmon were listed as a federally threatened species in 1989

(54 FR 32085: August 4, 1989) and reclassified as endangered in 1994 (59 FR 440: January 4, 1994). A subsequent proposal (69 FR 33102: June 14, 2004) to reclassify SRWCS as a threatened species in 2004 was not adopted and SRWCS were reaffirmed as an endangered species in 2005 (70 FR 37160: June 28, 2005) and through a status review in 2011 (76 FR

50447). Winter Chinook Salmon have also been listed as an endangered species under the

California Endangered Species Act since 1989. The SRWCS ESU includes fish spawning naturally in the Sacramento River and its tributaries and those that are part of the conservation hatchery operated by the USFWS (70 FR 37160: June 28, 2005). Recently, SRWCS have been declared as one of eight “Species in the Spotlight” by the National Oceanic and Atmospheric

Administration (NOAA), the parent agency of the National Marine Fisheries Service (NMFS;

https://www.fisheries.noaa.gov/topic/endangered-species-conservation/species-spotlight). The

Species in the Spotlight designation is intended to focus attention and recovery efforts on species that are considered to be at a high risk of extinction in the near future. Principal population characteristics that contribute to the endangered status of SRWCS are lack of both diversity and spatial structure. The recovery strategy developed by the NMFS for Central Valley Chinook

Salmon and steelhead is “to secure all extant populations and to reintroduce populations into https://www.fisheries.noaa.gov/topic/endangered-species-conservation/species-spotlight) historic habitat such that each salmonid diversity group in the Central Valley supports viable populations” (NMFS 2014). The term diversity group refers to salmonid ecoregions, which are delineated by climatological, hydrological, and geological characteristics. Historic habitats with the potential to support SRWCS include Battle Creek and upstream of Shasta Dam.

Winter Chinook Salmon Conservation Hatchery

Since 1989, the USFWS has operated a conservation hatchery for SRWCS, which is located on the Sacramento River at the base of Shasta Dam. The goal of the SRWCS conservation hatchery is to prevent extinction, conserve diversity, and increase abundance, thereby contributing to the preservation, stability, and recovery of SRWCS ESU.

The SRWCS Conservation Hatchery consists of two interrelated programs: the Integrated-

Recovery Supplementation Program, hereafter referred as the “Supplementation Program”, and the Captive Broodstock Program. The Supplementation Program is operated to increase abundance and conserve genetic resources of the at-risk SRWCS population. The Captive

Broodstock Program maintains a source of broodstock in a safe and secure captive environment, providing an added measure of insurance against catastrophic year-class failures. Together, the

Supplementation Program and Captive Broodstock Program are intended to increase resiliency and promote recovery of the endangered SRWCS ESU.

A complementary goal of the SRWCS Conservation Hatchery is to provide a source of fish for re-establishment of locally-extirpated natural spawning populations in Battle Creek and upstream of Shasta Dam. This hatchery role is consistent with the recovery strategy put forth in the NMFS

Recovery Plan (2014), which is “to secure all extant populations and to reintroduce populations into historic habitat such that each salmonid diversity group in the Central Valley supports viable populations”. The NMFS has identified reintroduction of SRWCS to Battle Creek and upstream of Shasta Dam as key recovery actions to address the threats facing SRWCS. Successful introductions into these historic spawning habitats would reduce the likelihood of extinction and contribute to the recovery goals (NMFS 2014).

Efforts to reintroduce SRWCS upstream of Shasta Dam and to Battle Creek will rely, to some extent, on the SRWCS Conservation Hatchery as a source of fish. The SRWCS Conservation

Hatchery has been identified as an integral component of the plan to reintroduce SRWCS to

Battle Creek (McConnaha et al. 2016). Implementation of the Battle Creek Winter-Run

Reintroduction Plan (Reintroduction Plan) currently has not been funded and, as a result, the timeline for implementing the program has yet to be established. Preliminary feasibility studies for the effort to reintroduce SRWCS to historic spawning habitats upstream of Shasta Dam are currently in progress, but a detailed reintroduction strategy has not been developed. This project, however, will also likely rely on the SRWCS Conservation Hatchery and associated fish trapping facilities as a source of fish for both preliminary studies and project implementation.

The term diversity group refers to salmonid ecoregions, which are delineated by climatological, hydrological, and geological characteristics (NMFS 2014).

