Livingston Stone Winter Chinook Program

Transcription

California Hatchery Review Project
Appendix VIII
Livingston Stone National Fish Hatchery
Winter Chinook
Program Report
June 2012
Introductory Statement from the California HSRG
This program report was developed by contractor staff tasked with providing background information to
the California HSRG on hatchery programs, natural population status and fisheries goals in California.
The resulting report is one of many sources of information used by the California HSRG in their review
process.
Information provided in this program report was developed through interviews with hatchery staff,
regional, state and tribal biologists working in the basins and a review and summarization of the
pertinent scientific literature. The draft program report was then provided to interview participants for
review and comment on multiple occasions. Comments received were incorporated into the report and
the report finalized.
Because of the review process, it is believed the report represents an accurate snapshot in time of
hatchery operations, natural salmon population status and fisheries goals in California as of 2012. This
program report may or may not be consistent with the consensus positions of the California HSRG
expressed in the main report, as their primary involvement was in the preparation of Section 4.3,
“Programmatic Strategies”, which compares existing program practices to the statewide Standards and
Guidelines developed by the California HSRG.
Table of Contents
1 Description of Current Hatchery Program ...............................................................................1 1.1 Programmatic Components ...............................................................................................1 1.2 Operational Components ...................................................................................................1 1.2.1 Facilities .....................................................................................................................1 1.2.2 Broodstock .................................................................................................................2 1.2.3 Spawning....................................................................................................................3 1.2.4 Incubation ..................................................................................................................4 1.2.5 Rearing .......................................................................................................................4 1.2.6 Release .......................................................................................................................4 1.2.7 Fish Health .................................................................................................................5 2 Populations Affected by the Hatchery Program ......................................................................5 2.1 Current Conditions of Affected Natural Populations ........................................................5 2.1.1 Sacramento River Spring, Fall, Late-fall and Winter Chinook Populations..............8 2.2 Long–term Goals for Natural Populations ......................................................................12 3 Fisheries Affected by the Hatchery Program .........................................................................13 3.1 Current Status of Fisheries ..............................................................................................13 3.2 Long-term Goals for Affected Fisheries .........................................................................14 4 Programmatic and Operational Strategies to Address Issues Affecting Achievement of
Goals .....................................................................................................................................15 4.1 Issues Affecting Achievement of Goals ..........................................................................15 4.1.1 Natural Production Issues ........................................................................................15 4.1.2 Ecological Interaction Issues ...................................................................................15 4.2 Operational Issues ...........................................................................................................16 4.3 Programmatic Strategies .................................................................................................16 4.3.1 Broodstock ...............................................................................................................16 4.3.2 Program Size and Release Strategies .......................................................................19 4.3.3 Incubation, Rearing and Fish Health .......................................................................20 4.3.4 Monitoring and Evaluation ......................................................................................26 4.3.5 Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial
Organisms. ...............................................................................................................30 5 Literature Cited ......................................................................................................................30 List of Figures
Figure 1. Figure 2. Estimated exploitation rate of Livingston Stone winter Chinook by brood year1998 - 2003. .............................................................................................................13 Livingston Stone winter Chinook percent of total harvest to fisheries: 1998 –
2003. ........................................................................................................................14 California Hatchery Review Project – Appendix VI
Livingston Stone National Fish Hatchery Winter Chinook Program / June 2012
i
List of Tables
Table 1. Table 2. Table 3. Table 4. Table 5. Table 6. Table 7. Table 8. Table 9. Table 10. Table 11. Table 12. Table 13. Table 14. Table 15. Table 16. Table 17. Table 18. Table 19. Table 20. Table 21. Table 22. Table 23. Table 24. Table 25. Table 26. Table 27. Table 28. Table 29. Table 30. Page ii
Winter Chinook broodstock collection at Keswick Dam and Red Bluff
Diversion Dam, return years 1990-2008d. .................................................................3 Total egg take targets, release targets and survival estimates for winter
Chinook salmon at Livingston Stone NFH. ..............................................................4 Populations in the Central Valley fall and late-fall Chinook ESU, ordered from
north to south (unlisted ESU). ...................................................................................7 Populations in the Central Valley spring Chinook ESU, ordered from north to
south (ESA listed threatened). ...................................................................................8 Spring Chinook salmon escapement in the mainstem Sacramento River (20012010). .........................................................................................................................9 Fall Chinook salmon escapement in the mainstem Sacramento River (20012010). .......................................................................................................................10 Late-fall Chinook salmon escapement in the mainstem Sacramento River
(2001-2010). ............................................................................................................10 Winter Chinook salmon escapement in the mainstem Sacramento River (20012010). .......................................................................................................................11 Estimated ocean contribution for winter Chinook salmon from the Livingston
Stone/Coleman National Fish Hatchery, by brood year, based on the number of
salmon released. ......................................................................................................12 Broodstock Source. .................................................................................................16 Broodstock Collection. ............................................................................................17 Broodstock Composition. ........................................................................................17 Mating Protocols. ....................................................................................................18 Program Size. ..........................................................................................................19 Release Strategy. .....................................................................................................20 Fish Health Policy. ..................................................................................................20 Hatchery Monitoring by Fish Health Specialists. ...................................................20 Facility Requirements..............................................................................................22 Fish Health Management Plans. ..............................................................................23 Water Quality. .........................................................................................................23 Best Management Practices.....................................................................................24 Hatchery and Genetic Management Plans...............................................................26 Hatchery Evaluation Programs. ...............................................................................26 Hatchery Coordination Teams.................................................................................26 In-Hatchery Monitoring and Record Keeping.........................................................26 Marking and Tagging Programs. .............................................................................28 Post-Release Emigration Monitoring. .....................................................................28 Adult Monitoring Programs. ...................................................................................29 Evaluation Programs. ..............................................................................................29 Direct Effects of Hatchery Operations. ...................................................................30 California Hatchery Review Project – Appendix VIII
Appendices
Appendix A-1 Hatchery Program Review Questions
Appendix A-2 Livingston Stone Winter Chinook Program Data Tables
Appendix A-3 Hatchery Program Review Analysis Benefit-Risk Statements
Appendix B
Natural Populations Potentially Affected by the Hatchery Program
California Hatchery Review Project – Appendix VI
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Published Date : 1/16/2012
1
Description of Current Hatchery Program
Livingston Stone National Fish Hatchery (NFH), a substation of Coleman NFH, was constructed
by the Bureau of Reclamation in late1997 to produce ESA-listed winter Chinook salmon to assist
in population recovery. This program is supported in the NMFS draft Recovery Plan for winter
Chinook salmon (NMFS 2009; USFWS 2011). Artificial propagation of winter Chinook salmon
at Livingston Stone NFH is intended to be a temporary measure that will cease when the naturally
spawning population has been recovered. A captive broodstock component of the winter
Chinook program was conducted from 1991 to 2007; it was discontinued when the abundance of
natural-origin adults increased. If the abundance level again falls to critically low levels, the
captive broodstock element of this program could be reconsidered (USFWS 2011).
1.1
Programmatic Components
The winter Chinook program at Livingston Stone NFH is managed to be integrated with the
natural population of winter Chinook in the upper Sacramento River, and to provide a
demographic boost to aid in population recovery (USFWS 2011). Hatchery-origin winter
Chinook are intended to return as adults to the upper Sacramento River, spawn in the wild, and
become reproductively and genetically assimilated into the natural population. Annual
broodstock collection targets for the Livingston Stone NFH are dependent on the estimated
number of adults returning to the upper Sacramento River. Annual egg collection targets are
based on the number of broodstock collected and thus vary from year to year. The maximum
production of winter Chinook at the Livingston Stone Hatchery is approximately 250,000.
Juvenile winter Chinook at 60 fish per pound (fpp) (or a minimum size of 80 fpp) are released in
late January or early February.
1.2
Operational Components
1.2.1
Facilities
Construction of the Livingston Stone NFH, a substation of the Coleman NFH, was completed in
1998. It is located on a 0.4-acre Bureau of Reclamation-owned site approximately 0.5 miles
downstream of Shasta Dam and upstream of Keswick Dam.
Adult winter Chinook salmon broodstock are collected from the Sacramento River at the Keswick
Dam fish trap. Broodstock collection facilities consist of a fish ladder, a brail-lift, and a 1,000gallon fish-tank elevator. Salmon and steelhead are attracted to the Keswick Dam fish ladder
with a 340 cfs jet pump that supplies water to the trap and fish ladder. The fish ladder is
approximately 170 feet long by 38 feet wide, and contains weirs which create pools. The top of
the ladder leads to a fyke weir. After passing through the fyke weir, adult fish are contained in a
large fiberglass brail enclosure. When the brail is raised, fish are directed into a 1,000-gallon
elevator which transports them up the face of the dam to a fish distribution vehicle (USFWS
2011).
Winter Chinook adults collected in the fish trap are transported to Livingston Stone in a fish
distribution vehicle. Following transport, fish are identified by run based on phenotypic
characteristics. Phenotypically identified broodstock are placed in a 20-foot circular quarantine
tank while awaiting the results of genetic analyses. Adult salmon genetically identified as winter
Chinook salmon are transferred into another 20-foot circular holding tank. The holding tanks are
connected to a carbon filter for removal of malachite green following prophylactic and
therapeutic antifungal treatments of broodstock.
California Hatchery Review Project – Appendix VIII
Page 1
The Livingston Stone spawning and rearing building contains egg and fry incubation units, sixty
30-inch-diameter circular tanks for early rearing, a walk-in freezer, and an office. The incubation
building also contains a 120-gpm chiller, and a 75 kilowatt back-up generator is being added
outside the building. Twenty-four 3-foot by 16-foot rectangular tanks are used for early-rearing.
Ten 12-foot-diameter circular tanks are used for juvenile rearing and can also be used for captive
broodstock holding and rearing.
Water is supplied to the hatchery from a pipe tapped into the Shasta Dam penstocks. This pipe is
plumbed to three of the four penstocks for fail-safe supply. Flow is routed to gas equilibration
units on top of the hatchery head tank from where it is delivered to all hatchery facilities. The
water delivery system for Livingston Stone NFH is equipped with a low-water alarm and a
telephone call-out system. In the event of an emergency (e.g., power outage), the penstock
supplying Livingston Stone NFH defaults to an open position. Total flow available to the
hatchery is 3,000 gpm, all withdrawn from Shasta Lake at a depth of 270 feet, where
temperatures are cooler and can be managed by the Shasta Dam temperature control device.
Hatchery outflow is released to Keswick Reservoir, just below Shasta Dam.
1.2.2
Broodstock
The winter Chinook propagation program was initiated at Coleman NFH in 1988 and relocated to
Livingston Stone in 1997 to improve integration with the naturally reproducing population in the
upper Sacramento River. The winter Chinook supplementation program obtains broodstock from
the Sacramento River at the Keswick Dam fish trap. Prior to 2007, winter Chinook broodstock
were also occasionally collected at the Red Bluff Diversion Dam (RBDD); however, this practice
proved ineffective. Winter Chinook broodstock are completely of natural-origin and are collected
from mid-February into July. A maximum of 10% hatchery-origin adults were used as
broodstock through 2009. Beginning in 2010, only natural-origin winter Chinook were used as
broodstock to further reduce the effects of domestication selection. There have been no transfers
of winter Chinook salmon into Livingston Stone NFH (USFWS 2011).
The collection target for winter Chinook salmon broodstock is 15% of the estimated run size, up
to a maximum of 120 natural-origin adults. A minimum of 20 winter Chinook adults are targeted
for capture during any year regardless of run size (e.g., run size <133) (USFWS 2011).
Allocation of the total collection target into monthly collection targets are determined based on
the percentages of historic run timing past the RBDD. All hatchery-origin winter Chinook and
any natural-origin fish in excess of broodstock requirements are returned to the Sacramento
River.
To be selected as hatchery broodstock, adult winter Chinook must satisfy both phenotypic criteria
(run/spawn timing, collection location, and physical appearance) and genetic criteria (based on
seven loci that provide effective discrimination of winter Chinook plus another marker [GHpsi] to
identify gender). In combination, the genetic and phenotypic criteria enable accurate
identification of winter Chinook salmon for use in the program (USFWS 2011). Winter Chinook
are collected and spawned throughout the duration of run/spawn timing to maintain variability.
Table 1 shows the number of winter Chinook spawned at Coleman NFH (1989-1997) and at
Livingston Stone NFH (1998-2008). Between 2000 and 2008, observed pre-spawn mortality
associated with the operation of Keswick Dam fish trap has averaged 8% (USFWS 2011).
Page 2
Table 1.
Winter Chinook broodstock collection at Keswick Dam and Red Bluff Diversion
Dam, return years 1990-2008d.
Number Spawned
Return Year
Collection Location
Females
Malesc
Total
1990
Keswick
1
1
2
1991
Keswick and RBDD
6
13
19
1992
Keswick
13
13
26
1993
Keswick and RBDD
11
3
14
1994
Keswick
16
11
27
Keswick
21
16
37
1995
Captive Broodstock
21
6
27
1996
Captive Broodstock
38
30a
68
1997
Captive Broodstock
109
45b
154
1998
Keswick
61
35
96
Keswick and RBDD
9
14
23
1999
Captive Broodstock
20
0
20
Keswick and RBDD
44
34
78
2000
Captive Broodstock
66
60
126
Keswick and RBDD
50
47
97
2001
Captive Broodstock
100
32a
132
Keswick
48
40
88
2002
a
Captive Broodstock
95
25
120
Keswick
45
33
78
2003
Captive Broodstock
99
21a
120
Keswick
37
36
73
2004
a
Captive Broodstock
45
23
68
Keswick
51
44
95
2005
Captive Broodstock
46
21a
67
Keswick
37
52
89
2006
Captive Broodstock
60
31a
91
2007
Keswick
19
25
44
2008
Keswick
46
47
93
Males were collected from the Sacramento River and were also used for natural-origin crosses.
cryopreserved milt from 19 captive broodstock males.
c Jacks (i.e., males with a fork length < 650 mm) are included with counts of “Males”
d Salmon were propagated at Coleman NFH (1989-1997) and at Livingston Stone NFH (1998-2008).
Source: USFWS 2011
a
b Includes
1.2.3
Spawning
Winter Chinook broodstock at the Livingston Stone NFH are examined twice weekly to assess
their state of sexual maturity. Hormone analogue implants are administered, as necessary, to
accelerate final gamete maturation to synchronize maturation of broodstock. When a female
salmon is identified as being sexually mature, she is removed from the tank, euthanized, and
assigned a number; each male is assigned a letter. Expelled eggs are separated into two
approximately equal groups. Each group is fertilized with milt from a different male, forming
two half-sibling family groups. After mixing semen and eggs, tris-glycine buffer is added to
extend sperm life and motility. Spawned males are either returned to the holding tank for
additional spawning or euthanized. Males are typically spawned twice, but may be spawned up to
four times. Winter Chinook jacks are randomly incorporated into the spawning matrix.
Page 3
Annual egg collection targets for winter Chinook salmon at Livingston Stone are based on the
number of broodstock collected and thus vary from year to year. Survival rates by life stage are
given in Table 2.
Table 2.
Total egg take targets, release targets and survival estimates for winter Chinook
salmon at Livingston Stone NFH.
Survival Rate
Green Egg
Broodstock
Eyed Egg to Ponding to Overall Egg Total Egg
Release
to Eyed
Ponding
Release
to Release
Target
Target
Egg
Livingston Stone
0.92
0.78
0.80
0.58
Variable
250,000a
Winter Chinook
a Survival
1.2.4
rates based on a 2-year average (2006-2007) that does not include captive broodstock crosses.
Incubation
After fertilization, winter Chinook eggs are placed in Heath incubator trays and disinfected in an
iodophor bath for 15 minutes. Incubating eggs are treated twice a week with formalin to prevent
excessive fungus. After eye-up, eggs are temperature-shocked, and non-viable eggs were
removed. Formalin treatments are discontinued just prior to hatching. Sac fry are left in the
incubator trays until button-up, at which time they were transferred to 30-inch-diameter circular
tanks and started on commercial feed (USFWS 2011).
Incubation units for winter Chinook salmon are sixteen-tray vertical fiberglass incubators.
Loading densities typically range between 1,700 and 3,000 eggs per tray. These densities are
lower than those used for other hatchery stocks of Chinook salmon because the progeny of each
winter Chinook mating (referred to as a “family group”) are maintained separately in order to
quantify relative contribution by each parent. Each female winter Chinook is mated with two
males, and each family group is incubated separately.
1.2.5
Rearing
Family groups are combined as fish size increases, due to limited tank space at the hatchery.
Rearing ponds are partially covered to provide shade. Feeding rates vary based on egg take date
(April through July) and are altered by egg lot to achieve the target release size for each lot. By
the time of release, the pond loading flow index (FI) is 1.5 and the density index (DI) is 0.2.
Winter Chinook are released at the pre-smolt stage with the intent that they rear in the freshwater
environment prior to smoltification.
1.2.6
Release
Winter Chinook juveniles are propagated at Livingston Stone until they reach a size of about 80
fpp (approximately 85 mm fork length). Facility capacity is approximately 250,000 pre-smolts.
Releases occur around late January or early February; however, actual release timing may occur
outside of this target to coincide with a high flow and high turbidity event. Winter Chinook are
released into the Sacramento River at Caldwell Park in Redding (RM 299), about 10 miles
downstream of the hatchery. Volitional releases are not possible at Livingston Stone, so juveniles
are transported to the release site in two groups. This is done to avoid the catastrophic loss of an
entire brood year during transport or release (e.g., traffic accident). Releases are conducted at
dusk to reduce predation risks while juveniles acclimate to the river (USFWS 2011). Release
targets are variable, depending upon the estimated upriver escapement of adults for any given
brood year.
Page 4
1.2.7
Fish Health
Pathogen outbreaks have been detected at the Livingston Stone NFH in returning feral hatchery
broodstock. Infection hematopoietic necrosis virus (IHNV) is commonly detected in 51-81% of
the winter-run Chinook returning to Livingston Stone NFH. With proper iodophor egg
disinfection protocols in place, IHNV has not occurred in juvenile/production fish.
Renibacterium salmoninarum, the causative bacterium for BKD, can be detected in winter-run
adults at low levels of infection; 3-30% by the Enzyme Linked Immunosorbent Assay (ELISA)
and 2-9% by Direct Fluorescent Antibody Technique (DFAT). Adult are prophylactically
injected with antibiotics prior to spawning to reduce vertical transmission of this pathogen.
Juvenile winter-run Chinook have low levels of BKD that do not result in clinical disease or
require antibiotic therapy. From 2006-2011, R. salmoninarum has been detected in three
production cycles at 2% by DFAT and 6-50% by the highly sensitive QPCR assay.
2
Populations Affected by the Hatchery Program
This section presents information about natural Chinook populations that could be affected to
some extent by the Livingston Stone NFH winter Chinook program. Together, the Coleman NFH
and the Livingston Stone NFH propagate three runs of Chinook salmon, as well as steelhead.
Central Valley fall and late-fall Chinook and Central Valley steelhead are propagated at Coleman
NFH, while Sacramento River winter Chinook are propagated at Livingston Stone. These
salmonid stocks are included within the evolutionarily significant unit (ESU) of their respective
natural population. Each Chinook program at Coleman and Livingston Stone is managed to be
integrated with naturally-spawning populations; that is, natural-origin Chinook are incorporated
into the mating plans. The steelhead program at the Coleman NFH is currently managed as a
segregated program, a change that was recently implemented due to a paucity of natural-origin
broodstock in Battle Creek.
Delta smelt are also propagated at Livingston Stone NFH. The Delta smelt program is managed
as a secondary refugial population and does not involve the collection or release of fish to the
natural environment.
2.1
Current Conditions of Affected Natural Populations
The Sacramento River has the sole distinction among the rivers of western North America of
supporting four runs of Chinook salmon. The fall and late-fall runs spawn soon after entering the
natal stream, while the spring and winter runs typically remain in their streams for up to several
months before spawning. Formerly, runs also could be differentiated on the basis of their typical
spawning habitats: spring-fed headwaters for the winter run, the higher-elevation streams for the
spring run, mainstem rivers for the late-fall run, and lower-elevation rivers and tributaries for the
fall run (Yoshiyama et al. 2001).
The Central Valley fall/late fall-run Chinook salmon ESU was listed as a federal Species of
Concern in 2004 due to specific risk factors. The ESU includes all natural-origin populations of
fall-run Chinook salmon in the Sacramento and San Joaquin river basins and their tributaries, east
of Carquinez Strait.