Severe Drought

The period from 2012 – 2015 was the driest four-year span in California since record keeping began in the late 1800s (PPIC; http://www.ppic.org/publication/what-if-californias-drought-continues). This period of record low precipitation was accompanied by exceptionally warm temperatures, which exacerbated the effects of drought by reducing an already diminished snowpack and increased societal demands for water. Cumulative effects of severe drought and exceptionally warm temperatures depleted the state’s reservoirs, which forced curtailing of water deliveries. The largest reservoir in the state, Lake Shasta, became exhausted of its cold water pool in the late summer of 2014 and 2015, thereby impeding the ability to maintain downstream temperatures within the range required for successful natural spawning of SRWCS. As a result, reproductive success of naturally-spawning SRWCS was severely diminished during two consecutive years. Estimates of egg-to-fry survival, which typically average about 25% for naturally spawning SRWCS, were reduced to only 5.9% and 4.5% during 2014 and 2015, respectively (Bill Poytress, pers. comm., USFWS, Red Bluff, CA). The scant few SRWCS juveniles that were produced were also challenged during their emigration to the ocean by unfavorable conditions of low flows and high temperatures in the Sacramento River and the Bay-

Delta, further reducing expectations of survival for SRWCS from these two year classes.

Cumulative effects of these events resulted in the near-complete failure of two consecutive years of naturally spawning SRWCS.

Hatchery Role in Mitigating the Effects of Drought

With pre-season temperature modeling predicting that the Sacramento River would likely exceed the thermal limit of successful natural SRWCS spawning during 2014 and 2015, the USFWS, NMFS, and the California Department of Fish and Wildlife, referred to collectively as the Fish

Management Agencies, anticipated the potential of a near-complete failure of natural production.

In response, the Fish Management Agencies enacted emergency measures to temporarily expand the size of the SRWCS Conservation Hatchery. Included in this emergency action was the decision to temporarily expand the size of the Supplementation Program. Broodstock collection goals for the Supplementation Program, which are typically set at 60 female and 60 male, were revised to collect and retain as many SRWCS as could be captured and accommodated at

LSNFH as hatchery broodstock. To facilitate this, the hatchery retained both hatchery- and natural-origin SRWCS; this is a deviation from the standard program protocol that use only naturally-produced fish as hatchery brood. As a result of these changes, broodstock collection at the LSNFH was substantially increased in 2014 and 2015 and total hatchery production of

SRWCS juveniles reached levels two- and three-fold larger than standard production levels.

Effects of Drought on Winter Chinook Abundance

Demographic effects of drought, which may persist for multiple generations, highlight the vulnerable status of the SRWCS ESU, which consists of only one population entirely dependent on releases of cold water from Shasta Lake. Viability of an ESU that is represented by a single population is at increased risk of extinction. A single catastrophic event lasting four or more years could extirpate the entire SRWCS ESU (Lindley et al. 2007). Furthermore, an ESU comprised of only one population is inherently vulnerable to limitations of genetic and life history diversity. Genetic variation of SRWCS substantially reduced, compared to other runs of salmon in the Central Valley and across the Pacific Coast, perhaps as a result of past bottlenecks and genetic drift (Banks et al. 2000). Because genetic variation provides the mechanism of http://www.ppic.org/publication/what-if-californias-drought-continues).

http://www.ppic.org/publication/what-if-californias-drought-continues).

adaptation through natural selection, further reductions of genetic variation are a primary concern for the conservation of SRWCS, as they may affect the ability of the population to adapt to changing environments.

Results of spawner escapement surveys support expectations of the Fish Management Agencies that the drought had resulted in the near-complete failure of SRWCS natural production during

2014 and 2015. Spawner escapement surveys estimated 975 SRWCS returned to the upper

Sacramento River in 2017 (California Department of Fish and Wildlife Grandtab -https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=84381&inline), marking the second-lowest annual spawner escapement estimate in the recent 20 year period. An estimated 85% of the SRWCS spawners in 2017 were hatchery-origin fish from LSNFH (K. Offill, USFWS, Red

Bluff, CA, unpublished data), evidence that emergency measures enacted at the LSNFH were successful at avoiding a complete year-class failure. Few natural-origin adults returning and high percent of hatchery-origin spawners suggests reproductive success of naturally spawning

SRWCS in 2014 was greatly diminished and increased propagation efforts enacted at the LSNFH substantially benefitted the abundance of spawners in 2017. Spawning area surveys of 2018 are currently underway at the time of drafting this document, and an estimate of total spawners is not yet available. However, preliminary data from daily surveys again supports expectations of severely limited natural production during 2015, with a low abundance of natural origin spawners and a high proportion of hatchery-origin fish (Kevin Niemela, USFWS, Red Bluff, CA, unpublished data).

Using Captive Broodstock to Improve Population Resiliency

With evidence that the drought had severely reduced natural reproductive success of the SRWCS for two consecutive year classes, and recognizing the potential conservation values of the captive broodstock at the LSNFH, the Fish Management Agencies made the decision to spawn captive broodstock and use their progeny to initiate reintroduction of SRWCS into historic spawning habitats of Battle Creek

. This method of reintroducing winter Chinook Salmon to Battle Creek differs from the recommendations from the Reintroduction Plan, which calls for using the progeny of wild-caught broodstock. Since this strategy of reintroducing SRWCS to Battle Creek differs from the recommended strategy contained in the Reintroduction Plan, the project was called the Winter Chinook Salmon “Jumpstart” Project. The Jumpstart Project is intended to transition into implementation of the Reintroduction Plan when funding becomes available.

The Jumpstart Project confers a key benefit of quickly increasing spatial structure of the SRWCS

ESU, which is a primary need for the conservation of SRWCS. It also provides an opportunity to learn about the suitability of Battle Creek for a secondary population of SRWCS while

Alternative options that were considered for using the captive broodstock to derive a conservation benefit included (1) increasing the size of the Supplementation Program in

Sacramento River; and 2) contributing to multi-agency efforts to reintroduce SRWCS upstream of Shasta Dam. These projects were evaluated for their feasibility and compared to the Battle

Creek reintroduction project with regards to their benefits and drawbacks (USFWS 2017). Based on this evaluation, these projects did not advance past this initial analysis and did not receive any progeny of the SRWCS captive broodstock from the 2017 spawning year, but may be reconsidered in future years.

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=84381&inline), presenting negligible risks of detrimental effects to the existing SRWCS population in the mainstem Sacramento River. The primary risk of this conservation action is that captive broodstock progeny may not be successful at developing a SRWCS population in Battle Creek, potentially failing to take full advantage of the conservation potential contained within the captive broodstock and thereby failing to achieve the conservation benefits envisioned for this valuable resource.

Jumpstarting the Battle Creek SRWCS Reintroduction Process The remainder of this document will discuss actions that were taken during the winter Chinook

Salmon hatchery production cycle of 2017 – 2018 to Jumpstart the reintroduction of Winter

Chinook Salmon to Battle Creek. The sequence of information in this section follows the timeline of management events associated with the hatchery production cycle, including:

spawning, incubation and rearing, marking and tagging, assessment of fish health, imprinting, and juvenile releases. Each of these sections has been formatted to first identify the management actions that were taken (shown in bold) to Jumpstart the reintroduction of winter Chinook

Salmon to Battle Creek, followed by an explanation of the rationale behind those actions (shown in italics). The intent of structuring the document in this manner is to allow the reader to quickly identify specific management actions that were taken and then, if necessary, to investigate the underlying logic/rationale.

Spawning

Management Action:

Spawning of captive broodstock at the LSNFH occurred from July 25 to September 19, 2017, corresponding to timing of sexual maturation. To promote synchronous maturation, male and female captive broodstock were combined in a common rearing unit during late stages of rearing. Luteinizing Hormone-releasing Hormone analogue (LH-RHa) implants were administered to accelerate the maturation of ten females. Four hundred seventy-seven different family group combinations were created by spawning 244 female captive broodstock with 168 male broodstock of the following origins: captive broodstock (BY14:

n=41, BY15: n=115), wild-caught broodstock remaining from the Supplementation

Program (n=10), and cryopreserved semen (RY17: n=2; Table 1).

Rationale:

Spawning of captive broodstock in 2017 (July 25 – September 19) was later than that of wild-caught SRWCS broodstock, including fish of hatchery and natural origin spawned in the

Supplementation Program (April 24 – August 7). Delayed spawning of captive broodstock is attributed to later timing of sexual maturation. Winter Chinook Salmon captive broodstock at

LSNFH typically exhibit seasonally delayed maturation relative to natural spawning winter

Chinook Salmon (Kevin Niemela, USFWS, Red Bluff, CA, unpublished data). Similar observations of delayed sexual maturation have been previously observed within other salmon captive brood programs (Patterson et al. 2004; Berejikian et al. 1997). Because spawning of captive broodstock was delayed relative to that of broodstock collected from the wild, timing of successive juvenile life history events (e.g., eye-up, hatching, button-up) and associated management activities (e.g., marking and tagging, target release size) were also delayed relative to the progeny of wild-caught broodstock used in the Supplementation Program.