The Central Valley spring Chinook salmon ESU was listed as threatened in 1999, a status that
was reaffirmed in 2005. The ESU includes all natural-origin spring Chinook salmon in the
Sacramento River and its tributaries in California, including the Feather River. The Sacramento
River winter-run Chinook salmon ESU was listed as endangered in 1994; endangered status was
Page 5
reaffirmed in 2005. The ESU includes all natural-origin winter Chinook in the Sacramento River
and its tributaries, as well as winter Chinook from the Livingston Stone NFH.
The fall run is currently the most abundant Chinook run in the Central Valley, and was probably
most abundant historically, as well (Moyle 2002, Williams 2006). Moyle (2002) observed that
the fall run life history strategy makes it ideal for hatchery production, almost to the exclusion of
other runs. Historically, the other seasonal runs were also large (Yoshiyama et al. 2001);
however, over the decades, the spring and winter runs dwindled so that they now consist of few
remnant populations (Lindley et al. 2004). The extensive system of dams in the Central Valley
affected these runs much more than the fall run because the dams blocked much access to cold
water habitats (Lindley et al. 2009). Recent estimates indicate that hatcheries may contribute the
majority of the spawning escapement of Central Valley fall Chinook (USFWS 2011).
Fall Chinook are produced at five Central Valley hatcheries (Coleman NFH, Feather River,
Nimbus, Mokelumne River, and Merced), which together release more than 32 million smolts
annually. As a result, they contribute significantly to commercial and recreational fisheries in the
ocean and popular sport fisheries in the freshwater streams.
While the fall run is the most abundant run in the Central Valley, the aggregate population has
declined during the last several years from an average of 450,000 (1992-2005), to less than
200,000 fish in 2006 and to about 90,000 spawners in 2007. The population includes both
natural- and hatchery‐origin fish, but the proportion of hatchery fish can be as high as 90%
depending on location, year, and surveyor bias (Barnett‐Johnson et al. 2007 as cited in Moyle et
al. 2008).
Central Valley fall Chinook migrate upstream as adults from July through December and spawn
from early October through late December. Run timing varies from stream to stream. Late-fall
Chinook migrate into the rivers from mid-October through December and spawn from January
through mid-April. In general, San Joaquin River populations tend to mature earlier and spawn
later in the year than Sacramento River populations. These differences could be phenotypic
responses to the generally warmer temperature and lower flow conditions in the San Joaquin
River Basin relative to the Sacramento River Basin. The majority of young salmon of these races
migrate to the ocean during the first few months following emergence, although some may
remain in freshwater and migrate as yearlings.
Present day abundance of spring Chinook has declined dramatically from historic levels.
Commercial harvest data comparing average catch from 1916 through 1957 showed a 90%
reduction in spring Chinook salmon harvest over that time period (Skinner 1958 as cited in
USFWS 2011). 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. Today, there are only a few isolated, naturally-spawning populations remaining and
these all exist at relatively low levels of abundance (typically <1,000) (Yoshiyama et al. 1998).
Streams that support wild, persistent, and long-term documented populations of spring Chinook
salmon are Mill, Deer, and Butte creeks (CDFG 1998 as cited in USFWS 2011).
Adult Central Valley spring Chinook leave the ocean to begin their upstream migration in late
January and early February (CDFG 1998, as cited in NMFS 2009), and enter the Sacramento
River between March and September, primarily in May and June (Yoshiyama et al. 1998). They
generally enter rivers as sexually immature fish and must hold in freshwater for up to several
months before spawning (Moyle 2002). Spawning normally occurs between mid‐August and
early October, peaking in September (Moyle 2002 as cited in NMFS 2009 Recovery Plan).
Page 6
Spring‐run fry emerge from the gravel from November to March (Moyle 2002). Juveniles may
reside in freshwater for 12 to 16 months, but some migrate to the ocean as young‐of‐the-year in
the winter or spring within 8 months of hatching (NMFS 2009).
Historically, winter Chinook salmon were abundant and comprised of populations in the
McCloud, Pit, Little Sacramento, and Calaveras rivers (USFWS 2011). Most of these
populations have been isolated from historic spawning and rearing habitats by the construction of
Shasta Dam. The ESU is confined to the mainstem Sacramento River below Keswick Dam.
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 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. Since the early 1990s, the winter
Chinook salmon population has generally shown signs of increasing abundance.
Winter‐run Chinook salmon are unique because they spawn during summer months when air
temperatures approach their yearly maximum. As a result, they require reaches with cold water
sources to protect embryos and juveniles. Adult immigration and holding (upstream spawning
migration) through the Delta and into the lower Sacramento River occurs from December through
July, with a peak from January through April (USFWS 1995, as cited in NMFS 2009).
Winter‐run Chinook salmon are sexually immature when upstream migration begins, and they
must hold for several months in suitable habitat prior to spawning. Primary spawning areas are in
the mainstem Sacramento River between Keswick Dam (RM 302) and RBDD (RM 243).
Spawning occurs between late‐April and mid‐August, with a peak generally in June. Fry rear in
the upper Sacramento River, with fry and juvenile emigration past RBDD from July through
March (although NMFS [1993 and 1997] reports juvenile rearing and outmigration extending
from June through April).
Except for Central Valley winter Chinook, which are largely restricted to the mainstem
Sacramento River between Keswick Dam and Red Bluff Dam, the existing Central Valley fall
Chinook population is unique among North American Chinook ESUs in having little or no
detectable geographically structured genetic variation (Williamson and May 2005; Banks et al.
2000). The degree of this diversity in the historical population is unknown, although it was
almost certainly much greater than at present (Lindley et al. 2009). Central Valley late-fall
Chinook are genetically distinguishable from fall Chinook, yet they are closely related and have
been included in the same ESU (Myers et al. 1998).
For this review, existing Central Valley Chinook populations were defined based on populations
described in the CDFG Grand Tab worksheet. Populations included in the analysis were those
reported in the last 5 years to have fall Chinook and are consistent with those described in ICF
Jones & Stokes (2010) (Table 3).
Table 3.
Populations in the Central Valley fall and late-fall Chinook ESU, ordered from north
to south (unlisted ESU).
Population
Location
Sacramento River Fall Chinook (natural)
Sacramento River
Clear Creek Fall Chinook (natural)
Sacramento River
Cow Creek Fall Chinook (natural)
Sacramento River
Cottonwood Creek Fall Chinook (natural)
Sacramento River
Battle Creek Fall Chinook
Sacramento River
Battle Creek Late-Fall Chinook
Sacramento River
Page 7
Population
Mill Creek Fall Chinook (natural)
Deer Creek Fall Chinook (natural)
Butte Creek Fall Chinook (natural)
Feather River Fall Chinook
Yuba River Fall Chinook (natural)
American River Fall Chinook
Mokelumne River Fall Chinook
Stanislaus River Fall Chinook (natural)
Tuolumne River Fall Chinook (natural)
Merced River Fall Chinook
Location
Sacramento River
Sacramento River
Sacramento River
Sacramento River
Sacramento River
Sacramento River
San Joaquin River
San Joaquin River
San Joaquin River
San Joaquin River
Historically, there were 19 independent populations and eight dependent populations of
spring‐run Chinook salmon in the Central Valley (Lindley et al. 2004). Currently, there are three
independent (Butte, Mill, and Deer) and six dependent (Antelope, Big Chico, Clear, Thomes,
Cottonwood/Beegum, and Stony) populations remaining, along with one “other” hatchery‐natural
integrated population in the Feather River and one “other” population in the Sacramento River
below Keswick Dam (Table 4).
Table 4.
Populations in the Central Valley spring Chinook ESU, ordered from north to south
(ESA listed threatened).
Population
Classification
Clear Creek Spring Chinook (natural)
Dependent
Beegum-Cottonwood Spring Chinook (natural)
Dependent
Battle Creek Spring Chinook (natural)
Dependent
Other Sacramento River Spring Chinook (natural Other
production above Red Bluff Diversion Dam)
Antelope Spring Chinook (natural)
Dependent
Mill Creek Spring Chinook (natural)
Independent
Thomes Spring Chinook (natural)
Dependent
Deer Creek Spring Chinook (natural)
Independent
Stony Creek Spring Chinook (natural)
Dependent
Big Chico Spring Chinook (natural)
Dependent
Butte Creek Spring Chinook (natural)
Independent
Feather River Spring Chinook (integrated)
Other
Currently, the Sacramento River winter Chinook salmon ESU consists of a single (independent)
population in the mainstem Sacramento between Keswick Dam and RBDD. The current
conditions of each of these populations, which could be affected by the Livingston Stone NFH
program, are described in Appendix B. The Sacramento River spring, fall, late-fall, and winter
Chinook populations are described below.
2.1.1
Sacramento River Spring, Fall, Late-fall and Winter Chinook Populations
The Sacramento River is approximately 384 miles long from its headwaters near Mount Shasta to
its mouth at the Delta with a watershed that covers approximately 27,000 square miles. It carries
an annual runoff of 22,000,000 acre-feet, approximately one-third of the total runoff in the state.
The upper watershed includes the drainages above Lake Shasta and Lake Oroville. Valley
Page 8
drainages include the upper Colusa and Cache Creek watershed on the west side of the valley,
and the Feather River and American River watersheds on the east side.
Historically, the Central Valley drainage as a whole is estimated to have supported spring‐run
Chinook salmon runs as large as 700,000 fish between the late 1880s and 1940s (Yoshiyama et al.
1998). The general indication is that the winter run once numbered in the high tens of thousands
and occasionally may have exceeded 100,000 fish. Similar estimates can be inferred from
historical catch data for the fall and late-fall runs. Pre-twentieth century run sizes, including
harvest, for the entire Central Valley may have approached 900,000 fall Chinook and 100,000
late-fall Chinook (Fisher 1994 as cited in Yoshiyama et al. 1998).
The upstream distribution of salmon in the Sacramento River is now limited by Keswick Dam, a
flow-regulating dam located 9 miles below Shasta Dam. The only known streams that currently
support viable populations of spring‐run Chinook salmon in the Central Valley are Mill, Deer and
Butte creeks (see below). Each of these populations is small and isolated (NMFS 2009);
however, between 2001 and 2010, an average of 152 spring Chinook also spawned sporadically
in the mainstem Sacramento River (Table 5).
Table 5.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Spring Chinook salmon escapement in the mainstem Sacramento River (20012010).
Mainstem Sacramento River
Upstream
Downstream
Total
of RBDD
of RBDD
600
21
621
195
0
195
0
0
0
370
0
370
0
30
30
0
0
0
248
0
248
0
52
52
0
0
0
0
0
0
141
10
152
Source: http://www.calfish.org/LinkClick.aspx?fileticket=Kttf%2boZ2ras%3d&tabid=104&mid=524
Fall-run and late-fall run Chinook salmon spawn in the mainstem Sacramento River where
spawning gravels occur for about 67 miles downstream of Keswick Dam. Between 2001 and
2010, an average of nearly 45,000 fall Chinook and approximately 11,000 late-fall Chinook
spawned in the mainstem Sacramento River, most spawning above the RBDD (Tables 6 and 7).
Those numbers were heavily influenced by fish produced in hatcheries on Battle Creek and the
Feather and American rivers. According to ICF Jones & Stokes (2010), approximately 38% of
the natural fall Chinook spawners and 52% of the natural spring Chinook spawners in the
Sacramento River above RBDD are hatchery-origin fish.
Page 9
Table 6.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall Chinook salmon escapement in the mainstem Sacramento River (2001-2010).
Upstream
Downstream
Total
of RBDD
of RBDD
57,920
17,376
75,296
45,552
20,138
65,690
66,485
22,744
89,229
34,050
9,554
43,604
44,950
12,062
57,012
46,568
8,900
55,468
14,097
2,964
17,061
23,134
1,609
24,743
5,311
516
5,827
13,824
2,548
16,372
35,189
9,841
45,030
Table 7.
Late-fall Chinook salmon escapement in the mainstem Sacramento River (20012010).
Downstream of
Year
Upstream of RBDD
RBDD
In-River
Coleman NFH*
Total
In-River (Total)
Nov 2000 – Apr 2001
18,351
18,351
925
Nov 2001 – Apr 2002
36,004
36,004
0
Nov 2002 – Apr 2003
5,346
38
5,384
148
Nov 2003 – Apr 2004
8,824
60
8,884
0
Nov 2004 – Apr 2005
9,493
79
9,572
1,031
Nov 2005 – Apr 2006
7,678
12
7,690
2,485
Nov 2006 – Apr 2007
7,678
66
7,744
1,470
Nov 2007 – Apr 2008
3,673
0
3,673
291
Nov 2008 - Apr 2009
3,424
32
3,456
65
Nov 9009 – Apr 2010
3,843
81
3,924
439
Average
10,431
46
10,468
685
* Transferred to Colman NFH from Keswick Dam and/or RBDD.
Historically, independent winter-run populations existed in Battle Creek, and in the Pit, McCloud,
and Little Sacramento rivers in the Upper Sacramento River. There is no evidence that winter
runs occurred in any of the other major drainages before the era of watershed development. Like
the spring run, winter run fish typically ascended far up the drainages to the headwaters
(Yoshiyama et al. 2001). All historic winter-run spawning habitat in the upper Sacramento River
has been blocked by Shasta and Keswick dams. The only remaining population in the mainstem
Sacramento River spawns between Keswick Dam (RM 302) and RBDD (RM 243).
In 1979, the winter-run population was over 200,000 adults, but today returns average less than
8,000 (Table 8). A rapid decline in adult abundance occurred from 1967 to 1979 after completion
of the RBDD. Over the next 20 years, the population remained static and reached a low point in
Page 10
1994 of only 186 adults. At that point, the run was basically extinct, as defined in the most recent
guidelines for recovery of Central Valley salmonids (Lindley et al. 2007; NMFS 2008).
Juvenile winter Chinook were first released from the Livingston Stone NFH in April 1998
(USFWS 2011). If not for the very successful supplementation program at the Livingston Stone
NFH, construction of a temperature control device on Shasta Dam, opening the RBDD gates, and
restrictions in the ocean harvest, the population would fail to exist in the wild (NMFS 2008).
Between 2001 and 2010, an average of approximately 7,500 winter-run Chinook spawned in the
Sacramento River (Table 8).
Table 8.
Winter Chinook salmon escapement in the mainstem Sacramento River (2001-2010).
Year
Upstream of
Downstream
Total In-River
RBDD
of RBDD
Dec 2001 - Aug 2002
7,325
12
7,337
Dec 2002 - Aug 2003
8,105
28
8,133
Dec 2003 - Aug 2004
7,784
0
7,784
Dec 2004 - Aug 2005
15,730
0
15,730
Dec 2005 - Aug 2006
17,149
48
17,197
Dec 2006 - Aug2007
2,487
0
2,487
Dec 2007 - Aug 2008
2,725
0
2,725
Dec 2008 - Aug 2009
4,416
0
4,416
Dec 2009 - Aug 2010
1,533
0
1,533
Average
7,473
10
7,482
Although Livingston Stone is a very good example of a conservation hatchery operated to
maximize genetic diversity and minimize domestication of the offspring produced in the
hatchery, it still faces some of the same issues as other hatcheries in reducing the diversity of the
naturally-spawning population (NMFS 2008). Lindley et al. (2007) characterizes hatchery
influence as a looming concern with regard to diversity. Even with a small contribution of
hatchery fish to the natural spawning population, hatchery contributions could compromise the
long-term viability and extinction risk of the winter-run. Despite these potential impacts,
Livingston Stone is expected to play a continuing role as a conservation hatchery for the
protection and enhancement of the existing winter‐run population below Keswick and Shasta
dams. It also is expected to play a role in re‐establishing winter-run Chinook to habitats above
Shasta Reservoir and to Battle Creek (NMFS 2009).
According to ICF Jones & Stokes (2010), the percentage of hatchery‐origin winter Chinook
spawning naturally averaged 12.4% in return years 2001‐2006. The PNI of the combined
hatchery and wild winter Chinook population was estimated to be 0.80 to 0.90. This is based on
the percent hatchery fish spawning naturally (pHOS) ranging from 10 to 20% and the proportion
of natural-origin fish in the broodstock (pNOB) of 90 to 95%. According to the pHOS and PNI
criteria described in ICF Jones & Stokes (2010), this supports population rebuilding. Artificial
propagation of winter Chinook salmon at Livingston Stone is expected to cease when the
naturally spawning population has recovered.
2.1.1.1
Harvest
According to USFWS (2011), an average of 149 winter Chinook salmon from Livingston Stone
and Coleman hatcheries were harvested in ocean commercial and sport fisheries from 1991 to
Page 11
2003 (Table 9). The overall ocean harvest rate on these hatchery winter Chinook salmon was
approximately 0.14%. Age composition of ocean-caught winter Chinook from Age 1 to Age 5 is
shown below.
Table 9.
Estimated ocean contribution for winter Chinook salmon from the Livingston
Stone/Coleman National Fish Hatchery, by brood year, based on the number of
salmon released.
Contribution
Brood
Release
Year
Number
Total
Percent
Age 1
Age 2
Age 3
Age 4
Age 5
1991
11,153
16
0.14
0
13
3
0
0
1992
26,433
98
0.37
0
98
0
0
0
1993
18,723
37
0.19
0
25
5
0
7
1994
43,346
36
0.08
0
9
27
0
0
1995
51,267
24
0.05
0
21
0
3
0
1996
4,718
0
0
0
0
0
0
0
1997
21,271
0
0
0
0
0
0
0
1998
153,908
157
0.1
8
137
5
7
0
1999
30,840
58
0.19
0
55
3
0
0
2000
166,207
83
0.05
0
77
5
0
0
2001
252,685
49
0.02
0
44
5
0
0
2002
233,612
910
0.39
0
843
67
0
0
2003
218,517
467
0.21
0
443
25
0
0
Average
92,822
149
0.14
1
136
11
1
1
SD
96,657
260
0.13
2
243
19
2
2
Age Structure
0.4%
0.40%
91.20%
7.50%
0.50%
The USFWS (2011) estimated that 96,400 Coleman NFH fall Chinook salmon and 8,677 late-fall
Chinook salmon were harvested in the Sacramento River sport fishery from 1998 to 2002. During
that period, over 400,000 hours were spent angling. Average freshwater harvest of fall Chinook
salmon was approximately 19,280 per year with the low of 14,340 in 1998 and a high of 24,509
in 2002. Average freshwater harvest of late-fall Chinook salmon was approximately 1,735 per
year with a low of 1,034 in 2002 and a high of 2,408 in 2000.
2.2
Long–term Goals for Natural Populations
NMFS has classified Upper Sacramento winter Chinook as a Core 1 population. A Core 1
population must meet the following low risk extinction criteria:
Page 12

Census population size is greater than 2,500 adults, or the effective population size is
greater than 500 adults;

No productivity decline is apparent;

No catastrophic events occurred or are apparent within the past 10 years.
3
Fisheries Affected by the Hatchery Program
3.1
Current Status of Fisheries
Harvest of Chinook salmon off the coast of California has declined from historic levels due to
decreases in many stocks and ESA listings. Since 1991, management objectives and harvest
allocations have required substantially lower ocean harvest rates on Klamath River fall Chinook.
Because Central Valley salmon intermingle in the ocean with Klamath River salmon stocks,
harvest restrictions intended to protect Klamath River fall Chinook have frequently limited
commercial seasons that would normally also target Central Valley stocks, including salmon from
Coleman NFH. Beginning in 1996, ocean fisheries were further constrained to protect
Sacramento River winter Chinook salmon. In 1999, coastal California Chinook stocks south of
the Klamath River were listed as threatened under the ESA.
Ocean harvest also has been affected during the last decade as a result of fishery restrictions off
the Washington and Oregon coasts. From the U.S.-Canada border to Cape Falcon, Oregon, ocean
fisheries are managed to protect depressed Columbia River fall Chinook salmon and Washington
coastal and Puget Sound natural coho salmon stocks, as well as to meet ESA requirements for
Snake River fall Chinook salmon. In 2008, the ocean commercial and recreational fisheries for
salmon were closed off the coast of Oregon and California as a result of the extremely low
abundance of Central Valley fall Chinook (USFWS 2011).
The exploitation rate of Livingston Stone winter Chinook by brood year is presented in Figure 1.
Average exploitation rate for brood years 1998-2003 was 21.3%.
30
25
27
26
23
23
20
%
18
15
11
10
5
0
1998
1999
2000
2001
2002
2003
Source: M. O’Farrell, NOAA Fisheries, personal communication, June 2011
Figure 1.
Estimated exploitation rate of Livingston Stone winter Chinook by brood year- 1998
- 2003.
Page 13
Figure 2 depicts the distribution of expanded coded-wire tag (CWT) recoveries in fisheries of
Livingston Stone Winter Chinook for brood years 1998-2003 (averages are shown). Among
fisheries, the largest percentage of CWT recoveries occurred in the California ocean sport
fisheries (75%), followed by the California ocean troll (12%). It should be noted that this harvest
was of 2-year-old “jacks”. Small numbers of adult recoveries (less than 6% in each fishery) were
also reported in the California freshwater sport fishery and the ocean troll and ocean sport fishery.
Oregon and British Columbia ocean troll fisheries also had rare recoveries of winter Chinook tags
(data not shown).
CDFG 10‐Ocean Troll
4%
CDFG 40‐ Ocean Sport
CDFG 46‐
3%
Freshwater Sport 6%
Jacks CDFG 40‐
Ocean Sport
75%
Figure 2.
Jacks CDFG 10‐
Ocean Troll
12%
Livingston Stone winter Chinook percent of total harvest to fisheries: 1998 – 2003.
Due to a lack of expanded CWT data available through RMIS for spawning ground CWT
recoveries, it is not possible to precisely calculate smolt to adult survival rates for Livingston
Stone winter Chinook. However, applying an average exploitation rate (21.3%) to an average
percent of total winter Chinook escapement estimated to be of hatchery-origin for return years
2001-2005 (11.2%) allows for calculation of the total adults produced by the hatchery. This was
divided by the total number of hatchery fish that were released for years that contributed to those
return years (90% as three-year-olds). Using this methodology, an estimate of average total smolt
to adult survival of 0.78% was calculated (range 0.32-2.25%) for brood years 1998-2003.
3.2
Long-term Goals for Affected Fisheries
Long-term harvest goals for the fisheries affected by the program have not been established.
Page 14
4
Programmatic and Operational Strategies to Address Issues
Affecting Achievement of Goals
This section describes programmatic and operational hatchery strategies that can be used in the
Livingston Stone NFH to address issues that potentially affect achieving the goals for the fish
populations. Issues to be considered in evaluating hatchery strategies are first identified,
followed by brief descriptions of how possible strategies relate to those issues.
4.1
Issues Affecting Achievement of Goals
A host of issues exist that might affect fishery, fish production, and conservation goals for the
Sacramento Basin. Many of these issues are habitat-related and are outside the control of what
can be done in the hatcheries. Patterns and magnitude of flow releases from dams or water
diversions, for example, are beyond the control of hatchery management. But some issues can be
addressed by specific programmatic and operational strategies employed at the hatcheries. A list
of issues that can be addressed, at least in part, by the hatchery programs and their operations is
given below. Important questions associated with the issues are also identified.
4.1.1
Natural Production Issues
Status of viable salmonid population (VSP) parameters for Livingston Stone winter
Chinook populations: What are the expected effects of the Livingston Stone winter Chinook
hatchery program on VSP parameters of natural Chinook populations? Can hatchery strategies be
updated to enhance the VSP parameters for the natural populations?
Hatchery stock genetic management: What are the effects of current management on genetic
diversity of the hatchery stock and possible effects of strays on natural-origin fish? Can hatchery
strategies be updated to improve hatchery stock genetic diversity and adaptation to the natural
environment (when fish leave the hatchery), both for fish that return to the hatchery and for those
that spawn in nature?
Natural population genetics: Is the hatchery program affecting the genetic integrity and
productivity of the natural populations and, if so, can the program be modified to reduce, or even
reverse, effects?
Performance of the hatchery stock unrelated to genetic composition:Do hatchery fish
released into nature exhibit behavioral traits that adversely affect their performance, unrelated to
domestication effects on genetics, prior to returning to the hatchery or if they spawn in nature,
and if so, can hatchery strategies be modified to ameliorate effects?
4.1.2
Ecological Interaction Issues
Predation effects: What are the predation effects of the hatchery fish released as part of this
program on sensitive natural populations? What are the predation effects of other hatchery
programs on fish released as part of this program? Can the hatchery strategies for this program
be updated to ameliorate these effects?
Competition: What are the competition effects of the hatchery fish released as part of this
program on sensitive natural populations? What are the competition effects of other hatchery
programs on fish released as part of this program? Can the hatchery strategies for this program
be updated to ameliorate these effects?
Page 15
Disease: Does this program exacerbate effects of disease in the basin on other species or
programs (including this program), and, if so, how can the hatchery strategies be updated to
ameliorate effects?
4.2
Operational Issues
Operational issues at the hatchery were identified from answers to a set of questions dealing with
all phases of hatchery operations. This questionnaire was initially developed as part the
Northwest Power and Conservation Council’s Artificial Production Review and Evaluation
(APRE) project for Columbia River hatcheries, and the scientific review process of Northwest
salmon hatcheries. The California HSRG reviewed and updated the questions for the purpose of
this review, and introduced a number of additional questions (see Appendix A-1). The questions
were answered by the hatchery manager, M&E biologists and the regional manager(s) in
workshops held in June 2011. Responses provided in the workshops (plus clarifying notes) can
be found in Appendix A-1.
Most of the questions required simple “yes”, “no” or “NA” replies. They are generally framed
such that a “yes” answer implies consistency with Best Management Practices (BMP) and “no”
answer implies a potential risk. The CA HSRG requested five-year disease histories from
resource managers as part of this questionnaire, but summaries were not provided for all years.
This limited their ability to assess current disease status of the program, or to quantitatively assess
the effectiveness of fish health management efforts. Data tables that were provided as follow up
to the set of question answers are presented in Appendix A-2, and a benefit-risk analysis of the
Appendix A-1 information is provided in Appendix A-3.
4.3
Programmatic Strategies
The California HSRG identified a suite of issues that are applicable to hatchery programs
statewide. These issues were organized under five topics (1) broodstock management; (2)
program size and release strategies; (3) incubation, rearing and fish health management; (4)
monitoring and evaluation; and (5) direct effects of hatchery operation on local habitat and
aquatic or terrestrial organisms. For each topic, hatchery standards to be achieved were defined
and in many cases, suggested implementation guidelines to meet the standard were developed.
All standards and guidelines are listed in Chapter 4 of the California Hatchery Review Report.
Standards that the California HSRG determined apply to this program are presented below.
Where their evaluation determined that this program complies with a standard, this is noted.
Where their evaluation determined that this program does not comply with a standard, “standard
not met” is noted, and recommended guidelines to resolve the issue are identified. In many cases,
the California HSRG provided program-specific comments as well.
4.3.1
Broodstock
Table 10.
Broodstock Source.
Standard
Standard 1.1: Broodstock is appropriate to the basin and the
program goals and should encourage local adaptation.
Guideline
Standard met.
Page 16
Table 11.
Broodstock Collection.
Standard
Standard 1.2: Trapping is done in such a way as to minimize
physical harm to both broodstock and non-broodstock fish.
Guideline
Consistency with Standard Unknown.
Comment: HORs can be trapped multiple times. This may
reduce their ability to reproduce naturally.
Standard 1.3: Collection methods are appropriate for the
program goals.
Standard met.
Comment: Egg take goals are achieved.
Comment: A trap constructed at ACID would provide
more flexibility and greater opportunity to intercept
actively migrating fish than Keswick Dam.
Standard 1.4: Trapping is designed to collect sufficient fish
as potential broodstock to be representative of the entire run
timing and life history distribution of the population or
population component with which it is integrated.
Standard NOT met.
Comment: The existing location for the trapping of
broodstock for Livingston Stone is very limited in the ability
to capture fish representing the entire spectrum of life history
diversity. Only fish that migrate to the furthest upstream
reaches are susceptible to capture. Habitat conditions in the
uppermost reaches where the trap is located are
substantially different from the area of primary spawning by
winter Chinook.
Standard 1.5: Hatcheries have effective facilities for the
extended holding of unripe fish and males that will be used
for multiple spawning.
Standard met.
Table 12.
Broodstock Composition.
Standard
Standard 1.6: Broodstock is primarily comprised of fish
native to the hatchery location, with incorporation of fish
from other locations not exceeding the rate of straying of
natural-origin fish.
Standard met.
Standard 1.7: The levels of natural-origin broodstock are
appropriate for program goals.
Standard met.
Guideline
Comment: It is recommended that managers
investigate the feasibility of collecting natural-origin
adult fish at the fish ladder at Anderson-Cottonwood
Irrigation District (ACID) Dam near Caldwell Park in
Redding. The existing trapping location (Keswick
Page 17
Standard
Guideline
Dam) is very limited in its ability to capture fish
representing the entire spectrum of winter-run Chinook
salmon life history diversity. Only fish that migrate to
the furthest upstream reaches are susceptible to
capture. Habitat conditions in the uppermost reaches
where the trap is located are substantially different
from the primary winter-run Chinook salmon spawning
area.
Standard 1.8: Fish from different runs are not crossed.
Standard met.
Standard 1.10: For Chinook and coho salmon, fish from all
age classes and sizes are incorporated into broodstock at
rates that are commensurate with their relative reproductive
success in natural areas, when known.
Standard met.
Table 13.
Mating Protocols.
Standard
Standard 1.11: The program uses genetically conscious
mating protocols to control or reduce inbreeding and genetic
drift (random loss of alleles), to retain existing genetic
variability and avoid domestication, while promoting local
adaptation for integrated stocks.
Guideline
Standard met.
Standard 1.12: Inbreeding is avoided.
Standard met.
Standard 1.13: The proportion of natural-origin fish used as
broodstock does not negatively affect the long-term viability
of the donor population. For conservation-oriented
programs, extinction risk of the ESU may take precedence.
Standard met.
Comment: Extinction risk of the ESU takes precedence.
Page 18
4.3.2
Program Size and Release Strategies
Table 14.
Program Size.
Standard
Standard 2.1: Program size is established by a number of
factors including mitigation responsibilities, societal benefits,
and effects on natural fish populations.
Guideline
Standard met.
Comment: Program purpose is conservation.
Standard 2.2: Program size is measured as adult
production.
Standard NOT met.
Comment: No explicit adult production goal has been
defined, but implicit goals must exist and could be readily
calculated based on the intent of the conservation program
to produce adults to contribute to the natural area spawning
population.
Standard 2.3: Annual assessments are made to determine if
adult production goals are being met.
Standard NOT met.
Comment: Program production goals should be
expressed in terms of the number of adult recruits just
prior to harvest (age-3 ocean recruits for Chinook).
Standard 2.4: Program size is based on consideration of
ecological and genetic effects on naturally spawning
populations, in addition to harvest goals or other community
values.
Standard met.
Comment: A conservation program of limited size and with
substantial post-release monitoring, there are apparently
minimal deleterious effects.
Standard 2.5: Natural spawning populations not integrated
with a hatchery program should have less than five percent
total hatchery-origin spawners (i.e., pHOS less than five
percent). Spawners from segregated hatchery programs
should be absent from all natural spawning populations (i.e.,
pHOS from segregated programs should be zero).
Comment: Populations have not been identified and
population boundaries have not been delineated. This
has been identified as an area of needed research
(Chapter 6.2 of the California Hatchery Review
Report).
Consistency with standard unknown
Page 19
Table 15.
Release Strategy.
Standard
Standard 2.6: Size, age, and date at release for hatcheryorigin fish produce adult returns that mimic adult attributes
(size at age and age composition) of the natural population
from which the hatchery broodstock originated (integrated
program) or achieve some other desired size or condition at
adult return (segregated programs).
Standard met.
Standard 2.7: Juveniles are released at or in the near vicinity
of the hatchery.
Standard met.
4.3.3
Guideline
Comment: This is a conservation program. The
intent of off-site release is for fish to return to winter
Chinook natural spawning areas. Straying to other
areas is not an issue. Deleterious ecological effects of
this program are considered unlikely.
Incubation, Rearing and Fish Health
Table 16.
Fish Health Policy.
Standard
Standard 3.1: Fishery resources are protected, including
hatchery and natural fish populations, from the importation,
dissemination, and amplification of fish pathogens and
disease conditions by a statewide fish health policy. The
fish health policy clearly defines roles and responsibilities,
and what actions are required of fish health specialists,
hatchery managers, and fish culture personnel to promote
and maintain optimum health and survival of fishery
resources under their care. The Fish Health Policy includes
the California HSRG’s Bacterial Kidney Disease (BKD)
management strategy (see Appendix V).
Guideline
Comment: The USFWS should develop a Hatchery
Procedure Manual for the program at Livingston Stone
NFH, which includes performance criteria and culture
techniques presented in IHOT (1995), Fish Hatchery
Management (Wedemeyer 2001) or comparable
publications.
Standard met.
Table 17.
Standard
Page 20
Hatchery Monitoring by Fish Health Specialists.
Guideline
Standard
Standard 3.2: Fish health inspections are conducted
annually on all broodstocks to prevent the transmission,
dissemination or amplification of fish pathogens in the
hatchery facility and the natural environment, as follows:
a)
Inspections are conducted by or under the
supervision of an AFS certified fish health specialist or
qualified equivalent. For state-operated anadromous fishery
programs, specific standards and qualifications are to be
defined during development of a fish health policy.
b)
Annual inspections follow AFS ‘Fish Health
Bluebook’ guidelines for hatchery inspections.
c)
Broodstocks are examined annually for the
presence of BKD and where the causative bacterium
Renibacterium salmoninarum recurs, the California HSRG’s
control strategy will be implemented.
Guideline
Standard met.
Comment: Adults are prophylactically injected; BKD has
been at very low levels in juveniles, not requiring treatment.
Standard 3.3: Frequent routine fish health monitoring is
performed to provide early detection of fish culture, nutrition,
or environmental problems, and diagnosis of fish pathogens,
as follows:
a)
Monitoring is conducted by or under the supervision
of an AFS certified fish health specialist or qualified
equivalent.
b)
Monitoring is conducted on a monthly, or at least bimonthly basis, for all anadromous species at each hatchery
facility.
c)
A representative sample of healthy and moribund
fish from each lot is examined. Results of fish necropsies
and laboratory findings are reported on a standard fish
health monitoring form.
Standard met.
Standard 3.4: All antibiotic or other treatments are preapproved by the appropriate fish health specialist for each
facility. If antibiotic therapy is advised, fish health personnel
will culture bacterial pathogens to verify drug sensitivity.
Post-treatment examinations of treated units are conducted
to evaluate and document efficacy of antibiotic or chemical
treatments.
Standard met.
Standard 3.5: Examinations of fish are conducted prior to
release or transfer to ensure fish are in optimum health
condition, can tolerate the stress associated with handling
and hauling during release, and can be expected to perform
well in the natural environment after release.
Page 21
Standard
Guideline
Standard met.
Standard 3.6: Annual reporting standards and guidelines will
be followed for fish health reports, including results of adult
inspections, juvenile monitoring and treatments
administered, and pre-liberation examinations for each
hatchery program. A cumulative five year disease history
will be maintained for each program and reported in annual
or other appropriate facility reports.
Standard met.
Standard 3.7: Fish health status of stock is summarized prior
to release or transfer to another facility.
Standard met.
Table 18.
Facility Requirements.
Standard
Guideline
Standard 3.8: Physical facilities and equipment are
adequate, and operated in a manner that promotes quality
fish production and optimum survival throughout the rearing
period. If facilities are determined to be inadequate to meet
all program needs, and improvements are not feasible, then
the hatchery program(s) must be re-evaluated within the
context of what the facility can support without compromising
fish culture and/or fish health, or causing adverse
interactions between hatchery and natural fish populations.
Standard met.
Standard 3.9: Distinct separation of spawning operations,
egg incubation, and rearing facilities is maintained through
appropriate sanitation procedures and biosecurity measures
at critical control points to prevent potential pathogen
introduction and disease transmission to hatchery or natural
fish populations, as follows:
a)
Disinfect/water harden eggs in iodophor prior to
entering “clean” incubation areas. In high risk situations,
disinfect eggs again after shocking and picking, or
movement to another area of the hatchery.
b)
Foot baths containing appropriate disinfectant will
be maintained at the incubation facility’s entrance and exit.
Foot baths will be properly maintained (disinfectant
concentration and volume) to ensure continual
effectiveness.
c)
Sanitize equipment and rain gear utilized in
broodstock handling or spawning after leaving adult area.
d)
Sanitize all rearing vessels after eggs or fish are
removed and prior to introducing a new group.
e)
Disinfect equipment, including vehicles used to
Page 22
Comment: A biosecurity plan that protects individual
programs (winter-run Chinook salmon and Delta
smelt) should be prepared and implemented.
Standard
Guideline
transfer eggs or fish between facilities, prior to use with any
other fish lot or at any other location. Disinfecting water
should be disposed of in properly designated areas.
f)
Sanitize equipment used to collect dead fish prior to
use in another pond and/or fish lot.
g)
Properly dispose of dead adult or juvenile fish,
ensuring carcasses do not come in contact with water
supplies or pose a risk to hatchery or natural populations.
Standard met.
Standard 3.10: All hatchery water intake systems follow
federal and state fish screening policies.
Standard NOT met.
Table 19.
Fish Health Management Plans.
Standard
Standard 3.11: Fish Health Management Plans (FHMP)
similar to or incorporated within an HGMP have been
developed. The FHMP will:
a)
Describe the disease problem in adequate detail,
including assumptions and areas of uncertainty about
contributing risk factors.
b)
Provide detailed remedial steps, or alternative
approaches and expected outcomes.
c)
Define performance criteria to assess if remediation
steps are successful and to quantify results when possible.
d)
Include scientific rationale, study design, and
statistical analysis for proposed studies aimed at addressing
disease problems or areas of uncertainty pertaining to
disease risks.
Guideline 3.10.1. Follow existing statutes, including
NEPA, CEQA, ESA, CESA, and current court
decisions.
Comment: Water supply is from Shasta Dam
penstock. CDFG statewide fish screening policy
provides that under the provisions of the Fish &
Wildlife Coordination Act the CDFG shall require the
installation of fish screens on all unscreened
diversions where fish are present (i.e., hatchery
intake).
Guideline
Guideline 3.11.1. Compliance with the FHMP should
be reviewed annually, through the hatchery
coordination team, and include any new data or
information that may inform actions or decisions to
address disease concerns.
Standard NOT met.
Comment: New standard to be initiated.
Table 20.
Water Quality.
Standard
Standard 3.13: Existing facilities strive for suggested water
chemistry and characteristics (IHOT 1995, Wedemeyer
2001) which may require water filtration and disinfection,
additional heating or cooling, degassing and/or aeration, or
other modifications to the quantity and quality of an existing
Guideline
Guideline 3.13.1. When surface water is used, a
biosecurity evaluation should be performed, and water
supplies protected to the extent feasible, to avoid
direct contamination of hatchery water supply by
potential disease vectors (i.e. live fish, amphibians,
Page 23
Standard
water supply, as follows:
a)
Pathogen-free water supplies will be explored for
each facility, particularly for egg incubation and early
rearing.
b)
Water supplies must provide acceptable
temperature regimes for egg incubation, juvenile rearing and
adult holding.
c)
Water supplies will have appropriate water
chemistry profiles, including dissolved gases: near
saturation for oxygen, and less than saturation for nitrogen.
d)
Water supplies for egg incubation must not contain
excessive organic debris, unsettleable solids or other
characteristics that negatively affect egg quality and survival.
Standard NOT met.
Comment: Water supply is not pathogen free.
Table 21.
Best Management Practices.
Standard
Standard 3.14: The rationale, benefits, risks, and expected
outcomes of any deviations from established best
management practices 1 for fish culture and fish health
management are clearly articulated in the hatchery
operational plan (including specific fish culture procedures),
Hatchery and Genetic Management Plan (HGMP), Fish
Health Management Plan, the hatchery coordination team
process, and/or in annual written reports.
Standard NOT met.
Standard 3.15: Information on hatchery operations is
collected, reviewed, and reported in a timely, consistent and
scientifically rigorous manner (see requirements and list of
reporting parameters in Section 4.4, Monitoring and
Evaluation (M&E)).
Standard NOT met.
Guideline
birds, or mammals).
Guideline 3.13.2. Cooling and/or heating of water
supplies may be necessary to meet water quality
standards and program goals, for example, when egg
incubation and early rearing water temperatures are
too low in fall and winter months to consistently
achieve desired fish size-at-release.
Guideline 3.13.3. Degassing columns or aeration
devices may be necessary to meet water quality
standards throughout the rearing cycle.