A partial factorial (2x2) mating design was used to increase the effective population size, as compared to single pair matings. Partial factorial matings increase effective population size by better equalizing the number of progeny produced per parent. To conduct partial factorial matings, eggs from each female were split into two groups and each group of eggs was fertilized using the milt from a different male. Ideally, each male would have been used to fertilize two groups of eggs, equivalent to the total egg production of one female; however, because the number of females exceeded the number of males, each male was used to fertilize an average of

3.0 groups of eggs (range 1 – 7). To reduce likelihood of mating closely related individuals, pairings of captive broodstock were informed by an assessment of genetic relatedness. Due to reduced viability associated with fertilizing eggs with cryopreserved semen, a prioritization scheme favored using semen from live males.

All female captive broodstock spawned were age-3 (i.e., brood year 2014). Relative to the number of female captive broodstock spawners, a reduced number of age-3 males were available due to mortality caused by maturation as age-2 “jacks” and a concurrent outbreak of bacterial gill disease (Attachment 2). A substantial portion (73.7%) of captive broodstock males were jacks (i.e., brood year 2015). A total of 288,134 eggs were hand counted from collections across

19 spawning dates occurring July 25 through September 19. Eggs from an additional three females were collected, but not counted due to the condition known as “soft shell” that prevented physical handling. Average fecundity of counted captive broodstock was 1,196 eggs/female

(range: 186 – 3,008).

Incubation and Rearing

Management Action:

Embryos were initially incubated in vertical stacks of fiberglass incubator trays (Heath Incubation Trays) at LSNFH. Survival to eyed stage was 86.6%, which is within the range previously observed for SRWCS captive broodstock spawned with wild-caught broodstock at LSNFH (BY2001 – BY2006; range: 39.2% – 99.3%, avg. = 81.3%, SD = 21.9; Table 1).

However, this rate of survival is less than the average (93.6%, range: 87.4% – 97.2%, SD =

2.8) observed for pairings of wild-caught broodstock spawned in the Supplementation Program since 1998.

Captive broodstock progeny were transferred to Coleman National Fish Hatchery (CNFH) between October 11 and November 2, 2017. First fourteen egg takes were transferred to the CNFH as button-up fry and final five egg takes were transferred to CNFH as eyed eggs

(Table 2).

At the button-up stage, juvenile SRWCS were moved from incubator trays into fiberglass tanks (16’ x 3’4”) to initiate feeding. Throughout period of early rearing, fry from 19 egg takes were aggregated into seven pooled groups, called ‘lots’. Lots ranged in size from approximately 23,000 to 38,000. Lots were transferred to outdoor 8’ x 80’ raceways between December 12, 2017 and February 23, 2018, where they were reared until release.

To improve imprinting to Battle Creek, captive broodstock progeny were transferred from

LSNFH to CNFH at the earliest possible life stage - either as eyed eggs or as button-up fry -dependent on timeline of embryo development relative to water temperature suitability at CNFH.

CNFH is located on Battle Creek; therefore, juvenile salmon that are transferred to CNFH during their early life history will be exposed to distinctive chemical cues of the watershed to promote imprinting and homing to Battle Creek. Embryos from five egg takes were transferred to CNFH from 3 – 16 days prior to hatch and button-up fry from 14 egg takes were transferred to CNFH from 25 – 40 days after hatch. A temperature of ≤60°F (daily maximum) was used as a threshold to indicate suitable temperatures for transferring fry to CNFH; this threshold was met on October 1, triggering the transfer of SRWCS to the CNFH soon thereafter (Figure 1). A temperature of ≤56°F (daily maximum) was the threshold used to indicate suitable temperatures for transferring SRWCS eggs to CNFH; this threshold was met on October 9, triggering the transfer of SRWCS to CNFH soon thereafter.

To facilitate ponding within the 8’x 80’ raceways, juvenile SRWCS from 19 egg takes were aggregated into seven pooled groups at CNFH. To promote a uniform size distribution and improve feeding, growth, and survival of pooled groups, it was necessary to manipulate (i.e., accelerate or retard) the growth of several egg lots prior to combining them in a raceway.