Guideline 3.13.4. If unable to remediate siltation
problems for egg incubation, alternative incubation
sites, water supplies, or incubation methods should be
considered.
Guideline
Guideline 3.14.1. Develop required plans.
Comment: Develop HGMP. Develop the hatchery
operational plan (specific Fish Culture Procedures), an
annual written reports. CNFH currently has a
functional Hatchery Evaluation Team (HET) in place to
coordinate hatchery operations, fish health, and
monitoring activities for the winter-run program at
Livingston Stone NFH.
Guideline 3.15.1. An annual report containing
monitoring and evaluation information (see M&E
standards), including pathogen prevalence, fish
disease prevalence, and treatment efficacies, should
be produced in a time such that the information can be
used to inform hatchery actions during the following
brood cycle.
1
Best management practices are procedures for operating hatchery programs in a defensible scientific manner to: 1)
utilize well established and accepted fish culture techniques and fish health methodologies to ensure hatchery
populations have the greatest potential to achieve program goals and, 2) minimize adverse ecological interactions
between hatchery and natural-origin fish.
Page 24
Standard
Standard 3.16: Eggs are incubated using best management
practices and in a manner that ensures the highest survival
rate and genetic contribution to the hatchery population, as
follows:
a)
Eggs are incubated at established temperatures,
egg densities, and water flows for specific species.
Appropriate egg incubation parameters are identified in
Hatchery Performance Standards (IHOT 1995, Chapter 4) or
Fish Hatchery Management (Wedemeyer 2001).
b)
Incubation techniques should allow for
discrimination of individual parents/families where required
for program goals (e.g., for conservation-oriented programs
and steelhead programs, or to exclude families for genetic
(hybridization) or disease culling purposes).
c)
Eggs in excess of program needs are discarded in
a manner that is consistent with agency policies and does
not pose disease risks to hatchery or natural populations.
Guideline
Standard met.
Standard 3.17: Fish are reared using best management
practices and in a manner that promotes optimum fish health
to ensure a high survival rate to the time of release, and
provides a level of survival after-release appropriate to
achieve program goals, while minimizing adverse impacts to
natural fish populations, as follows:
a)
Fish performance standards (i.e., species-specific
metrics for size, weight, condition factor, and health status)
will be established for all life stages (fry, fingerling, and
yearling) at each facility.
b)
Fish nutrition and growth rates are maintained
through the proper storage and use of high quality feeds.
Appropriate feeding rates will be closely monitored and
adjusted as needed to accommodate fish growth/biomass in
rearing units.
c)
Juvenile fish will be reared at density and flow
indices and temperature that promote optimum health.
Appropriate density and flow requirements for anadromous
fish are identified in Hatchery Performance Standards Policy
(IHOT 1995, Chapter 4) or in a comparable reference such
as Fish Hatchery Management (Wedemeyer 2001).
d)
Appropriate growth strategies will be developed,
with particular attention to photoperiod, temperature units
and feeding rates to optimize parr-to-smolt transformation, to
ensure juvenile fish reach target size-at-release and are
physiologically ready to out-migrate and survive salt-water
entry.
Standard met.
Page 25
4.3.4
Monitoring and Evaluation
Table 22.
Hatchery and Genetic Management Plans.
Standard
Guideline
Standard 4.1: Each hatchery program is thoroughly
described in a detailed operational plan such as an HGMP
or Biological Assessment. Operational plans are regularly
updated to reflect updated data, changes to goals and
objectives, infrastructure modifications, and changing
operational strategies.
Standard met.
Comment: A BA for Coleman and Livingston Stone NFHs
was completed in 2001. An updated draft was completed in
2011.
Table 23.
Hatchery Evaluation Programs.
Standard
Standard 4.2: For each hatchery, a Monitoring and
Evaluation program dedicated to reviewing the hatchery’s
achievement of program goals and assessing impacts to
naturally produced fishes must be established. Each M&E
program will describe and implement a transparent, efficient,
and timely process to respond to requests for experimental
fishes, samples, and data.
Guideline
Standard met.
Comment: Hatchery has an evaluation team and a written
Adaptive Management Plan.
Table 24.
Hatchery Coordination Teams.
Standard
Standard 4.3. A Hatchery Coordination Team has been
created for each hatchery.
Guideline
Standard met.
Table 25.
In-Hatchery Monitoring and Record Keeping.
Standard
Guideline
Standard 4.4: The monitoring and record keeping
responsibilities listed below are carried out on an annual
basis in-hatchery for each anadromous salmonid program.
Summaries of data collected, with comparisons to
established targets, are included in annual hatchery program
reports, and individual measurements (unless otherwise
indicated) are store in electronic data files. Sample sizes
indicated are provisional pending further consideration (see
Page 26
Standard
Section 6.2). A complete list of required and recommended
data collection and reporting is provided in Appendix IV.
a) Record date, number, size, age (if available), gender, and
origin (natural or hatchery; hatchery- and basin-specific
when available) of (a) all hatchery returns and (b) fish
actually used in spawning. (Summaries in annual reports;
individual measurements in electronic files.)
b) Record age composition of hatchery returns, as
determined by reading scales and/or tags, from a systematic
sample of the hatchery returns (n>550, or all returns for
programs with less than 550 returns).
c) Record sex-specific age composition of the fish spawned,
as determined by reading scales and/or tags, from a
systematic sample of the fish spawned (n>550, or all
spawned fish for programs with less than 550 spawned fish).
d) Describe in detail the spawning protocols used for each
program (by family group for conservation-oriented
programs), including the number of times individual males
were used.
e) Describe in detail the culling protocols used for each
program, including purpose.
f) Calculate and record effective population size (in
conservation-oriented programs).
g) Measure and record mean egg size, fecundity, and fish
length for each individual in a systematic sample of spawned
females (n>50), to establish and monitor the relation
between fecundity, egg size, and length in the broodstock.
(Include a table of all measurements in annual report.)
h) Record survival through the following life stages: green
egg to eyed egg, eyed egg to hatch, hatch to ponding,
ponding to marking/tagging, and marking/tagging to release.
i) Record mean, standard deviation, and frequency
distribution based on n>100 measurements of fish length, by
raceway, at periodic intervals (no less than monthly) prior to
release and at time of release for all release types, to
assess trends and variability in size throughout the rearing
process. (Report means and standard deviations in annual
reports; individual measurements and frequency
distributions in electronic files.)
j) Maintain records of disease incidence and treatment,
including monitoring of treatment efficacy.
k) Report CWT releases and recoveries to relevant
databases (i.e., RMIS) on a timely annual basis.
Guideline
Standard met.
Comment: Detailed in-hatchery data by life stage is
available.
Page 27
Table 26.
Marking and Tagging Programs.
Standard
Standard 4.5: Chinook salmon marking and tagging
programs allow for:
a)Estimation of ocean and freshwater fishery impacts, and
natural area and hatchery escapement at the age-, stockand release group-specific levels,
b)Estimation of the proportion of hatchery-origin fish in
natural spawning areas,
c) Estimation of the proportion of natural-origin fish in
hatchery broodstock,
d) Real-time identification of hatchery-origin juveniles and
adults (i.e., hatchery vs. non-hatchery origin),
e) Identification of stock of origin for hatchery-origin fish,
f) Real-time identification of yearling vs. fingerling releasetype fish at the adult stage.
Guideline
Standard met.
Comment: Fish are 100% coded wire tagged and adipose
fin-clipped.
Table 27.
Post-Release Emigration Monitoring.
Standard
Guideline
Standard 4.8: The quantities listed below are monitored in
the freshwater environment following release of juvenile
Chinook and coho. Summaries of collected data and
associated estimates, along with comparisons to established
targets, are included in annual or periodic (every 5 to 10
years) reports produced by the monitoring agencies/entities.
a) Annual: Document length (mean, standard deviation, and
frequency distribution) of hatchery fish at release as
compared to naturally produced smolts.
b) Periodic: Document the number of days (mean, standard
deviation, and frequency distribution) from release of
hatchery fish to passage at a location near entry to salt
water (e.g., using PIT tags/detectors or acoustic tags/arrays)
and the degree of overlap with natural-origin fish.
c) Periodic: Estimate the percent hatchery-origin fish among
outmigrating juveniles and, where feasible, estimate total
juvenile production.
Standard NOT met.
Comment: Annual comparisons of the size of NOR and
HOR juveniles is not done.
Page 28
Table 28.
Adult Monitoring Programs.
Standard
Standard 4.10: Monitoring programs for Chinook salmon
allow for estimation of the following on an annual basis.
a) Total recreational and commercial ocean harvest,
Guideline
and harvest of hatchery-origin fish at the age-, stock-,
and release group-specific (CWT) level,
b) Total freshwater harvest, and harvest of hatchery-origin
fish at the age-, stock-, and release group-specific (CWT)
level,
c) Total returns (hatchery -and natural-origin) to hatchery,
and returns at the age-, stock-, and release group-specific
(CWT) level,
d) Age composition of hatchery returns,
e) Total escapement by tributary and by species/run,
f) Proportion of hatchery-origin fish among natural area
spawners (pHOS) by tributary and at age-, stock-, and
release group-specific (CWT) level,
g) Age composition of individual tributaries important for
natural production.
Standard met.
Table 29.
Evaluation Programs.
Standard
Standard 4.13: Evaluation programs for Chinook salmon
assess the following fundamental issues on a brood-specific
basis:
a) Survival from release to pre-fishery recruitment,
b) Age-specific maturation schedules,
c) Straying (here defined as failure of hatchery-origin fish to
return to the hatchery from which they originated or to the
watershed in the immediate vicinity of the hatchery),
d) Age-specific fishery contribution rates,
e) Pre-fishery age-3 ocean recruitment.
Evaluation programs for Chinook salmon assess the
following fundamental issues on a periodic basis (e.g., every
5 to 10 years):
f) The relationship of hatchery fish survival rates and
maturation schedules to size and/or date of release;
g) Long-term trends in phenotypic traits (age, maturity,
fecundity at size, run/spawn timing, size distribution) and
genetic traits (divergence among year classes, effective
population size, divergence from natural populations) of
hatchery populations;
h) Spatial and temporal overlap and relative sizes of
emigrating juvenile hatchery- and natural-origin fish and total
(hatchery plus natural-origin) spawner distribution and
densities to assess the likelihood or magnitude of
Guideline
Guideline 4.13.1. Use tag recovery data and cohort
reconstruction (cohort analysis) methods to estimate
the following quantities. In the future, alternative
technologies or analytical methods may generate
other data suitable for estimating these quantities.
• Brood survival from release to ocean age-2 at
the release group-specific (CWT) level,
• Brood maturation schedule (age-specific
conditional maturation probabilities) at the
• Straying and geographic distribution of stray
hatchery-origin fish at the release groupspecific (CWT) level,
• Age-specific ocean and freshwater fishery
contributions and exploitation rates at the
• Pre-fishery ocean recruitment of hatcheryorigin fish at age-3 at the release groupspecific (CWT) and program level.
Page 29
Standard
deleterious effects of hatchery-origin fish on naturally
spawning fish due to competition, predation, or behavioral
effects.
Guideline
Standard NOT met.
4.3.5
Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial
Organisms.
Table 30.
Direct Effects of Hatchery Operations.
Standard
Guideline
Standard 5.1: Hatchery operations/infrastructure is
integrated into local watershed restoration efforts to support
local habitat restoration activities.
Standard met.
Standard 5.2: Hatchery infrastructure is operated in a
manner that facilitates program needs while reducing
impacts to aquatic species, particularly listed anadromous
salmonids.
Standard met.
Standard 5.3: Effluent treatment facilities are secure and
operated to meet NPDES requirements.
Standard met.
Standard 5.4: Current facility infrastructure and construction
of new facilities avoid creating an unsafe environment for the
visiting public and staff and provide adequate precautions
(e.g., fencing and signage) where unsafe conditions are
noted.
Standard met.
5
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Central Valley of California, USA. North American Journal of Fisheries Management 25:9931009.
Yoshiyama, R. M., E. R. Gerstung, F. W. Fisher, and P. B. Moyle. 2001. Historical and present
distribution of Chinook salmon in the Central Valley drainage of California. Pages 71-176 in
Contributions to the biology of Central Valley salmonids, R. L. Brown, editor. California
Department of Fish and Game, Fish Bulletin 179.
Yoshiyama, R.M., F.W. Fisher, and P.B. Moyle. 1998. Historical abundance and decline of Chinook
salmon in the Central Valley region in California. North American Journal of Fisheries
Management 18: 487–521.
Page 32
Appendix VIII
Winter Chinook
Program Report
Appendix A-1
June 2012
APPENDIX A-1
CALIFORNIA SCIENCE REVIEW PANEL
HATCHERY PROGRAM REVIEW QUESTIONS
BACKGROUND INFORMATION
1
Hatchery and Program Name
Hatchery:
Livingston Stone NFH
Program:
Winter Chinook Salmon
2
Species and Population (or stock) under Propagation and ESA Status
Species:
Winter Chinook
ESA Status:
Endangered
3
Responsible Organization and Individuals
Lead Contact:
Dan Castleberry, Assistant Regional Director – Fisheries
US Fish and Wildlife Service
Pacific Southwest Region
Room W-2606
2800 Cottage Way
Sacramento, CA 95825
(916) 978-6178
[email protected]
Hatchery Manager:
Scott Hamelberg, Project Leader
Coleman National Fish Hatchery
24411 Coleman Fish Hatchery Road
Livingston Stone National Fish Hatchery Winter Chinook Program /Appendix A-1 /
June 2012
Page A-1 1
Anderson, CA 96007
(530) 365-8781
[email protected]
John C. Rueth, Assistant Hatchery manager
16349 Shasta Dam Boulevard
Shasta Lake, CA 96019
(530) 273-0549
[email protected]
Other Contacts:
Hatchery Evaluation and Permitting Contact
James G. Smith, Project Leader
Red Bluff Fish and Wildlife Office
10950 Tyler Road
Red Bluff, CA 96080
(530) 527-3043
[email protected]
Reclamation Contact
Brian Person, Area Manager
US Bureau of Reclamation
16349 Shasta Dam Blvd.
Shasta Lake, CA 96019
(530) 275-1554
4
Funding Source, Staffing Level, and Annual Hatchery Program
Operational Costs
Livingston Stone National Fish Hatchery (NFH) is a substation of Coleman NFH. Coleman
NFH employs 23 FTE, and two additional FTEs are employed at Livingston Stone NFH. The
Coleman facility (and Livingston Stone substation) operates on an annual budget of $2.7 million,
funded by the US Bureau of Reclamation (Reclamation). This budget does not include the
evaluation or fish health budgets. Operations, evaluation and fish health costs are $4.3 million
annually.
5
Location(s) of Hatchery and Associated Facilities (weirs, etc.)
Livingston Stone NFH is located on the west side of the Sacramento River, approximately 0.5
miles below the base of Shasta Dam (Keswick Reservoir).
Page A-1 2
June 2012
6
Type of Program
The USFWS’s artificial propagation program for winter Chinook salmon at Livingston Stone
NFH is an integrated-recovery type program. That is, hatchery propagated winter Chinook are
managed to be integrated with the natural population of winter Chinook in the upper Sacramento
River, and are intended to provide a demographic boost to aid in the recovery of that population.
Hatchery-origin winter Chinook are intended to return as adults to the upper Sacramento River,
spawn in the wild, and become reproductively and genetically assimilated into the natural
population.
7
Purpose (Goal) of Program
The primary goal of the Service’s artificial production program at Livingston Stone NFH is to
provide a demographic boost to the natural spawning component of the population in the upper
Sacramento River, assisting in the recovery of that population.
8
Justification for the Program
Livingston Stone NFH, a substation of Coleman NFH, was constructed by Reclamation in late
1997. The facility was constructed for the explicit purpose of propagating ESA-listed winter
Chinook salmon to assist in the recovery of that population. This program is supported in
NMFS’s draft Recovery Plan for winter Chinook salmon (NMFS 2009b).
Additional: Please provide a summary of the program history.
The USFWS initially attempted to propagate winter Chinook salmon at Coleman NFH in 1955.
This first attempt, as well as subsequent efforts from 1958 through 1967, was largely
unsuccessful. From 1978 through 1985, attempts to propagate winter Chinook salmon at
Coleman NFH again met with limited success. High water temperatures at Coleman NFH
caused considerable mortality of adult broodstock, eggs, and juveniles.
In 1988, a Cooperative Agreement between the NMFS, Reclamation, USFWS, and CDFG
outlined a 10-point plan to implement actions to improve the status of winter Chinook salmon in
the Sacramento River basin. Included in this plan was the development of an artificial
propagation program at Coleman NFH, including necessary facilities and operations to meet
hatchery production goals. With the population of winter Chinook in severe decline, the USFWS
reinitiated a winter Chinook salmon propagation program at Coleman NFH in 1989. The goal of
the winter Chinook hatchery propagation program was to supplement natural spawning in the
upper Sacramento River. To improve the likelihood that fish reared at the Coleman NFH would
return to the upper Sacramento River and integrate with the naturally spawning population,
juvenile winter Chinook were released at the pre-smolt stage in the vicinity of Redding.
The first major production group of winter Chinook salmon juveniles (911,582 fish) from the
Coleman NFH was released in 1992; however, none of the fish from this release were observed
during monitoring efforts in the upper mainstem Sacramento River in 1994, the year the majority
of these fish were expected to return. Subsequently, monitoring conducted by the USFWS’s
Hatchery Evaluation Program observed that a considerable portion of hatchery-propagated
June 2012
Page A-1 3
winter Chinook adults were returning to Battle Creek and not assimilating with the natural
population in the Sacramento River. These observations suggested that rearing and release
strategies intended to imprint hatchery-origin winter Chinook juveniles to the mainstem
Sacramento River were ineffective. This situation, combined with evidence of possible
hybridization with spring Chinook in the propagation program, resulted in a two year (19961997) moratorium on the capture of natural winter Chinook broodstock. Hatchery spawning of
winter Chinook adults in 1996 and 1997 was limited to only a small number of adults that were
available from the captive broodstock program.
Construction of the Livingston Stone NFH in 1997 and refined genetic methods for broodstock
selection ameliorated concerns of straying and hybridization that led to the moratorium, so
collection of winter Chinook broodstock was re-initiated in 1998. Juvenile winter Chinook were
first released from the Livingston Stone NFH in April 1998.
HATCHERY OPERATION PHASE: BROODSTOCK CHOICE
1
Do the broodstocks represent natural populations native to the
watersheds in which hatchery fish will be released?
Clarification:
The watershed populations are those that will be evaluated by the Review Panel. Does
broodstock represent a) one native population, b) a mixture of local native populations, or c) one
or more nonnative populations?
Relationship to Outcomes/Goals:
This program uses a broodstock representing populations native to the watershed, which
increases the likelihood of long-term survival of the stock, helps avoid loss of population
diversity, and reduces the likelihood of unexpected ecological interactions.
Answer:
Yes. Broodstock origin is upper Sacramento River.
2
Was the best available broodstock selected for this program?
Clarification:
This question applies to situations where the native populations are extirpated. The concern is
that the best possible broodstock may not be the one selected.
Page A-1 4
June 2012
Choice of a broodstock with a similar life history and evolutionary history to the extirpated stock
improves the likelihood of successful reintroduction.
Answer:
Yes.
3
Does the broodstock display morphological and life history traits
similar to the natural population?
Clarification:
The Review Panel will need to distinguish lineage of a population (that may be connected to an
environment that no longer exists) from current environment and current fish performance.
Choice of a broodstock with similar morphological and life history traits improves the likelihood
of the stock's adaptation to the natural environment.
Answer:
Yes.
4
Does the broodstock have a pathogen history that indicates no threat
to other populations in the watershed?
Clarification:
Request a 5-year pathogen history.
The broodstock chosen poses no threat to other populations in the watershed from pathogen
transmission.
Answer:
Yes, there is no pathogen threat to other populations in the watershed.
5
Does the broodstock have the desired life history traits to meet
harvest goals (e.g., timing and migration patterns that result in full
recruitment to target fisheries)?
Clarification:
This question applies only to segregated programs with the sole purpose of providing fish for
harvest.
June 2012
Page A-1 5
The broodstock chosen is likely to have the life history traits to meet harvest goals for the target
stock without adversely affecting other stocks.
Answer:
N/A.
10
Is the percent natural-origin fish used as broodstock for this program
estimated?
Clarification:
[This question is out of order based on ID number, but should go before the next question.]
Estimating the proportion of natural fish used for broodstock makes it possible to determine
whether composition targets have been met and prevents masking of the status of both the
hatchery and natural populations.
Answer:
Yes.
6
What is the percent natural-origin fish in the hatchery broodstock?
Clarification:
Estimating the proportion of natural fish used for broodstock makes it possible to determine
whether composition targets have been met and prevents masking of the status of both the
hatchery and natural populations.
Answer:
100%.
7
Do natural-origin fish make up less than 5% of the broodstock for this
program?
Clarification:
This question does not apply to integrated programs. [It it may be relevant in the Central Valley.]
Maintaining a segregated hatchery population composed of less than 5% natural fish reduces the
risk of loss of population diversity.
Page A-1 6
June 2012
Answer:
No.
HATCHERY OPERATION PHASE: BROODSTOCK COLLECTION
11
Are adults returned to the river?
Clarification:
If the answer is YES, then describe the purpose of returning fish to the river. For example, fish
returned to river may be subject to additional harvest. Alternatively, fish may be returned to
river to supplement the natural population (a conservation purpose).
Not returning adults to the lower river to provide additional harvest reduces the likelihood of
straying and unintended contribution to natural spawning.
Answer:
Yes. Both hatchery and natural origin returns that are not used as broodstock are returned to the
river to spawn naturally.
12
Are representative samples of natural and hatchery population
components collected with respect to size, age, sex ratio, run and
spawn timing, and other traits important to long-term fitness?
Clarification:
For integrated populations, consider both natural and hatchery components.
For segregated populations, consider only the hatchery component.
Ask the following questions twice: first about hatchery fish; second about wild fish being
incorporated into hatchery stock:
How many males and females are collected for broodstock? Are adults collected over entire
migration/spawn period? How many females and males are collected, and does the hatchery
program attempt to equalize the number of males and females?
Collecting representative samples of both the natural and hatchery populations reduces the risk
of domestication and loss of within-population diversity.
June 2012
Page A-1 7
Answer:
Hatchery Fish: Length, gender, phenotypic data are collected, then fish are Floy-tagged and
returned to the river.
Wild Fish: Yes, phenotypic characteristics of broodstock have been compared to other
subcomponents of the population spawned elsewhere in the basin and been found similar. The
exception may be for fish that spawn below Keswick Dam, as these fish are not sampled.
13
Does the proportion of the spawners brought into the hatchery follow
a “spread-the-risk” strategy that attempts to improve the probability
of survival for the entire population (hatchery and natural
components)?
Clarification:
The Review Panel will also consider timing of run and collection over all components of the run.
The proportion of spawners brought into the hatchery improves the likelihood that the population
will survive a catastrophic loss from natural events or hatchery failure.
Answer:
Yes. No more than 15% of the run is captured. No more than 120 adults are taken from the
natural environment.
14
Is the effective population size being estimated each year?
Clarification:
How many fish are mated each year? What is the age of fish mated, the family size variation,
and how many total parents were used to produce offspring released? The Review Panel will use
this information to evaluate program’s effective population size.
Sufficient broodstock are collected to maintain genetic variation in the population.
Answer:
Yes, the effective population size is estimated annually.
15
Within the last 10 years, has the program used only eggs or fish from
within the watershed?
Clarification:
If YES, is there a fish health policy that is in place for egg/fish transfers? If so, please provide a
copy.
Page A-1 8
June 2012
If the answer is NO, how many years and how many fish? Have fish been exported from this
program in the last 10 years?
If the answer is NO, were transfers into this population extensive in the more distant past? (This
question may be especially important in a segregated program where few natural fish are
included in broodstock but large number of hatchery fish stray and spawn naturally.)
Avoiding stock transfers from outside of the watershed promotes local adaptation and reduces
the risk of pathogen transmission.
Answer:
Yes. There have been no egg or fish transfers.
16
Is the broodstock collected and held in a manner that results in less
than 10% pre-spawning mortality?
Clarification:
If NO, ask questions to help the Review Panel evaluate the cause and consequences of prespawning mortality. What is the pre-spawning mortality in the program? Why does it exceed
10%? Are there any issues with bias in pre-spawning mortality? Are there facility needs that
would reduce mortality?
Maintaining pre-spawning survival higher than 90% maintains an effective population size and
reduces domestication selection.
Answer:
Yes. Pre-spawn mortality is highly variable, with an average of 8% for return years 2000
through 2008 and a range of 0% to 16.4%.
17
Does the program have guidelines for acceptable contribution of
hatchery-origin fish to natural spawning?
Clarification:
If YES, describe your guidelines.
Having established guidelines for acceptable contribution of hatchery-origin fish to natural
spawning provides a clear performance standard for evaluating the program.
Answer:
Yes. No hatchery origin fish are used in broodstock, so all surviving returns are expected to
spawn in the wild. The percent HOR on spawning grounds has not exceeded 18%.
June 2012
Page A-1 9
18
Are guidelines for the hatchery contribution to natural spawning met
for all affected naturally spawning populations?
Clarification:
Request a table of the estimated hatchery contribution to the spawning population.
The rate of hatchery contribution to natural spawning populations maintains population diversity
and promotes adaptation to the natural environment.
Answer:
Yes.
HATCHERY OPERATION PHASE: ADULT HOLDING
19
Is the water source [for adult holding] pathogen free?
Clarification:
If NO, what specific pathogens are in the water supply?
Fish health is promoted by the absence of specific pathogens during adult holding.
Answer:
No. There is a single water source for the hatchery – Shasta Lake. Pathogens present include:
BKD, Yersinia ruckeri, Flavobacterium columnaris, Ceratomyxa shasta, Ichthyophthirius
multifilis, and Nanophyetus salmincola. Numerous other bacterial, parasitic, and fungal species
have also been identified as being pathogenic to hatchery populations under appropriate
conditions.
The hatchery water source is currently free of anadromous fish.
20
Does the water used [for adult holding] result in natural water
temperature profiles that provide optimum maturation and gamete
development?
Clarification:
Are there any issues with egg quality (fertilization, soft-shell, coagulated yolk, etc.) at the
facility?
Page A-1 10
June 2012
Use of water resulting in natural water temperature profiles for adult holding ensures maturation
and gamete development synchronous with natural stocks.
Answer:
Yes.
21
Is the water supply [for adult holding] protected by flow alarms?
Clarification:
Broodstock security is maintained by flow and/or level alarms at the holding ponds.
Answer:
Yes.
22
Is the water supply [for adult holding] protected by back-up power
generation or a fail-safe back-up water supply?
Clarification:
Broodstock security is maintained by back-up power generation for the pumped water supply.
Answer:
Yes. Water is from penstocks and there is a back-up flow. If power is lost, the penstocks open
and the head tank goes to overflow mode, providing 100% of water needed to operate the
hatchery.
HATCHERY OPERATION PHASE: SPAWNING
23
Does the program have a protocol for mating?
Clarification:
If yes, what is the protocol?
Random mating maintains within-population diversity.
June 2012
Page A-1 11
Answer:
Yes. Hormones are used to increase maturation of males and females. The facility uses factorial
mating, 1:2 with males reused no more than 4 times. Typically males are used two times, with
an occasional third use. Males are cryopreserved for future generations, for use when live males
are not available.
Eggs from a single female are split into two lots and fertilized with two separate males, one male
per pan.
24
Does the program conduct single-family pairing prior to fertilization?
Clarification:
Single family pairing increases the effective population size of the hatchery stock.
Answer:
Yes. The facility uses factorial mating, 1:2 with males reused no more than 4 times. Typically
males are used two times, with an occasional third use. Males are cryopreserved for future
generations for use when live males are not available.
Eggs from a single female are split into two lots and fertilized with two separate males, one male
per pan.
25
Are multiple males used in the spawning protocol?
Clarification:
Use of back-up males in the spawning protocol increases the likelihood of fertilization of eggs
from each female.
Answer:
No. Back-up males are not used.
26
Are precocious fish (jacks and jills) used for spawning according to a
set protocol?
Clarification:
Is the rate of juvenile male precocity tracked near release time? If so, provide the rate for the
past 5 years (if available).
Page A-1 12
June 2012
Use of precocious males for spawning as a set percentage or in proportion to their contribution to
the adult run promotes within population diversity.
Answer:
Yes. Jacks and jills are used in the proportion they return to the trap (100% natural origin fish
used as brood).
26A Additional Question: Does the program have guidelines or policies
for ensuring long-term phenotypic and genetic distinctions between
populations/runs/species?
Clarification:
For example, is more than one run of a given species produced at your hatchery (e.g., spring and
fall Chinook; fall and late fall Chinook; summer and winter steelhead)?
If YES, what are these guidelines or policies? If NO, please explain.
Answer:
Yes. All adults collected for the propagation program have genetic analysis done to determine
whether they are from the winter run stock.
HATCHERY OPERATION PHASE: INCUBATION
27
Is the water source for incubation pathogen-free?
Clarification:
If NO, what specific pathogens are in the water supply?
Fish health is promoted by the use of pathogen-free water during incubation.
Answer:
No. All water used at the hatchery is taken from the river.
June 2012
Page A-1 13
29
Does the water used for incubation provide natural water temperature
profiles that result in hatching/emergence timing similar to that of the
naturally produced stock?
Clarification:
Use of water resulting in natural water temperature profiles for incubation ensures hatching and
emergence timing similar to naturally produced stocks with attendant survival benefits.
Answer:
Yes.
30
Can incubation water temperature be modified?
Clarification:
If YES, why is the temperature manipulated? This question will be asked for all programs to
provide information about the facility use (e.g., otolith marking).
The ability to heat or chill incubation water to approximate natural water temperature profiles
ensures hatching and emergence timing similar to naturally produced stocks with attendant
survival benefits.
Answer:
Yes. Water is chilled when necessary and water is also run through 10-, 20- and 150-micron
filters.
31
Is the incubation water supply protected by flow alarms?
Clarification:
Security during incubation is maintained by flow alarms at the incubation units.
Answer:
Yes.
Page A-1 14
June 2012
32
Is the water supply for incubation protected by back-up power
Clarification:
Security during incubation is maintained by back-up power generation for the pumped water
supply.
Answer:
Yes. There is automatic back-up for the head tank.
33
Are eggs incubated under conditions that result in equal survival of
all segments of the population to ponding?
Clarification:
The Review Panel wants to know if any portion of the eggs derives a survival advantage or
disadvantage from incubation procedures. Respond NO if there is a survival advantage.
Please describe the survival profile during incubation. How does the program go about ensuring
representation throughout the run?
Incubation conditions that result in equal survival of all segments of the population reduce the
likelihood of domestication selection and loss of genetic variability.
Answer:
Yes. All eggs go into heath trays and are incubated under the same conditions.
34
Are families incubated individually? (Include both eyeing and
hatching)
Clarification:
Request information about when families are combined and what protocols are used. This
question will be asked for all programs.
Are progeny from R. salmoninarum (BKD+) adult segregation? If so, for how long?
Incubating families individually maintains genetic variability during incubation.
Answer:
Yes, to both eyeing and hatch.
June 2012
Page A-1 15
36
Are agency or tribal species-specific incubation recommendations
followed for flow rates?
Clarification:
Request information about these incubation recommendations or protocols.
Use of flow recommendations/protocols during incubation promote survival of eggs and alevin
and allow for optimum fry development.
Answer:
Yes, incubation flows are 4-6 gpm.
37
followed for substrate?
Clarification:
Request information about substrate recommendations or protocols.
Use of substrate during incubation limits excess alevin movement and promotes energetic
efficiency.
Answer:
No. There are no recommendations and no substrate is used.
38
followed for density parameters?
Clarification:
Request information about density recommendations or protocols. What density index (DI) is
targeted? Is the facility able to maintain the prescribed DI throughout the entire rearing period?
Are there facility needs that would assist in meeting optimum rearing conditions?
Use of density recommendations/protocols during incubation promote survival of eggs and
alevin and allow for optimum fry development.
Answer:
Yes, no more than one female (5,500 eggs) is incubated per tray. The numbers are based on
stock-specific guidelines for endangered species program. Numbers for green eggs are based on
eggs from one female per tray.
Page A-1 16
June 2012
39
Are disinfection procedures implemented during spawning and/or
incubation that prevent pathogen transmission within or between
stocks of fish on site?
Clarification:
Are there written protocols for egg disinfection following spawning and during incubation for
the program? If so, what are they?
Proper disinfection procedures increase the likelihood of preventing dissemination and
amplification of pathogens in the hatchery.
Answer:
Yes. Eggs are partially water-hardened in stacks for 15 minutes with iodophor solution of 100
ppm.
40
Are eggs culled and if so, how is culling done?
Clarification:
Are eggs from Renibacterium salmoninarum (BKD +) adults culled?
If YES, what are the criteria for initial egg culling? How are progeny segregated (what disease
levels), and for how long (what determines when segregated rearing can be discontinued)?
Random culling of eggs over all segments of the egg-take maintains genetic variability during
incubation.
Answer:
No.
40A Additional Question: Would the program benefit by having an ability
to chill or heat incubation water supply?
Answer:
Yes, program has the ability to chill water and it seems to be beneficial based on one year of
data.
June 2012
Page A-1 17
HATCHERY OPERATION PHASE: REARING
41
Is the water source [for rearing] pathogen free?
Clarification:
If NO, what specific pathogens are in the water supply? Are standards in place for “acceptable
mortality rates” for each component of the production cycle (eggs, fry, fingerlings)? What
mortality level initiates fish health intervention?
Fish health is promoted by the absence of specific pathogens during rearing.
Answer:
No. All water used at the hatchery is taken from the river. Pathogens present include: BKD,
Yersinia ruckeri, Flavobacterium columnaris, Ceratomyxa shasta, Ichthyophthirius multifilis,
and Nanophyetus salmincola. Numerous other bacterial, parasitic, and fungal species have also
been identified as being pathogenic to hatchery populations under appropriate conditions.
42
Does the water used [for rearing] provide natural water temperature
profiles that result in fish similar in size to naturally produced fish of
the same species?
Clarification:
Use of natural water temperature profiles for rearing promotes growth of fish and smoltification
synchronous with naturally produced stocks.
Answer:
Yes.
43
Does the hatchery operate to allow all migrating species of all ages to
bypass or pass through hatchery related structures?
Clarification:
If NO, explain the reason(s) why not all species or ages are passed.
Providing upstream and downstream passage for juveniles and adults of the naturally produced
stocks supports natural distribution and productivity.
Page A-1 18
June 2012
Answer:
N/A. The facility is above anadromous fish passage.
44
Is the water supply [for rearing] protected by flow alarms?
Clarification:
Security during rearing is maintained by flow and/or level alarms at the rearing ponds.
Answer:
Yes.
45
Is the water supply [for rearing] protected by back-up power
Clarification:
Security during rearing is maintained by back-up power generation for the pumped water supply.
Answer:
Yes.
46
Are fish reared under conditions that result in equal survival of all
segments of the population to release? (In other words, does any
portion of the population derive a survival advantage or disadvantage
from rearing procedures? If so, then mark NO.)
Clarification:
Request the survival profile during rearing.
What are the juvenile mortality rates for the past five years?
Rearing conditions that result in equal survival of all segments of the population reduce the
likelihood of domestication selection and loss of genetic variability.
Answer:
Yes.
June 2012
Page A-1 19
47
Does this program avoid culling of juvenile fish? If fish are culled,
how are they selected to be culled? In the response, make sure to
capture the number culled, and the rational for culling.
Clarification:
Are Rs clinical juveniles culled? If so, what are the criteria for culling?
Avoiding culling of juveniles maintains genetic variability during rearing.
Answer:
Yes.
48
Is there a growth rate pattern that this program is trying to achieve?
Clarification:
If YES, what is the pattern?
If NO, what are the constraints to achieving this pattern?
Following proper feeding rates to achieve the desired growth rate improves the likelihood of
producing fish that are physiologically fit, properly smolted, and that maintain the age structure
of natural populations.
Answer:
Yes. The growth rate is based on release size target. Feeding rate varies by need to achieve
target release size at release date. Release size target is 80 fpp minimum and target length is 85
mm, which allows for calculation of a targeted condition factor at release.
The growth rate pattern varies based on egg take date (April through July) and is changed in
order to achieve target release size at date for all lots of fish. Release date is last week of
January or first week of February.
49
Is there a specified condition factor that this program is trying to
achieve?
Clarification:
If YES, what is this condition factor?
If NO, what are the constraints to achieving this condition factor?
Page A-1 20
June 2012
Feeding to achieve the desired condition factor is an indicator of proper fish health and
physiological smolt quality.
Answer:
Yes. The target condition factor is 4 (see Piper’s Table Appendix I). Release size is 80 fpp
minimum and length is 85 mm, which allows for calculation of a targeted condition factor at
release.
50
Does the program use a diet and growth regime that mimics natural
seasonal growth patterns?
Clarification:
If NO, describe the diet and growth regime used in the program and how it may differ from more
natural patterns.
Are there any problems with male precocity rates in juveniles? If known, please provide rates.
Use of diet and growth regimes that mimic natural seasonal growth patterns promote proper
smoltification and should produce adults that maintain the age structure of the natural population.
Answer:
Yes. Growth pattern for juvenile hatchery-origin winter Chinook salmon result in juveniles that
are within expected size range of naturally-produced juveniles. The natural life history for
winter Chinook salmon includes freshwater residency of juveniles from 5-10 months. Hatcheryorigin winter Chinook salmon are released into the Sacramento River below Keswick Dam at the
end of January at a target size of greater than or equal to 80mm. The size of natural-origin
winter Chinook salmon at that time is estimated to be approximately 65-136mm. The growth
rate of juvenile salmonids at the hatchery, as well as in the Sacramento River below Keswick
Dam, is influenced by the release of cold water from Shasta Lake.
51
Does the program employ any NATURES-type rearing measures, e.g.,
by providing natural or artificial cover, feeding, structures in
raceways, predator training, etc.?
Clarification:
Is bird/wildlife predation a problem at this facility? If so, what proportion of juvenile production
do you estimate may be lost to predation in a given production period?
Providing artificial cover increases the development of appropriate body camouflage and may
improve behavioral fitness.
June 2012
Page A-1 21
Answer:
Yes, raceways are covered halfway with camouflage netting. All feeding is done with automatic
surface feeders.
52
Are fish reared in multiple facilities or with redundant systems to
reduce the risk of catastrophic loss?
Clarification:
This question applies to conservation programs.
Maintaining the stock in multiple facilities or with redundant systems reduces the risk of
catastrophic loss from facility failure.
Answer:
No. Releases are, however, split into two trucks to prevent catastrophic loss of entire population
in one truck.
53
Are agency or tribal juvenile rearing standards followed for flow
rates?
Clarification:
Request information about these standards.
Following standards for juvenile loading maintains proper dissolved oxygen levels. This
promotes fish health, growth and survival, and increases the likelihood of preventing
dissemination and amplification of fish pathogens.
Answer:
Yes, flow rates have a maximum flow index (FI) of 1.5.
54
Are agency or tribal juvenile rearing standards followed for density?
Clarification/Input:
Request information about density standards for juveniles.
Are there prescribed Density Indices for juvenile rearing? If so, please provide.
Following standards for juvenile density maintain fish health, growth, and survival, and increases
the likelihood of preventing dissemination and amplification of fish pathogens.
Page A-1 22
June 2012
Answer:
Yes. At the time of final rearing, the maximum DI is 0.25.
54A Additional Question
How are fish selected for programming and
release as subyearlings vs. yearlings?
Clarification:
Request information about how subyearling and yearling fish are selected.
Answer:
N/A.
HATCHERY OPERATION PHASE: RELEASE
59
Is there a protocol to produce fish to a set size at release (fpp and
length)?
Clarification:
If so, what is the protocol? What is the basis for the set size at release?
Producing fish that are qualitatively similar to natural fish in size may improve performance and
reduce adverse ecological interactions.
Answer:
Yes. Release size is a minimum of 80 fpp and length is 85 mm, which allows for calculation of a
targeted condition factor at release. Targeted release date is last week in January or first week of
February.
60
Are there protocols for fish morphology at release?
Clarification:
If so, what is the protocol?
Are standards in place for functional morphology characteristics at release (general fish health
condition such as minimal fin and/or opercular erosion, degree of silver coloration scale loss, or
any noted gross abnormalities)?
June 2012
Page A-1 23
Producing fish that are qualitatively similar to natural fish in morphology may improve
performance and reduce adverse ecological interactions.
Answer:
No, there are no morphology protocols. Release is based on weight and size.