Marking and Tagging

Management Action:

Marking and tagging were conducted from January 23 to February 26, 2018, by a contracted crew from the Pacific States Marine Fishery Commission. Juvenile SRWCS were first processed through the automated Marking and Tagging System trailer (MATS:

Northwest Marine Technology, Shaw Island, WA), which applied an adipose fin clip and coded-wire tag (CWT) to each fish. Each of the seven raceways received a uniquely numbered CWT. After a raceway of juvenile fish was completely processed in the MATS trailer, the lot was again processed through another trailer, where the left pelvic fin was manually removed from each fish. The rate of ventral fin clipping was approximately 250 fish/person/hour, which includes time for project preparations and shut-down.

Approximately four days were required to completely process each lot of salmon through both tagging trailers (e.g., one day for CWT and removal of adipose fin plus three days for removal of pelvic fin). Total cost of tagging is estimated to be approximately $73,000.

Effectiveness of marks and tags was assessed for at least 21-days after the final tag date.

Assessments indicated a high level of mark-tag effectiveness (Table 3). Overall retention rates of adipose-fin clip, CWT, and left pelvic-fin clip averaged 99.3% (range: 98.5% – 100.0%, SD = 0.5) among the seven CWT groups. Increased rates of direct mortality from marking and tagging were not apparent, however, see Fish Health section, below.

Ability to identify Jumpstart SRWCS after they are released into the wild has important implications for their monitoring and management throughout their geographical range. Of particular importance is to distinguish introduced Jumpstart SRWCS from late-fall Chinook

Salmon at CNFH during their adult migration into Battle Creek. Migration timing of SRWCS overlaps considerably with that of late-fall Chinook Salmon, and adults of both stocks coincide at the hatchery during their spawning migration. During a typical year, several thousand hatchery-origin late-fall Chinook return to the CNFH and must be quickly distinguishable from

Jumpstart SRWCS so that the hatchery can continue late-fall Chinook Salmon spawning operations while avoiding unnecessary handling and associated impacts to winter Chinook

Salmon. All late-fall Chinook Salmon produced at the CNFH are coded-wire tagged and marked with an adipose-fin clip, so a different marking and tagging strategy was needed for Jumpstart

SRWCS. It is also important that introduced Jumpstart SRWCS be distinguishable from naturally produced spring Chinook Salmon in Battle Creek, which do not receive a mark or tag.

Lastly, monitoring of California ocean commercial and recreational fisheries and inland sport fishery also rely on monitoring programs, which are based on adipose fin clips and coded wire tags. Any marking and tagging strategy for introduced Jumpstart SRWCS that doesn’t include, at minimum, an adipose-fin clip and coded-wire tag would not be detected by existing harvest monitoring programs.

Alternative strategies for marking and tagging SRWCS were considered during development of the Reintroduction Plan (McConnaha et al. 2016) and the reader is referred to that document for a more thorough discussion of alternative strategies. The plan’s authors recognized the challenges of selecting a marking and tagging strategy that meets all objectives of management and monitoring while, at the same time, is both practical and avoids negative effects to marked fish. Each marking and tagging strategy considered in that document conferred at least one tangible disadvantage in regards to cost, feasibility, the ability to achieve all of the management and monitoring objectives, or the potential to impose a survival disadvantage to marked fish.

Since no identified strategy for marking and tagging was unequivocally superior to others, the authors of the Reintroduction Plan deferred recommendation of a marking and tagging strategy until a later time.

Based on the assessment of marking and tagging contained in the Reintroduction Plan

(McConnaha et al. 2016), and with consideration given to the aforementioned monitoring and management needs, the Fish Management Agencies selected a marking and tagging strategy for

Jumpstart SRWCS consisting of an adipose fin clip, coded-wire tag, and removal of the left pelvic fin (i.e., ventral fin). The rational for this decision is that this marking and tagging strategy is feasible and will allow captive broodstock progeny to be reliably identified in all existing management and monitoring programs throughout their life cycle and geographic range. A principal benefit of this marking and tagging strategy compared to others being considered was the ability to identify captive broodstock progeny in existing ocean fishery monitoring programs. Primary uncertainties of this marking and tagging strategy are associated with the permanence of the pelvic fin clip as a life-long mark (e.g., permanence depends on application proficiency) and the possibility that removal of a pelvic fin negatively may affect post-release survival. Previous evaluations of fin clip effects on salmonid survival have produced mixed results, ranging from no detectable effects (Bumgarner et al. 2009 and

Jones et al. 1997, as cited in McConnaha et al. 2016) to reductions in excess of 50% (Eriksen et

al. 2011 and Mears and Hatch 1976, as cited in McConnaha et al. 2016). A large reduction in survivability resulting from the marking and tagging process could compromise the success of

Jumpstart reintroduction efforts and fail to take advantage of the full potential value of captive broodstock. It has been recommended that studies be developed to determine negative consequences of using a pelvic clip as the additional identifiable mark, and USFWS may pursue these studies in the future.

Fish Health

Management Action:

Weekly fish health monitoring of captive broodstock progeny during tagging operations was conducted to assess stress and other potential impacts of double tagging (CWT and left pelvic fin clip) operations. Pre-liberation health examinations of captive broodstock progeny were initiated on February 5 and completed on February 23, 2018. Fish health screening included virology, culturable bacteria, and Renibacterium salmoninarum; and no pathogens were detected (Attachment 1). One raceway of juvenile SRWCS contracted a low-level infection of cold-water disease Flavobacterium psychrophilum after examination but prior to their release into Battle Creek.

Monitoring and evaluations of fish health must be completed prior to releasing fish from a federal fish hatchery. Fish health examinations of Jumpstart SRWCS were conducted by the

USFWS California-Nevada Fish Health Center.

In early March 2018, after completion of pre-liberation health examinations, but prior to releasing all of the Jumpstart SRWCS into Battle Creek, one raceway (Raceway 42; CWT

056176) of SRWCS juveniles were diagnosed with a low level infection of cold-water disease

Flavobacterium psychrophilium. Level of infection, and increasing water temperatures prevented further progression of Flavobacterium psychrophilium infections, and treatment was not warranted for this group of fish. The raceway was released upon recommendation of the

California-Nevada Fish Health Center.

Fine-scale Imprinting

Management Action:

No action taken

To promote imprinting to specific reaches of Battle Creek where SRWCS are desired to return to spawn, a multi-stakeholder team investigated opportunities to develop an acclimation-imprinting facility on North Fork Battle Creek. North Fork Battle Creek is considered to be more suitable than South Fork Battle Creek or the mainstem of Battle Creek because of cooler temperatures and higher base flows, resulting in improved SRWCS spawning habitats. More specifically, the

Feeder Reach, which extends from North Battle Creek Feeder Diversion Dam (river mile [RM]

9.42) downstream to Eagle Canyon Diversion Dam (RM 5.23), is regarded as optimal for

SRWCS (Figure 3; Ward and Keir 1999). By rearing juvenile SRWCS in water from North Fork

Battle Creek for a period of time prior to release, it may be possible to improve their homing to the specific stream sections where SRWCS spawning is likely to be most successful. Coleman

NFH is located on the mainstem Battle Creek (RM 5.97), approximately 16 miles downstream from their optimal habitat and 11 miles downstream from the confluence of North Fork Battle

Creek and South Fork Battle Creek (RM 16.80), precluding imprinting on only North Fork Battle

Creek water. Efforts to develop an acclimation/imprinting facility in the watershed of North

Fork Battle Creek, however, were hindered by several factors, including;

1) Limited stream access points to North Fork Battle Creek due to the steep terrain.

Especially limited are access points with sufficient space and access to water for an acclimation facility;

2) Properties of the Pacific Gas and Electric Company (PG&E) currently have access restrictions associated with construction, modifications, and testing of hydropower facilities associated with the BCRP, and;

3) Limited time and funding were available to identify and develop a suitable acclimation/imprinting facility.

As a result of these impediments, an acclimation/imprinting facility was not developed on North

Fork Battle Creek for Jumpstart SRWCS spawned in 2017. Development of an acclimation-imprinting facility may be reconsidered for releases from the Jumpstart project in future years.

Because winter Chinook Salmon could not be reared for an extended period in North Fork Battle

Creek, we believe that there is an increased likelihood that captive broodstock progeny may not imprint to the most suitable spawning areas; this increases the uncertainty about where adults from this brood year will return to spawn in future years.

Juvenile Releases

Management Action:

Progeny of winter Chinook captive broodstock were released into the North Fork Battle

Creek at Wildcat Road Bridge (Figure 3) on four dates between March 2 and April 6, 2018

(Table 4). Number of fish in each release group ranged from approximately 25,000 (April 6, 2018) to more than 92,000 (March 14, 2018). Average fork length of fish at liberation ranged from 71 – 80mm; to take advantage of favorable environmental conditions, several groups of fish were released at a size marginally smaller than winter Chinook typically released from the Sacramento River Supplementation Program. Three of four releases coincided with precipitation events in the northern Central Valley, which resulted in increased flows and turbidity in Battle Creek and the Sacramento River (Figure 2). Battle

Creek flow exceeded 7,800 cfs coincident with the final release into Battle Creek, subjecting fish to potential diversion at a compromised levee in lower Battle Creek.