61
Are there protocols for fish behavior characteristics at release?
Clarification:
Producing fish that are qualitatively similar to natural fish in behavior may improve performance
and reduce adverse ecological interactions.
Answer:
No; however, established time and size at release are consistent with expected smoltification.
62
Are there protocols for fish growth rates up to release?
Clarification:
Answer:
Yes, the growth rate is based on release size target. Feeding rate varies by need to achieve target
release size at release date. Release size is 80 fpp minimum and length is 85 mm, which allows
for calculation of a targeted condition factor at release.
Pattern varies based on egg take date (April through July) and is changed in order to achieve
target release size at date for all lots of fish. Release date is last week of January or first week of
February.
63
Are there protocols for physiological status of fish at release?
Clarification:
If so, what is the protocol? Are gill ATPase and blood chemistry tested prior to smolt releases?
Page A-1 24
June 2012
Answer:
No.
64
Are there protocols for fish size and life history stage at release?
Clarification:
Releasing fish at sizes and life history stages similar to those of natural fish of the same species
may improve performance and reduce adverse ecological interactions.
Answer:
Yes. Release size is minimum 80 fpp and length is 85 mm, which allows for calculation of a
targeted condition factor at release. This size is believed to achieve smoltification.
65
Are volitional releases during natural out-migration practiced?
Clarification:
The Review Panel noted that in some cases, a non-volitional release may be the best practice.
Follow up with implementation questions (how long is the volitional release period, what occurs
if fish remain, etc.).
Volitionally releasing smolts during the natural outmigration timing may improve homing,
survival, and reduce adverse ecological interactions.
Answer:
No. Fish cannot be volitionally released from the hatchery. Passage is blocked downstream.
66
Are there protocols for fish release timing?
Clarification:
If so, what are the protocols? When are fish released? What are the natural out-migration
characteristics?
June 2012
Page A-1 25
Releasing fish in a manner that simulates natural seasonal migratory patterns improves the
likelihood that harvest and conservation goals will be met and may reduce potential adverse
ecological impacts.
Answer:
Yes, based on expected time of smoltification. Site-specific research has identified the optimum
time and size at release to achieve program objectives. Fish are always released at dusk to
reduce predation.
67
Are all hatchery fish released at or adjacent to the hatchery facility
(on-site)?
Clarification:
If NO, describe off-site release locations. Describe the extent to which off-site release locations
are used, and explain why they are used.
Answer:
No. Fish are released at Caldwell Park boat ramp at RM 298. Shasta Dam is at RM 309.
68
Are data routinely collected for released fish?
Clarification:
If YES, provide a table describing all releases for the last 10 years (including date, size, type,
release method, location, number, purpose, and mark groups). The Review Panel has asked that
the table include fish released for experimental purposes.
Are pre-release exams done? If so, are results provided to the hatchery manager or appropriate
staff prior to release?
Answer:
Yes. Data collected include release date, species, race, brood year, production log number,
number released, CWT status, CWT code, length, weight, release location, tag retention rate and
mark rate. There is also a pre-release disease screen by fish health.
Winter Chinook are 100% ad clipped/CWT by combination of family groups that equal 10,00012,000.
Page A-1 26
June 2012
69
Has the current carrying capacity of the watershed used by migrating
fish (i.e., lower river or estuary) been taken into consideration in
sizing the number of releases from this program?
Clarification:
Considering the carrying capacity of the watershed when sizing the hatchery program increases
the likelihood that stock productivity will be high and may limit the risk of adverse ecological
and harvest interactions.
Answer:
No. But current abundance is believed to be far below both the juvenile and adult carrying
capacity. This is an endangered species program. The size of the program is aimed at
preventing extinction while not reducing effective population size rather than dramatically
increasing abundance.
69A Additional Question:
Are fish trucked to alternative release sites?
Clarification/Input:
If YES, what proportion of the release is trucked? Where are fish released and how are fish
released?
Answer:
Yes, Caldwell Park boat ramp.
69B Additional Question: Is more than one release type (e.g., June and
October releases) released from a typical brood year?
Clarification:
If YES, are all the fish used for each release type representative from throughout the hatchery’s
production (i.e., the same fraction of fish originating from each week’s spawning are used for
each release type so that releases originated from parents spawned throughout the spawning
run)?
If YES, what is the basis for this allocation among release types?
If NO, please describe how fish used for each release type are selected.
Answer:
No.
June 2012
Page A-1 27
69C Additional Question: Does the hatchery have a method to estimate
the number of fish released?
Clarification:
If YES, what are these inventory procedures?
If NO, does the hatchery estimate the numbers of fish released and how?
Answer:
Yes. There is an adjusted inventory between tagging and release. A count is completed when
100% of fish are clipped and mortalities are tracked until release (usually no more than thirty
days between marking and release).
HATCHERY OPERATION PHASE: FACILITIES
71
Does hatchery intake screening comply with California State,
National Marine Fisheries Service, and/or other agency facility
standards?
Clarification:
Compliance with these standards reduces the likelihood that intake structures cause entrapment
in hatchery facilities and impingement of migrating or rearing juveniles.
Answer:
N/A. The intake is upstream of anadromous fish zone.
72
Does the facility operate within the limitations established in its
National Pollution Discharge Elimination System (NPDES) permit?
Clarification:
Compliance with NPDES discharge limitations is designed to maintain water quality in
downstream receiving habitat.
Answer:
Yes
Page A-1 28
June 2012
73
If the production from this facility falls below the minimum
production requirement for an NPDES permit, does the facility
operate in compliance with state and/or federal regulations for
discharge?
Clarification:
Compliance with NPDES discharge limitations maintains water quality in downstream receiving
habitat.
Answer:
Yes.
74
Is the facility sited so as to minimize the risk of catastrophic fish loss
from flooding or other disasters?
Clarification:
Clarify the disposition of fish if the program manager anticipates a catastrophic loss.
Locating the facility where it is not susceptible to flooding decreases the likelihood of
catastrophic loss.
Answer:
Yes.
75
Is staff notified of emergency situations at the facility through the use
of alarms, auto-dialer, and/or pagers?
Clarification:
Notification to staff of emergency situations using alarms, auto-dialers, and/or pagers reduces the
likelihood of catastrophic loss.
Answer:
Yes, alarms and auto-dialers are used to alert staff in an emergency
June 2012
Page A-1 29
76
Is the facility continuously staffed to ensure the security of fish
stocks on-site?
Clarification:
Continuous facility staffing reduces the likelihood of catastrophic fish loss.
Answer:
Yes, there is one resident on-site.
76A Additional Question:
procedures manual?
Does the hatchery have an emergency
Clarification:
How are fish handled under emergency scenarios?
Answer:
Yes, there is a SOP that addresses water loss and a safety manual for emergency situations.
76B Additional Question: Does the hatchery have an emergency
procedures plan in case of loss of water?
Clarification:
How are fish handled under emergency scenarios (addressed in the program HGMP)?
Answer:
Yes. Water is from penstocks and there is a back-up flow. If power is lost, penstocks open and
head tank goes to overflow mode, providing 100% of water needed.
76C Additional Question: Does the hatchery have the ability/procedures
to protect fish on station from excessive predation/predators?
Clarification:
Is predator loss excessive (estimated loss)?
Are there ANS issues at this facility (snails, macrophytes, or other organisms in the water
supply)? If so, what problems result and how do you address them?
Relationship to Outcome:
Limiting predator loss promotes accurate accounting of fish numbers. Limiting predator contact
with fish and rearing units also reduces the risk of introducing predator-transmitted pathogens.
Page A-1 30
June 2012
Answer:
Yes. Raceways have chicken-wire covers.
HATCHERY OPERATION PHASE: MONITORING & EVALUATION
M&E1
Additional Question:
program?
Is there a formal fish health monitoring
Clarification:
Please provide information about the disease status of juveniles and returning adults.
If NO, does the facility have any of the following components of a fish health program:
•
•
•
•
Fish health policy or guidelines
Biosecurity plan
Pathogen segregation program (BKD): prescribed prophylactic treatments/vaccination
protocols for adults and/or juveniles?
Juvenile monitoring program (prior to release)
Please provide guidance and protocols for each of above.
Answer
Yes. Service guidelines 713FW1-5 are followed. There is no biosecurity plan, but SOPs for
biosecurity include disinfection of eggs between spawning and incubation, disinfection plan for
tagging equipment, and equipment disinfection between rearing units. The facility segregates for
BKD and all females are injected with erythromycin. Juvenile monitoring programs include
mid-term diagnostic checks and pre-liberation inspections.
M&E2
Does the program monitor stock
Answer:
Yes. Data is collected from hatchery and upper Sacramento River. Data collected includes
spawning ground surveys, population metrics such as spawn timing, adult age and size, spawning
locations, spawning success, reproductive success, scale samples and genetic sampling.
June 2012
Page A-1 31
M&E3
developing an HGMP?
Does this program have or is it
Clarification:
If YES, at what stage of the HGMP process is the program? When did this process start and is
the program in compliance? If the program is not in compliance - why?
Answer:
Yes. A BA for Coleman and Livingston Stone NFHs was completed in 2001. An updated draft
was completed in 2011.
M&E4
Additional Question: Is there an ongoing genetic monitoring
program? If so, please describe.
Clarification:
Answer:
Yes. Abernathy Lab does rapid response sampling to identify run, sex and origin. There has
been a parentage and grandparentage analysis (in 2007).
M&E5
Additional Question: Does the agency and/or hatchery
program have staff dedicated to monitoring and evaluation of this
program?
Clarification:
If YES, what data is collected?
Answer:
Yes. Data is collected from hatchery and upper Sacramento River spawning populations. Data
collected includes spawning ground surveys, population metrics such as spawn timing, adult age
and size, spawning locations, spawning success, reproductive success, scale samples and genetic
sampling. There are also annual estimates of the total number of natural- and hatchery-origin
fish spawning naturally.
M&E6
Additional Question: Does the program have a consistent
long-term marking or tagging program?
Clarification:
If YES, please describe the program and its recent 10-year history. Is continued funding
reasonably secure for this program?
Answer:
Yes, there is a program, and funding is secure. Hatchery has always performed 100% marking.
Page A-1 32
June 2012
M&E7
Additional Question: Are the fish selected for marking or
tagging representative of all hatchery release and production
groups?
Clarification:
Please provide information about how fish are selected for marking and/or tagging.
Answer:
Yes, 100% of winter Chinook are marked. Every fish is ad clipped and receives a CWT.
M&E8
Additional Question: Are routine protocols followed annually
to characterize attributes (e.g., run timing, age, size, sex structure,
etc.) of hatchery fish trapped and fish actually used in broodstock?
Clarification:
If YES, what are the protocols and attributes?
Answer:
No hatchery fish are used for brood, only natural fish are used for brood. Brood is collected
across run timing using monthly collection targets, sex ratio targets. Most natural-origin winter
Chinook that are trapped are spawned in most years.
Project managers would like to have a trap lower in the system to improve the opportunity to
collect fish that better represent the return curve.
M&E9
Additional Question: Is there coordination in tagging and
recovery of marks/tags among watersheds, hatcheries and/or other
programs?
Answer:
Information is collected at hatcheries/watershed and is shared.
Hatchery (and other) Project Work Teams meet to discuss Livingston Stone hatchery issues and
issues related to Central Valley hatcheries.
Prior to release, Red Bluff announces what fish may be present in the watershed and what mark
they may carry.
HATCHERY OPERATION PHASE: EFFECTIVENESS
81
What is the percent of hatchery-origin fish (first generation) in the
natural spawning areas (for the same species/race) and how does
June 2012
Page A-1 33
this percent vary geographically within the watershed (e.g., reaches
or tributaries adjacent to the hatchery often experience much greater
straying than do more remote areas)?
Clarification:
If YES, please provide this information for the last 10 years. If available, ask for the distribution
of natural spawners within the watershed to see if it matches or contrasts with the distribution of
naturally spawning hatchery fish, even if only a qualitative comparison.
This question is used to evaluate the level of hatchery influence on the population.
Answer:
An average of 11.8% of the run was hatchery-origin from 2001-2009, with a range from 5.8% to
19.5%.
85
Is the percent hatchery-origin fish (first generation) in natural
spawning areas estimated?
Clarification:
If YES, provide information about how the contribution to spawning is estimated (via weir
counts, live counts, carcass recovery, etc.). Provide information on the relative reproductive
success of hatchery fish on the spawning grounds.
Estimating the proportion of hatchery fish spawning in the wild allows evaluation of composition
targets and prevents hatchery returns from masking the status of the natural population.
Answer:
Yes. Proportion of natural influence (PNI) is estimated, as well.
HATCHERY OPERATION PHASE: ACCOUNTABILITY
86
Are standards specified for in-culture performance of hatchery fish?
Clarification:
If YES, please describe these standards.
If NO, are there standards for some in-culture performance? These might include standards for
overall health (free of clinical disease signs/behavior, free of gross abnormalities [i.e., gills and
fins]); feed conversion and growth rates; or size and condition factor at release.
Page A-1 34
June 2012
Explicit standards for survival, size, condition, etc., make it easier to detect culture problems
before they become impossible to rectify.
Answer:
Yes. There are goals based on site-specific successes. Goal for green to eyed is 0.92, eyed to
ponding is 0.78, ponding to release is 0.80, and overall egg to release is 0.58.
87
Are in-culture performance standards met? How often?
Meeting these standards is assumed to be the best management practice.
Answer:
Yes. However, due to individual family successes, there can be a lot of variation. In-culture
performance results are adaptively managed based on site-specific standards, i.e. modifications
to incubation infrastructure and strategies when required.
88
Are standards specified for pre-release characteristics to meet postrelease performance standards of hatchery fish and their offspring?
Clarification:
If YES, please describe these standards.
Explicit standards for post-release survival make it easier to detect culture problems before they
become impossible to rectify.
Answer:
Yes. Hatchery managers expect to have high enough smolt-to-adult return ratio (SAR) to
provide a small boost demographically to the endangered population, with limited negative
genetic impacts to the population.
89
Are post-release performance standards met?
Clarification:
How are myxozoan disease impacts on juveniles post release being addressed (Ceratomyxa
shasta and Parvicapsula minibicornis)?
Are there alternative strategies for post-release performance when adverse disease or
environmental conditions (e.g., elevated temperatures) occur at the scheduled time of release?
How often are standards met?
June 2012
Page A-1 35
Answer:
Yes. Post-release standards have been met for at least the last 10 years.
90
Are hatchery programming and operational decisions based on an
Adaptive Management Plan? For example, is an annual report
produced describing hatchery operations, results of studies, program
changes, etc.? If a written plan does not exist, then the answer is No.
An Annual Report or review process that presents results of studies and that specifies responses
to be taken ensures that the program managers can respond to adverse or unforeseen
developments in a timely manner.
Answer:
Yes, there is an annual report noting problems and successes that is discussed at quarterly
meetings.
Page A-1 36
June 2012
HATCHERY PROGRAM REVIEW ANSWERS
The Hatchery Program Review Questions were answered by regional managers, hatchery
managers, and the M&E biologist associated with the hatchery program during meetings held at
Livingston Stone National Fish Hatchery, June 7, 2011.
Attendee
Affiliation
Andy Appleby
Kurtis Brown
Scott Foote
Brett Galyean
Scott Hamelberg
Kevin Malone
Kevin Niemela
Bob Null
Robyn Redekopp
John Rueth
DJ Warren & Associates
USFWS
USFWS
USFWS
USFWS
Malone Environmental
USFWS
USFWS
Meridian Environmental, Inc.
USFWS
June 2012
Page A-1 37
Appendix VIII
Winter Chinook
Program Report
Appendix A-2
June 2012
Appendix A‐2 Livingston Stone National Fish Hatchery Winter Chinook Program Data Tables Table 1.
Disease history from pathologist reports for Livingston Stone National Fish Hatchery
Winter-run Chinook, 2000-2010. Results from adult inspections and combined juvenile
monitoring, diagnostics and pre-release examinations. Methodology and prevalence of
infection for the bacterium Renibacterium salmoninarum is given in parentheses.
Date
Stock
Virus
Bacteria1
Parasites
2000
Adult
IHN
Renibacterium salmoninarum
(ELISA 3%)
Aeromonas salmonicida
Ceratomyxa shasta
2000
Juvenile
Negative
(ELISA 13%)
Negative
2001
Adult
IHN
(ELISA 14%)
Ceratomyxa shasta
2001
Juvenile
Negative
Negative
Negative
Ceratomyxa shasta
2002
Adult
IHN
(ELISA 5%)
Yersinia ruckeri
2002
Juvenile
Negative
(ELISA 17%)
Negative
2003
Adult
IHN
(ELISA 9%)
Ceratomyxa shasta
2003
Juvenile
Negative
Negative
Negative
2004
Adults
IHN
Negative
Ceratomyxa shasta
2004
Juvenile
Negative
(ELISA 25%)
Negative
2005
Adult
IHN
(DFAT 9%)
Ceratomyxa shasta
2005
Juvenile
Negative
Renibacterium salmoninarum (ELISA
30%)
Negative
June 2012
Page A-2 1
Date
Stock
Virus
Bacteria1
Parasites
2006
Adult
IHN
(DFAT 6%)
Ceratomyxa shasta
Parvicapsula minibicornis
Negative
2006
Juvenile
Negative
(QPCR 50%)
Flavobacterium branchiophilum
Aeromonas hydrophila
2007
Adult
IHN
Ceratomyxa shasta
2007
Juvenile
Negative
(QPCR 6%)
Flavobacterium branchiophilum
Negative
2008
Adult
IHN
Ceratomyxa shasta
2008
Juvenile
Negative
(DFAT 2%)
Flavobacterium columnare
Negative
2009
Adult
IHN
Ceratomyxa shasta
2009
Juvenile
Negative
Negative
Negative
2010
Adult
IHN
Yersinia ruckeri
Ceratomyxa shasta
2010
Juvenile
Negative
Negative
Negative
1 Screening method(s) for Renibacterium salmoninarum, the bacterium causing Bacterial Kidney Disease, include Direct Fluorescent Antibody
Test (DFAT), Enzyme Linked Immunosorbent Assay (ELISA), or Quantitative Polymerase Chain Reaction (QPCR). All presumptive test results
were confirmed by DNA testing using QPCR.
Page A-2 2
June 2012 Table 2. Egg to release survival of natural-origin fish reared at Livingston Stone NFH, 2000-2010.
Fish
Ponded
Smolts
Released
Egg to
Release
Survival
-
179,399
166,556
77.08%
225,845
-
214,954
190,732
80.52%
231,375
220,189
-
176,882
164,806
71.23%
2003
223,269
195,689
-
180,205
152,011
68.08%
2004
192,387
177,507
-
165,878
148,385
77.13%
2005
267,803
243,525
-
196,211
160,212
59.82%
2006
279,853
259,348
-
189,881
161,212
57.61%
2007
121,341
111,686
-
100,909
71,883
59.24%
2008
260,370
235,279
-
200,696
146,211
56.16%
2009
324,321
302,544
-
267,819
198,582
61.23%
2010
139,349
129,512
-
125,153
123,857
88.88%
Average
226,637
208,967
-
181,635
153,132
68.82%
Release
Year
Egg
Take
Eyed
Eggs
2000
216,075
197,511
2001
236,864
2002
Eggs
Culled
Source: Livingston Stone National Fish Hatchery Staff.
June 2012
Page A-2 3
Table 3.
Actual release number, location, and size of winter Chinook salmon releases from
Livingston Stone NFH, 2000-2008.
Brood
Year
Release Location
Release
Method
Purpose
Number
Released
2000
- Captive Brood
Trucked
Captive
Brood
216
95 Complete
2000
Bodega Bay Marine
Lab - Captive Brood
Trucked Captive
Brood
504
93 Complete
2000
Steinhart Aquarium Captive Brood
Trucked Captive
Brood
504
94 Complete
2000
Caldwell Park Sacramento River
Trucked 166,207
81 Complete
2001
- Captive Brood
Trucked Captive
Brood
208
107 Complete
2001
Bodega Bay Marine
Lab - Captive Brood
Trucked Captive
Brood
208
110 Complete
2001
Trucked Mitigation
61,952
98 Complete
2002
Trucked Mitigation
164,805
82 Complete
2002
Trucked Mitigation
68,807
122 Complete
2002
- Captive Brood
Trucked Captive
Brood
201
79 Complete
2002
Bodega Bay Marine
Lab - Captive Brood
Trucked Captive
Brood
201
88 Complete
2003
- Captive Brood
Trucked Captive
Brood
217
79 Complete
2003
Trucked Mitigation
151,911
68 Complete
2003
Trucked Mitigation
66,606
84 Complete
2004
Trucked Mitigation
148,384
67 Complete
2004
Trucked Mitigation
19,876
111 Complete
Page A-2 4
Mitigation
Size
(fpp)
CWT
Status
June 2012 Brood
Year
Release Location
Release
Method
2005
Trucked 2005
Trucked 2006
Trucked 2006
Trucked 2007
Trucked 2008
Lake Redding Park
Trucked
Purpose
Number
Released
Size
(fpp)
CWT
Status
Mitigation
160,272
58 Complete
Mitigation
13,071
94 Complete
Mitigation
161,192
51 Complete
Mitigation
35,076
68 Complete
Mitigation
71,883
62 Complete
Mitigation
146,211
57 Complete
Source: USFWS 2011.
Table 4.
Number of winter Chinook returns by sex, age, females spawned and eggs harvested,
2000-2010.
Brood
Year
Adult Collection
Location
2000
Keswick and RBDD
60
42
0
44
216,000
4,909
2000
Captive Brood
n/a
n/a
n/a
66
88,001
1,333
2001
Keswick and RBDD
88
117
0
50
236,864
4,737
2001
Captive Brood
n/a
n/a
n/a
100
105,958
1,060
2002
Keswick and RBDD
104
90
0
48
231,375
4,820
2002
Captive Brood
n/a
n/a
n/a
95
122,411
1,289
2003
Keswick and RBDD
157
128
0
45
223,269
4,962
2003
Captive Brood
n/a
n/a
n/a
99
140,641
1,421
Females
Males
Females
Spawned
Jacks
June 2012
Total
Eggs
Fecundity
Page A-2 5
Brood
Year
Adult Collection
Location
2004
Keswick
68
278
0
37
192,387
5,200
2004
Captive Brood
n/a
n/a
n/a
45
42,129
936
2005
Keswick
224
169
0
51
267,803
5,251
2005
Captive Brood
n/a
n/a
n/a
46
50,063
1,088
2006
Keswick
149
163
0
52
279,853
5,382
2006
Captive Brood
n/a
n/a
n/a
60
81,814
1,364
2007
Keswick
84
71
0
24
121,341
4,854
2008
Keswick
102
96
0
48
260,370
5,314
2009
Keswick
169
109
0
62
324,321
5,231
2010
Keswick
230
192
0
27
139,349
5,161
Females
Males
Females
Spawned
Jacks
Total
Eggs
Fecundity
Source: USFWS 2011.
Table 5.
Winter Chinook salmon spawner population estimates in the Sacramento River, 20012009.
Year
Sacramento
River Mainstem
Percent Natural
2001
8,120
93.8%
2002
7,337
87.7%
2003
8,133
94.2%
2004
7,784
92.0%
2005
15,730
80.5%
2006
17,197
86.2%
2007
2,487
92.6%
2008
2,725
94.0%
2009
4,416
89.7%
Average
8,689
90.1%
Source: Grandtab, USFWS 2011 and CAMP 2010.
Page A-2 6
June 2012 Table 6. Egg to release survival of captive broodstock-origin fish reared at Livingston Stone NFH,
2001-2006.
Release
Year
Egg Take
Eyed
Eggs
Eggs
Culled
Fish
Ponded
Smolts
Released
Egg to
Release
Survival
20011
100,959
85,099
3,0903
67,270
61,952
64.42%
20021
123,825
104,121
8,5003
73,088
68,807
62.43%
20031
139,398
98,432
7,1883
80,548
66,606
52.94%
20042
49,129
34,281
-
26,075
19,876
40.46%
20052
50,063
20,044
-
15,089
13,071
26.11%
20062
81,814
38,475
-
37,654
35,076
42.87%
Average
BML
121,394
95,884
6,259
73,635
65,788
59.93%
Average
LS
60,335
30,933
0
26,273
22,674
36.48
1 Fish
from Bodega Marine Lab (BML) were reared from 2001 to 2003.
Fish from Livingston Stone were reared from 2004 to 2006.
3 BML eggs were culled due to high BKD parents and to keep release size close to 60.00.
Source: Livingston Stone National Fish Hatchery Staff.
2
June 2012
Page A-2 7
Appendix VIII
Winter Chinook
Program Report
Appendix A-3
June 2012
Appendix A‐3 Hatchery Program Review Analysis Livingston Stone National Fish Hatchery Winter Chinook Benefit‐Risk Statements Question
ID
1
2
3
Category
Broodstock
Choice
Question
Does the broodstock chosen
represent natural populations
native or adapted to the
watersheds in which hatchery
fish will be released?
Broodstock
Choice
Was the best available
broodstock selected for this
program?
Broodstock
Choice
display morphological and life
history traits similar to the natural
population?
Correct
Answer
Y
Y
Y
Answer
Provided
by
Managers
Benefit
Risk
Y
This program uses a broodstock
representing populations native or
adapted to the watershed, which
increases the likelihood of long
term survival of the stock, helps
avoid loss of among population
diversity, and reduces the
likelihood of unexpected ecological
interactions.
Selection of a broodstock not
representing populations native
or adapted to the watershed
poses a risk of loss of among
population diversity and may
pose additional risks of adverse
ecological interactions with nontarget stocks.
NA
Choice of a broodstock with a
similar life history and evolutionary
history to the extirpated stock
improves the likelihood of
successful re-introduction.
Y
Choice of a broodstock with similar
morphological and life history traits
improves the likelihood of the
stock's adaptation to the natural
environment.
Livingston Stone National Fish Hatchery Winter Chinook Program /Appendix A-3 / June 2012
Choice of a broodstock with a
dissimilar life history and
evolutionary history to the
extirpated stock reduces the
likelihood of successful reintroduction.
Choice of a broodstock with
dissimilar morphological and life
history traits poses a risk that
the stock will not adapt well to
the natural environment.
Page A-3 1
Question
ID
Category
Broodstock
4
Choice
5
Broodstock
Choice
Broodstock
7
Choice
10
11
Page A-3 2
Broodstock
Choice
Broodstock
Collection
Question
have a pathogen history that
indicates no threat to other
populations in the watershed?
have the desired life history traits
to meet harvest goals? (e.g.,
timing and migration patterns that
result in full recruitment to target
fisheries)?
Do natural origin fish make up
less than 5% of the broodstock
for this program?
Is the percent natural origin fish
used as broodstock for this
program estimated?
Are adults returned to the river?
Correct
Answer
Y
Y
NA
Y
N
Answer
Provided
by
Managers
Benefit
Y
The broodstock chosen poses no
threat to other populations in the
watershed from pathogen
transmission
NA
The broodstock chosen is likely to
have the life history traits to meet
harvest goals for the target stocks
without adversely impacting other
stocks.
N
Maintaining a hatchery population
composed of less than 5% natural
fish reduces the risk of loss of
among population diversity.
Y
Estimating the proportion of natural
fish used for broodstock makes it
possible to determine whether
composition targets have been met
and prevents masking of the status
of both the hatchery and natural
populations.
Y
Not recycling adults to the lower
river to provide additional harvest
reduces the likelihood of straying
and unintended contribution to
natural spawning
Risk
The broodstock chosen poses a
risk to other populations in the
watershed from pathogen
transmission
The broodstock chosen is
unlikely to have the life history
traits to successfully meet
harvest goals and may
contribute to overharvest of
comingled stocks.
Maintaining a hatchery
population composed of more
than 5% natural fish increases
the risk of loss of among
population diversity.
Percent wild fish used as
broodstock for this program is
not accurately estimated. Not
estimating of the proportion of
natural fish used for broodstock
makes it impossible to
determine whether composition
targets have been met and it
masks the status of both the
hatchery and natural
populations.
Recycling adults to provide
additional harvest benefits can
increase the likelihood of
straying and increase the
contribution of hatchery fish on
the spawning grounds
Question
ID
12
Category
Broodstock
Collection
Question
Are representative samples of
natural and hatchery population
components collected with
respect to size, age, sex ratio,
run and spawn timing, and other
traits important to long-term
fitness?
Does the proportion of the
spawners brought into the
hatchery follow a “spread-therisk” strategy that attempts to
improve the probability of survival
for the entire population
(hatchery and natural
components)?
Correct
Answer
Answer
Provided
by
Managers
Y
Failure to collect representative
samples of both the natural and
hatchery populations poses a
risk of loss of within population
diversity and viability.
Y
Y
The proportion of spawners
brought into the hatchery improves
the likelihood that the population
will survive a catastrophic loss
from natural events or hatchery
failure.
The proportion of spawners
brought into the hatchery
increases the risk that the
population not will survive a
catastrophic loss from natural
events or hatchery failure.
Sufficient broodstock are collected
to maintain genetic variation in the
population
Avoidance of stock transfers from
outside the watershed promotes
local adaptation and reduces the
risk of pathogen transmission.
Sufficient broodstock are not
collected to maintain genetic
variation in the population
Stock transfers from outside the
watershed pose a risk to local
adaptation and increases the
risk of pathogen transmission.
Pre-spawning mortality greater
than 10% poses a risk to
maintaining effective population
size and a risk of domestication
selection
Lack of established guidelines
for acceptable contribution of
hatchery origin fish to natural
spawning makes program
evaluation difficult.
Y
Broodstock
Collection
14
Broodstock
Collection
Is the effective population size
being estimated each year?
Y
Y
15
Broodstock
Collection
Within the last 10 years, has the
program used only eggs or fish
from within the watershed?
Y
Y
Broodstock
Collection
Is the broodstock collected and
held in a manner that results in
less than 10% pre-spawning
mortality?
Broodstock
Collection
Do you have guidelines for
acceptable contribution of
hatchery origin fish to natural
spawning?
17
Risk
Collection of representative
samples of both the natural and
hatchery populations reduces the
risk of domestication and loss of
within population diversity.
13
16
Benefit
Y
Y
Y
Maintaining pre-spawning survival
higher than 90% maintains
effective population size and
reduces domestication selection.
Y
Having established guidelines for
acceptable contribution of hatchery
origin fish to natural spawning
provides a clear performance
standard for evaluating the
Page A-3 3
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Benefit
Risk
The rate of hatchery contribution to
natural spawning populations
maintains among population
diversity and promotes adaptation
to the natural environment.
Fish health is promoted by the
absence of specific pathogens
during adult holding.
Use of water resulting in natural
water temperature profiles for adult
holding ensures maturation and
gamete development synchronous
with natural stocks.
The rate of hatchery
contribution to natural spawning
populations poses a risk of loss
of among population diversity
and domestication selection.
There is a risk to fish health due
to the lack of specific-pathogen
free water for adult holding.
Lack of natural water
temperature profiles may lead to
domestication selection for adult
maturation and gamete
development.
Absence of flow and/or level
alarms at the holding pond may
pose a risk to broodstock
security.
Lack of back-up power
generation for the pumped
water supply may pose a risk to
broodstock security.
Non-random mating increases
the risk of loss of within
Pooling of gametes poses a risk
to maintaining genetic diversity
in the hatchery population.
program.
Are guidelines for hatchery
contribution to natural spawning
met for all affected naturally
spawning populations?
Y
Y
19 Adult Holding
Is the water source [for adult
holding] pathogen free?
Y
N
20 Adult Holding
Does the water used [for adult
holding] result in natural water
temperature profiles that provide
optimum maturation and gamete
development?
Y
Y
21 Adult Holding
Is the water supply [for adult
holding] protected by flow
alarms?
Y
Y
Broodstock security is maintained
by flow and/or level alarms at the
holding ponds.
22 Adult Holding
Is the water supply [for adult
holding] protected by back-up
power generation or a fail-safe
back-up water supply?
Y
Y
Broodstock security is maintained
by back-up power generation for
the pumped water supply.
23 Spawning
Does the program have a
protocol for mating?
Y
Y
Random mating maintains within
24 Spawning
Does the program conduct
single-family pairing prior to
fertilization?
Y
Single family pairing increases the
effective population size of the
hatchery stock.
18
Page A-3 4
Broodstock
Collection
Y
Question
ID
Category
25 Spawning
Question
Are multiple males used in the
spawning protocol?
Correct
Answer
Y
Answer
Provided
by
Managers
N
Use of back-up males in the
spawning protocol increases the
likelihood of fertilization of eggs
from each female.
Use of precocious males for
spawning as a set percentage or in
proportion to their contribution to
the adult run promotes within
26 Spawning
Are precocious fish (jacks and
jills) used for spawning according
to a set protocol?
Y
Y
27 Incubation
Is the water source [for
incubation] pathogen-free?
Y
N
Y
NA
28 Incubation
29 Incubation
This question is dropped - Is the
water source [for incubation]
specific-pathogen free?
Does the water used [for
incubation] provide natural water
temperature profiles that result in
hatching/emergence timing
similar to that of the naturally
produced population?
Y
Benefit
Y
30 Incubation
Can incubation water
temperature be modified?
Y
Y
31 Incubation
Is the water supply [for
incubation] protected by flow
Y
Y
Fish health is promoted by the use
of pathogen-free water during
incubation.
during incubation.
water temperature profiles for
incubation ensures hatching and
emergence timing similar to
naturally produced stocks with
attendant survival benefits.
The ability to heat or chill
incubation water to approximate
natural water temperature profiles
ensures hatching and emergence
timing similar to naturally produced
stocks with attendant survival
benefits.
Security during incubation is
maintained by flow alarms at the
Risk
Not using of back-up males in
the spawning protocol increases
the risk of unfertilized eggs and
loss of genetic diversity in the
broodstock.
Not using precocious males for
spawning as a set percentage
or in proportion to their
contribution to the adult run
increases the risk of loss of
within population diversity.
to the lack of pathogen-free
water for incubation.
free water for incubation.
temperature profiles may
contribute to domestication
selection during incubation.
The inability to heat or chill
incubation water to approximate
natural water temperature
profiles may contribute to
domestication selection during
incubation.
Absence of flow alarms at the
incubation units may pose a risk
Page A-3 5
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Benefit
alarms?
incubation units.
32 Incubation
Is the water supply [for
incubation] protected by back-up
power generation or a fail-safe
back-up water supply?
Security during incubation is
maintained by back-up power
generation for the pumped water
supply.
33 Incubation
Are eggs incubated under
conditions that result in equal
survival of all segments of the
population to ponding?
Y
Y
34 Incubation
Are families incubated
individually? (Includes both eying
and hatching.)
Y
Y
36 Incubation
Are agency or tribal speciesspecific incubation
recommendations followed for
flow rates?
37 Incubation
substrate?
38 Incubation
density parameters?
Page A-3 6
Y
Y
Y
Y
Y
Incubation conditions that result in
equal survival of all segments of
the population reduce the
likelihood of domestication
selection and loss of genetic
variability.
Incubating families individually
maintains genetic variability during
incubation.
Y
Use of IHOT flow
recommendations during
incubation promote survival of
eggs and alevin and allow for
optimum fry development.
N
Use of IHOT recommendations for
use of substrate during incubation
limits excess alevin movement and
promotes energetic efficiency.
Y
Use of IHOT density
incubation promote survival of
eggs and alevin and allow for
Risk
to the security of incubating
eggs and alevin.
Absence of back-up power
the security of incubating eggs
and alevin.
Incubation conditions that result
in unequal survival of all
segments of the population
pose a risk of domestication
variability.
Not incubating families
individually poses a risk of loss
of genetic variability.
Failing to meet IHOT flow
incubation poses a risk to the
survival of eggs and alevin and
may not allow for optimum fry
development.
Failing to meet IHOT
recommendations for using
substrate during incubation may
allow excess alevin movement
and reduces energetic
efficiency.
Failing to meet IHOT density
incubation poses a risk to the
survival of eggs and alevin and
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Benefit
optimum fry development.
39 Incubation
Are disinfection procedures
implemented during spawning
and/or incubation that prevent
pathogen transmission within or
between stocks of fish on site?
40 Incubation
Are eggs culled and if so, how is
culling done?
Y
N
41 Rearing
Is the water source [for rearing]
pathogen free?
Y
N
42 Rearing
Does the water used [for rearing]
provide natural water
temperature profiles that result in
fish similar in size to naturally
produced fish of the same
species?
43 Rearing
Does the hatchery operate to
allow all migrating species of all
ages to by-pass or pass through
hatchery related structures?
44 Rearing
Is the water supply [for rearing]
protected by flow alarms?
Y
Y
Proper disinfection procedures
increase the likelihood of
preventing dissemination and
amplification of pathogens in the
hatchery.
Random culling of eggs over all
segments of the egg-take
incubation.
during rearing.
Y
water temperature profiles for
rearing promotes growth of fish
and smoltification synchronous
with naturally produced stocks.
Y
NA
Providing upstream and
downstream passage of juveniles
and adults supports natural
distribution and productivity of
naturally produced stocks.
Y
Y
Y
Security during rearing is
maintained by flow and/or level
alarms at the rearing ponds.
Risk
may not allow for optimum fry
development.
Lack of proper disinfection
procedures increase the risk of
dissemination and amplification
of pathogens in the hatchery.
Non-random culling of eggs
genetic variability during
incubation.
free water for rearing.
temperature profiles may lead to
domestication selection during
rearing.
Inhibiting upstream and
downstream passage of
juveniles and adults poses a
risk to distribution and
productivity of naturally
produced stocks.
Absence of flow and/or level
alarms at rearing ponds may
pose a risk to the security of the
cultured fish.
Page A-3 7
Question
ID
Category
45 Rearing
46 Rearing
47 Rearing
Question
Is the water supply [for rearing]
protected by back-up power
generation or a fail-safe back-up
water supply?
Are fish reared under conditions
that result in equal survival of all
segments of the population to
release? (In other words, does
any portion of the population
derive a survival advantage or
disadvantage from rearing
procedures? If yes, then mark
NO in box.)
Does this program avoid culling
of juvenile fish? If fish are culled,
how are they selected to be
culled? In the response, make
sure to capture the number
culled, and the rational for
culling.
48 Rearing
Is there a growth rate pattern that
this program is trying to achieve?
49 Rearing
Is there a specified condition
factor that this program is trying
to achieve?
Page A-3 8
Correct
Answer
Y
Y
Y
Y
Y
Answer
Provided
by
Managers
Benefit
Risk
Y
Security during rearing is
maintained by back-up power
generation for the pumped water
supply.
Absence of back-up power
the security of the cultured fish.
Y
Rearing conditions that result in
equal survival of all segments of
the population reduce the
likelihood of domestication
variability.
Rearing conditions that result in
unequal survival of all segments
of the population pose a risk of
domestication selection and
loss of genetic variability.
Y
Random culling of juveniles over
all segments of the population
rearing.
Non-random culling of juveniles
genetic variability during
rearing.
Y
Following proper feeding rates to
achieve the desired growth rate
improves the likelihood of
producing fish that are
physiologically fit, properly
smolted, and that maintain the age
structure of natural populations.
Y
Feeding to achieve the desired
condition factor is an indicator of
proper fish health and
physiological smolt quality.
Improper feeding that does not
achieve desired growth rate
increases the risk of producing
fish that are not physiologically
fit, that are not properly smolted,
and that exhibit an age structure
not representative of natural
populations.
Feeding that does not achieve
the desired condition factor may
be an indicator of poor fish
health and physiological smolt
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Benefit
Risk
quality.
50 Rearing
Does the program use a diet and
growth regime that mimics
natural seasonal growth
patterns?
51 Rearing
Does the program employ any
NATURES-type rearing
measures, e.g., by providing
natural or artificial cover, feeding,
structures in raceways, predator
training, etc?
52 Rearing
Are fish reared in multiple
facilities or with redundant
systems to reduce the risk of
catastrophic loss?
53 Rearing
Are agency or tribal juvenile
rearing standards followed for
flow rates?
54 Rearing
Are agency or tribal juvenile
rearing standards followed for
density?
Y
Y
Y
Y
Y
Y
Use of diet and growth regimes
that mimic natural seasonal growth
patterns promote proper
smoltification and should produce
adults that maintain the age
structure of the natural population.
Use of diet and growth regimes
that do not mimic natural
seasonal growth patterns pose
a risk to proper smoltification
and may alter the age structure
of the hatchery population.
Y
Providing artificial cover increases
the development of appropriate
body camouflage and may improve
behavioral fitness.
Lack of overhead and in-pond
structure does not produce fish
with the same cryptic coloration
or behavior as do using
enhanced environments.