Strategy for releasing juvenile SRWCS into Battle Creek can have a large influence on post-release survival, and thereby affect the success of the jumpstart project. Release strategy for the jumpstart project focused on achieving high levels of abundance and diversity as the two primary objectives. Release strategies that encourage high survival will promote larger numbers of SRWCS adults returning to Battle Creek, retaining more of the genetic and phenotypic diversity of their parents. Genetic diversity provides the basis for adaptation to novel habitats. Abundance and diversity are the same priorities used in developing the overall

Reintroduction Plan (McConnaha et al. 2016). Considerations associated with the release of

SRWCS captive broodstock progeny into Battle Creek to promote high levels of abundance and diversity are discussed below.

Release Location-

Location where hatchery salmon are released can affect survival and homing. Juvenile salmon are “imprinted” to the distinctive odors of their natal tributary, which enables them to “remember” olfactory cues and relocate the particular stream (i.e., homing) when they return as adults to spawn (Hasler and Scholz 1983). This adaptation reduces reproductive loss by ensuring that spawning will occur in suitable spawning areas.

Timing of imprinting in salmon is highly linked to elevated thyroxine levels associated with the parr-smolt transformation process. This explains why salmon that are raised at a hatchery but released as smolts at another location tend to return as adults to the release site, not the rearing site. However, populations of salmon that emigrate soon after emergence are also able to imprint properly as alevins and emergent fry, demonstrating that the imprinting process is flexible both spatially and temporally

(Dittman and Quinn 1996).

To promote homing to the locations of Battle Creek where SRWCS will have the best chances for successful reproduction, we attempted to release captive broodstock progeny at or near the smolt stage and at the area they are desired to return to spawn. The

Feeder Reach has been identified as the area where SRWCS are likely to have the best likelihood of successful reproduction (Ward and Kier 1999), therefore, release in this stream reach is preferred. However, the number of potential release sites in North Fork

Battle Creek is constrained by rough terrain and limited access points. A multi-stakeholder team identified and considered the following possible release locations on

North Fork Battle Creek, listed in order of preference based on proximity to favorable spawning habitats: (1) North Battle Creek Feeder Diversion Dam, (2) Wilson Hill Road

Bridge, and (3) Wildcat Road Bridge (Figure 3). If none of these options were feasible, releasing the progeny of SRWCS captive broodstock into Battle Creek at CNFH was a fourth, albeit less desirable, option.

Releasing progeny of SRWCS captive broodstock near to PG&E’s North Battle Creek

Feeder Diversion Dam and Eagle Canyon Diversion Dam hydropower facilities could subject juvenile fish to impacts associated with construction and start-up testing of the new hydropower and fish facilities. Planned testing of facility automation programming and operations, which are necessary for facility start-up and transfer, were scheduled to occur between March and September 2018, potentially overlapping with the release of

SRWCS into Battle Creek. Juvenile SRWCS released in the proximity of these activities could be subject to diversion or dewatering. Exact timing of these tests was unknown and dependent on a variety of factors, including stream flow in Battle Creek. Due the uncertainties associated with the timing of facilities testing, the decision was made to abandon consideration of the two upper-most release locations - North Battle Creek

Feeder Diversion Dam and Wilson Hill Road Bridge - to avoid the potential for impacts to juvenile salmon. The selected release site, located at the Wildcat Road Bridge, is the next-most upstream release location considered by the multi-stakeholder team. The

Wildcat Road Bridge is on North Fork Battle Creek (0.9 mile from confluence with South

Fork Battle Creek), downstream of the preferred spawning area. By releasing juvenile

SRWCS at the Wildcat Road Bridge, impacts associated with facilities testing were avoided while, at the same time, promoting imprint to the North Fork Battle Creek, near to the preferred spawning location.

Release Timing-

Several factors associated with the timing of salmon releases from a hatchery are known to influence their survival. Juvenile salmon from the SRWCS Supplementation Program are typically released in February, when fish approach smolt stage and when winter storm events are expected to create favorable environmental conditions in the emigration corridor. However, spawning of captive broodstock occurred later than that of naturally-reared SRWCS, and progeny of captive broodstock were not sufficiently developed for a February release. Later in the spring, environmental conditions are likely to be a constraining factor, as water temperature in lower Sacramento River and

Delta typically increase during April, potentially resulting in thermal stress and increased predation. Based on these constraints, we targeted a March release for progeny of SRWCS captive broodstock. Timing the release of SRWCS captive broodstock progeny in March appeared to reasonably balance the goals of releasing juveniles at or near the smolt stage, at a time when spring storm events are expected to create favorable conditions for emigration, and prior to the deterioration of water conditions in the lower

Sacramento River and Delta.

Because of inherent uncertainties associated with forecasting juvenile growth and environmental conditions, identifying specific release dates for SRWCS captive broodstock progeny was an adaptive process, based on ‘real-time’ information associated with several factors, including: (1) fish size and life stage, (2) weather and environmental conditions, (3) managed flow releases (i.e., discharge) from Shasta Dam,

(4) number of fish in a release group, and (5) flooding at a compromised levee in lower

Battle Creek. Each of these factors is thought to be influential to survival of juvenile

SRWCS released into Battle Creek. Likely effects of these factors on survival of juvenile

SRWCS are briefly discussed below.

1. Size and Life Stage

Size and life stage at the time of release from a hatchery are known to influence the survival of juvenile salmon. Generally, salmon that are larger and older at the time of their release survive to maturity more than fish that are younger and smaller. Substantial data support releasing juvenile salmon at or near the smolt stage to produce increased returns of adult salmon, as compared to releases at earlier life stages (Kevin Niemela, USFWS, Red Bluff CA, unpublished data). To promote increased returns of adult SRWCS to Battle Creek, juveniles produced in the Supplementation Program are released at or near pre-smolt/smolt life stage.

Releasing fish at the pre-smolt/smolt life stage attempts to strike a balance between achieving a reasonably high rate of survival while, at the same time, subjecting hatchery fish to some of the natural selective forces during their early life history. Releases at pre-smolt/smolt life stage are also recommended in the

Reintroduction Program.

2. Weather and Environmental Conditions

Environmental conditions at the time of release from a hatchery are a primary influence on their survival. Ideally, releases of SRWCS would be timed to occur in association with winter/spring storm events in the northern Central Valley.

Storm events associated with substantial precipitation result in increased flows and high turbidity in Battle Creek and the Sacramento River; these conditions are generally associated with increased rates of emigration and decreased predation on juvenile salmon. Alternatively, low flows and clear water are generally associated with slower rates of emigration and increased predation; conditions that lead to decreased survival.

3. Managed Flow Releases from Shasta Dam

Emigrating juvenile salmonids are thought to be aided in their downstream migration by increased flows (Raymond 1968; Connor et al. 2011). The downstream migration of salmon smolts may be initiated by increased water flow

(see review in Jonsson 1991). Additionally, increased river flows may reduce likelihood of predation and diversion, as emigrating juveniles are able to disperse across a broader area of the river corridor. Timing releases of hatchery SRWCS to coincide with a period of increased discharge from Shasta Dam, including the possibility of a managed pulse flow, may contribute to increased survival during emigration of hatchery releases. However, we hypothesize that it is unlikely that increased discharge from Shasta Dam would have a similar benefit to the survival of juvenile hatchery salmon compared to equivalent flow increases resulting from natural precipitation events; this difference is due to limitations of the magnitude, duration and lack of turbidity associated with managed flow events. Therefore, we considered synchronizing juvenile releases to coincide with natural flow events to be a higher priority.

4. Number of Fish in a Release Group

Anecdotal and experimental evidence and ecological theory suggest that releasing very large numbers of juvenile salmon at a single place and time may improve their survival through the emigration corridor by overwhelming or satiating predators, thereby conferring increased protection for the masses

(Furey 2016, Pitcher 1986). Benefit of en masse releases is expected to be greatest when the number of fish released is large and size (i.e., length and area) of the emigration corridor small. However, ability to achieve significant benefits to survival by conducting an en masse release of winter Chinook into Battle Creek is highly uncertain. An association between number of fish in a release group and survival was not evident in a previous acoustic tagging study of late-fall

Chinook from the CNFH (R. Null, Pers. Comm. USFWS, Anderson, CA).

Furthermore, because total number (~215,000) of SRWCS to be released into

Battle Creek is relatively small and length and area of the emigration corridor are large, we anticipate that potential benefits to survival would be attenuated as fish move throughout the emigration corridor.

We believe that any benefits resulting from an en masse release would likely be localized near the release location in Battle Creek and unlikely to persist downstream as fish distribute across time and space. However, it is also possible that release of SRWCS into Battle Creek could be timed to coincide with a release of fall Chinook Salmon from the CNFH. In this situation, the number of juveniles released simultaneously could be substantially increased, potentially affording an increased level of protection through the river corridor.