N
Maintaining the stock in multiple
facilities or with redundant systems
reduces the risk of catastrophic
loss from facility failure.
Y
Following IHOT standards for
juvenile loading maintains proper
dissolved oxygen levels promoting
fish health, growth and survival,
and increases the likelihood of
preventing dissemination and
amplification of fish pathogens.
Y
Following IHOT standards for
juvenile density, fish health,
growth, and survival increases the
likelihood of preventing
dissemination and amplification of
Not maintaining the stock in
multiple facilities or with
redundant systems increases
the risk of catastrophic loss from
facility failure.
Not following IHOT standards
for juvenile loading poses a risk
to maintaining proper dissolved
oxygen levels, compromising
fish health and growth and
increases the likelihood of
of fish pathogens.
Not following IHOT standards
for juvenile density poses a risk
to maintaining fish health,
growth, and survival, and
Page A-3 9
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Benefit
fish pathogens.
55 Rearing
For captive broodstocks, are fish
maintained on natural
photoperiod to ensure normal
maturation?
Y
NA
Maintaining captive broodstock on
natural photoperiods ensures
normal maturation.
56 Rearing
For captive broodstocks, are fish
maintained reared at 12C to
minimize disease?
Y
NA
Maintaining captive broodstock on
rearing water below 12oC reduces
the risk of loss from disease.
57 Rearing
For captive broodstocks, are
diets and growth regimes
selected that produce potent,
fertile gametes and reduce
excessive early maturation of
fish?
NA
Producing viable gametes and
maintaining age structure of the
population in captive breeding
increases the likelihood of meeting
conservation goals.
58 Rearing
For captive broodstocks, are
families reared individually to
maintain pedigrees?
NA
Rearing families separately for
captive broodstock programs
maintains pedigrees to reduce the
risk of inbreeding depression.
59 Release
Is there a protocol to produce
fish to a set size at release (fpp
and length)?
Y
Producing fish that are qualitatively
similar to natural fish in size may
improve performance and reduce
adverse ecological interactions.
N
similar to natural fish in
morphology may improve
performance and reduce adverse
ecological interactions.
60 Release
Page A-3 10
Are there protocols for fish
morphology at release?
Y
Y
Y
Y
Risk
of fish pathogens.
Maintaining captive broodstock
on unnatural photoperiods
poses a risk to normal
maturation.
Maintaining captive broodstock
on rearing water above 12oC
increases the risk of loss from
disease.
Failure to produce viable
gametes and maintain age
structure of the population in
captive breeding reduces the
likelihood of meeting
conservation goals.
Inability to rear families
separately for captive
broodstock programs increases
the risk of inbreeding
depression.
Producing fish that are not
qualitatively similar to natural
fish in size may adversely affect
performance and increase
fish in morphology may
adversely affect performance.
Question
ID
Category
61 Release
62 Release
63 Release
Question
behavior characteristics at
release?
growth rates up to release?
Are there protocols for
physiological status of fish at
release?
64 Release
Are there protocols for fish size
and life history stage at release?
65 Release
Are volitional releases during
natural out-migration timing
practiced?
Correct
Answer
Y
Y
Y
Y
Y
Answer
Provided
by
Managers
Benefit
Risk
N
similar to natural fish in behavior
may improve performance and
reduce adverse ecological
interactions.
Y
similar to natural fish in growth rate
interactions.
N
similar to natural fish in
physiological status may improve
performance and reduce adverse
ecological interactions.
Y
Releasing fish at sizes and life
history stages similar to those of
natural fish of the same species
interactions.
N
Volitionally releasing smolts during
the natural outmigration timing
may improve homing, survival, and
interactions.
fish in behavior may adversely
affect performance and increase
fish in growth rate may
adversely affect performance
and increase adverse ecological
interactions.
fish in physiological status may
adversely affect performance
and increase adverse ecological
interactions.
Releasing fish at sizes and life
history stages dissimilar to
those of natural fish of the same
species may reduce
performance and increase the
risk of adverse ecological
interaction.
Failure to volitionally release
smolts during the natural
outmigration timing may
adversely affect homing,
survival, and increase risk of
Page A-3 11
Question
ID
Category
66 Release
67 Release
Question
release timing?
Are all hatchery fish released at
or adjacent to the hatchery
facility (on-site)?
Correct
Answer
Y
Y
Answer
Provided
by
Managers
Benefit
Y
Releasing fish in a manner that
simulates natural seasonal
migratory patterns improves the
likelihood that harvest and
conservation goals will be met and
may reduce potential adverse
ecological impacts.
N
Releasing fish within the historic
range of that stock increases the
likelihood that habitat conditions
will support the type of fish being
released and does not pose new
risks of adverse ecological
interactions with other stocks.
68 Release
Are data routinely collected for
released fish?
Y
Y
69 Release
Has the carrying capacity of the
subbasin been taken into
consideration in sizing this
program in regards to
determining the number of fish
released?
Y
N
Page A-3 12
Releasing fish in the same
subbasin as the rearing facility
reduces the risk of dissemination
of fish pathogens to the receiving
watershed.
Taking the carrying capacity of the
subbasin into consideration when
sizing the hatchery program
increases the likelihood that stock
productivity will be high and may
limit the limit the risk of adverse
ecological and harvest
interactions.
Risk
Failing to release fish in a
manner that simulates natural
seasonal migratory patterns
decreases the likelihood that
harvest and conservation goals
will be met and may increase
the potential for adverse
ecological impacts.
Releasing fish outside the
historic range of that stock
poses a risk that habitat
conditions will not support the
type of fish being released and
poses new risks of adverse
ecological interactions with
other stocks.
Not releasing fish in the same
subbasin as the rearing facility
increases the risk of
dissemination of fish pathogens
to the receiving watershed.
Failing to take the carrying
capacity of the subbasin into
consideration when sizing the
hatchery program poses a risk
to the productivity of the stock
and may increase the risk of
adverse ecological and harvest
interactions.
Question
ID
Category
Question
70 Release
Are 100% of the hatchery fish
marked so that they can be
distinguished from the natural
populations?
71 Facilities
Does hatchery intake screening
comply with California State,
National Marine Fisheries
Service, and/or other agency
facility standards?
72 Facilities
73 Facilities
74 Facilities
75 Facilities
Does the facility operate within
the limitations established in its
National Pollution Discharge
Elimination System (NPDES)
permit?
If the production from this facility
falls below the minimum
production requirement for an
NPDES permit, does the facility
operate in compliance with state
or federal regulations for
discharge?
Is the facility sited so as to
minimize the risk of catastrophic
fish loss from flooding or other
disasters?
Is staff notified of emergency
situations at the facility through
Correct
Answer
Y
Y
Answer
Provided
by
Managers
NA
NA
Benefit
Risk
Marking 100% of the hatchery
population allows them to be
distinguished from the natural
population and prevents the
masking of the status of that
population and prevent
overharvest of weaker stocks.
Compliance with IHOT or National
Marine Fisheries Service
standards reduces the likelihood
that intake structures cause
entrapment in hatchery facilities
and impingement of migrating or
rearing juveniles.
Not marking 100% of the
hatchery population prevents
them from being distinguished
from the natural population and
may the mask the status of that
population and cause over
harvest of weaker stocks.
Failure to comply with IHOT or
National Marine Fisheries
Service standards increases the
risk of entrapment in hatchery
facilities and impingement of
migrating or rearing juveniles
Y
Compliance with NPDES
discharge limitations maintain
water quality in downstream
receiving habitat
Hatchery discharge may pose a
risk to water quality in
downstream receiving habitat
Y
For facilities that fall below the
minimum production requirement
for an NPDES permit, compliance
with these discharge limitations
maintain water quality in
For facilities that fall below the
minimum production
requirement for an NPDES
permit, hatchery discharge may
pose a risk to water quality in
Y
Y
Siting the facility where it is not
susceptible to flooding decreases
the likelihood of catastrophic loss.
Y
Y
Notification to staff of emergency
situations using alarms,
Y
Y
Siting the facility where it is
susceptible to flooding
catastrophic loss.
Inability to notify staff of
emergency situations using
Page A-3 13
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
the use of alarms, autodialer,
and pagers?
76 Facilities
Is the facility continuously staffed
to ensure the security of fish
stocks on-site?
77 M&E
Question was dropped - Do you
have a numerical goal for total
catch in all fisheries?
78 M&E
have a goal for broodstock
composition (hatchery vs.
natural) in the hatchery?
79 M&E
have a goal for spawning
escapement composition
(hatchery vs. natural) in the wild?
80 M&E
have a goal for smolt-to-adult
return survival?
Page A-3 14
Y
Y
Y
Y
Y
Benefit
Risk
autodialers, and pagers reduces
alarms, autodialers, and pagers
catastrophic loss.
Lack of continuous facility
staffing increases the likelihood
of catastrophic loss.
Lack of numerical goals for
fishery contributions from this
program makes it impossible to
define and evaluate its success
and difficult to implement
information responsive
management.
This program lacks a specific
policy for hatchery broodstock
natural), which makes it difficult
to monitor and evaluate its
effectiveness and to test the
validity of the policy.
This program lacks a specific
policy for natural spawning
natural), which makes it difficult
to monitor and evaluate its
effectiveness and to test the
validity of the policy.
This program does not have a
specified smolt to adult survival
goal making it difficult to define
success and evaluate
effectiveness.
Y
Continuous facility staffing reduces
NA
This program has a numerical goal
for total catch in all fisheries, which
makes it possible to evaluate its
success and implement
management.
NA
This program has a specific policy
for hatchery broodstock
composition (hatchery vs. natural),
which makes it possible to monitor
and evaluate its effectiveness and
to test the validity of the policy.
NA
This program has a specific policy
for natural spawning composition
(hatchery vs. natural), which
makes it possible to monitor and
evaluate its effectiveness and to
test the validity of the policy.
NA
This program has an explicit goal
smolt to adult survival, which
makes it possible to evaluate
success and implement
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Benefit
Risk
management.
82 Effectiveness
Question Dropped - Do adults
from this program make up less
than 5% of the natural spawning
escapement (for the
species/race) in the subbasin?
Y
NA
Maintaining a natural spawning
population composed of less than
5% hatchery fish reduces the risk
of loss of among population
diversity.
Y
Estimating the proportion of
hatchery fish spawning in the wild
allows evaluation of composition
targets and prevents hatchery
returns from masking the status of
the natural population.
Having in-culture performance
goals provides clear performance
standards for evaluating the
program.
85 Effectiveness
Is the percent hatchery-origin fish
(first generation) in natural
spawning areas estimated?
86 Accountability
Are standards specified for inculture performance of hatchery
fish?
Y
Y
87 Accountability
Are in-culture performance
standards met? How often?
Y
Y
88 Accountability
Are standards specified for prerelease characteristics to meet
post-release performance
standards of hatchery fish and
their offspring?
Y
Y
89 Accountability
Are post-release performance
standards met?
Y
Y
Y
Having post release performance
goals provides clear performance
standards for evaluating the
program.
Maintaining a natural spawning
population composed of greater
than 5% hatchery fish increases
the risk of loss of among
Percent hatchery fish spawning
in the wild is not estimated! Not
estimating the proportion of
hatchery fish spawning in the
wild prevents evaluation of
composition targets and allows
hatchery returns to mask the
status of the natural population.
The program lacks standards
for in-culture performance. Of
hatchery fish, making it difficult
to determine causes for
program successes and
failures.
The program lacks specified
standards for post release
performance of hatchery fish
and their offspring, making it
difficult to determine success
and failures and their causes.
Page A-3 15
Question
ID
Category
90 Accountability
Question
Are hatchery programming and
operational decisions based on
an Adaptive Management Plan?
For example, is an annual report
produced describing hatchery
operations, results of studies,
program changes, etc.? If a
written plan does not exist, then
the answer is No.
Correct
Answer
Y
Answer
Provided
by
Managers
Y
Benefit
This program has an annually
updated written adaptive
management plan describing
program goals, operations, and
results. This makes it possible to
base hatchery operations on
adaptive management principles.
Risk
This program lacks an annually
updated, written plan describing
program goals, operations, and
results. This makes it difficult to
base hatchery programming
and operations on adaptive
management principles.
Page A-3 16
Appendix VIII
Winter Chinook
Program Report
Appendix B
June 2012
Sacramento River Winter Chinook
Appendix B
Natural Populations Potentially Affected by the Hatchery Program
In addition to the natural populations of spring, fall, late-fall, and winter Chinook in the
Sacramento River, numerous other salmonid populations may be affected by operation of this
program. These are summarized below.
1
Clear Creek (Spring and Fall Chinook)
The Clear Creek watershed begins in the Trinity Mountains east of Trinity Lake and flows
approximately 50 miles to its confluence with the Sacramento River just south of Redding. The
watershed is divided into upper and lower Clear Creek, with Whiskeytown Reservoir forming the
boundary. Below Whiskeytown Reservoir, Clear Creek flows approximately 18.1 river miles to
the Sacramento River with a watershed area of about 48.9 square miles. Inflow is contributed
from a cross-basin transfer between Lewiston Lake in the Trinity River watershed and
Whiskeytown Reservoir. Most of the land in the lower Clear Creek watershed is undeveloped,
with scattered private residences, gravel mining operations, light industrial and commercial uses.
Land ownership is a combination of private, commercial, state, and federal entities (including the
Bureau of Land Management and National Park Service) (Greenwald et al. 2003).
For the 50-year period from 1954 to 1994, fall-run Chinook salmon populations in lower Clear
Creek averaged around 2,000 fish annually, ranging from around 500 to as many as 10,000
depending on the year. In recent years, CALFED and its member agencies, and the Western
Shasta Resource Conservation District have invested heavily in restoration work to enhance
anadromous fish populations, while at the same time, the BLM has aggressively pursued
acquisition of private lands in lower Clear Creek to expand public access and recreation
opportunities. 1 Beginning in 1995, Clear Creek flows were increased to benefit fall and late-fall
Chinook spawning and rearing. The flows improved fish passage into Clear Creek, improved
water temperatures during spawning and rearing periods, increased the amount of spawning and
rearing habitat, and contributed to record numbers of fall Chinook salmon spawning in Clear
Creek (Brown 1996 as cited in Greenwald et al. 2003). Beginning in 1999, stream flows were
also increased in the summer to benefit spring-run Chinook and steelhead. Other significant
actions taken specifically for spring-run Chinook and steelhead have included the removal of
McCormick-Saeltzer Dam in 2000, and placement of spawning-sized gravel for steelhead below
Whiskeytown Dam and the Placer Road Bridge (Greenwald et al. 2003).
As a direct result of these enhancements, Clear Creek currently supports a substantial population
of fall-run Chinook salmon, though large numbers of spawners are believed to be of hatchery
origin (IFC Jones & Stokes 2010). Between 2001 and 2010, an average of over 8,900 fall
Chinook returned to Clear Creek annually (Table B-1). There is also a small run of late-fall
Chinook present in the system, perhaps numbering at least 100 fish (Matt Brown, USFWS,
personal communications). In order to reestablish spring Chinook in Clear Creek, 200,000
juveniles from the Feather River Hatchery were planted in 1991, 1992 and 1993. As a result,
Clear Creek also currently supports a relatively small spring Chinook population. Between 2001
and 2010, an average of 87 spring Chinook returned to Clear Creek each year (Table B-1).
1
http://www.sacriver.org/documents/2010/Roadmap/Westside_ClearCreek.pdf
Livingston Stone National Fish Hatchery Winter Chinook Program /Appendix B /
June 2012
Page B 1
In a Programmatic Data Gathering Workshop on June 14, 2011, USFWS staff based in Red Bluff
reported that a relatively small component of the Clear Creek fall Chinook spawning population
is composed of hatchery strays, and the largest fraction of those are from hatcheries other than
Coleman NFH. In contrast, the late-fall Chinook run into Clear Creek has been comprised of an
increasing number of Coleman NFH late-fall strays in recent years (Giovannetti and Brown
2010). In 2009, an estimated 72% of the Clear Creek late-fall run was comprised of strays from
Coleman NFH. The high stray rate of late-fall fish is believed to be due to trucking of hatchery
juveniles to the bay, a practice that has been stopped for this race at this hatchery.
Table B-1.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall and spring Chinook salmon escapement in Clear Creek (2001-2010).
Fall
Spring
Chinook
Chinook
Total
10,865
0
10,865
16,071
66
16,137
9,475
25
9,500
6,365
98
6,463
14,824
69
14,893
8,422
77
8,499
4,129
194
4,323
7,677
200
7,877
3,228
120
3,348
7,192
21
7,213
8,825
87
8,912
2
Cow Creek (Fall Chinook)
The 275,000-acre Cow Creek watershed is a generally uncontrolled tributary to the Sacramento
River located in eastern Shasta County. The watershed is unique in that land ownership is
divided almost evenly among commercial forestland, commercial agriculture (predominantly
cattle ranching), and small private residential properties, with minimal public ownership. The
watershed includes five principal tributaries: North Fork Cow, Oak Run, Clover, Old Cow, and
South Fork Cow creeks. It provides important habitat for both fall-run and late fall-run Chinook
salmon and steelhead. There are no major reservoirs in the watershed, but numerous small dams
divert water for irrigation and hydropower production.
The distribution of fall-run Chinook is generally restricted to the valley floor and lower foothill
elevations of Cow Creek and its major tributaries; however, smaller portions of the population
can be expected to ascend to the upper-most waterfall barriers in the system (typically to an upper
limit of 1,000 feet of elevation). More detailed study and analysis is required to precisely
describe the distribution of spawning activity in the creek system (SHN 2001).
While historical information describing fall Chinook abundance in Cow creek is limited, during
1953–1969, the Cow Creek drainage supported a fall-run that averaged 2,800 fish (Yoshiyama et
al. 2001). Fall-run salmon presently occur in the mainstem Cow Creek up to where the South
Fork joins, and they ascend the South Fork up to Wagoner Canyon. In the North Fork Cow
Creek, fall Chinook are stopped by falls near the Ditty Wells fire station. Occasionally, late-fall
run salmon occur in Cow Creek (Yoshiyama et al. 2001). From 2006-2010 (the period of
available data), the annual number of fall Chinook retuning to Cow Creek ranged from 261 to
4,130 fish, and averaged 1,490 (Table B-2).
Page B 2
June 2012
Table B-2.
Fall Chinook salmon escapement in Cow Creek (2001-2010).
Year
Fall Chinook
2006
4,130
2007
2,044
2008
478
2009
261
2010
536
Average
1,490
According to SHN (2001), data describing the late-fall-run Chinook salmon are very limited.
There are no estimates of the late fall-run population in Cow Creek, although their presence has
been documented. According to California Department of Fish and Game (CDFG) file data, the
most recent survey for late-fall-run spawning was an aerial survey of Cow Creek on February 26,
1965. Fifty-four carcasses and 14 live fish were observed in the entire Cow Creek watershed.
Most of the live salmon were observed below the Highway 44 Bridge, while the carcasses were
evenly distributed between Millville and the confluence with the Sacramento River.
3
Beegum-Cottonwood Creek (Spring and Fall Chinook)
The Cottonwood Creek drainage area lies within Shasta and Tehama counties on the northwest
side of the Central Valley. The lower two-thirds of the drainage is part of the Central Valley
uplands, extending to slopes of the North Coast Mountain Range, Klamath Mountains and the
Trinity Mountains. The creek flows eastward through the valley to the Sacramento River, the
confluence lying approximately 16 miles north of Red Bluff and about 150 miles northwest of
Sacramento. The watershed has three main tributaries: North Fork, Middle Fork (flowing along
the Shasta-Tehama County line), and the South Fork. The watershed drains approximately 938
square miles. With an annual runoff of 586,000 acre-feet, Cottonwood Creek is the third largest
watershed tributary west of the Sacramento River. Cottonwood Creek has a natural pattern of
high flows and peak runoff events in winter and low flows in the summer and fall (CH2M Hill
2002).
Cottonwood Creek historically supported both spring and fall runs and, presumably, also a latefall run. The spring-run fish formerly migrated to the headwaters of the South and Middle forks
of Cottonwood Creek above Maple Gulch on the South Fork and about 8 miles into Beegum
Creek on the Middle Fork (Yoshiyama et al. 2001). The CDFG has not monitored fall-run
escapement into Cottonwood Creek on a consistent basis. From 1953 to 1969, seventeen annual
estimates were made based on carcass counts and occasional aerial redd counts. During this
period, an average of approximately 2,500 fall Chinook spawned in Cottonwood Creek annually
(range 350 to 6,000). From 2007 through 2010, an average of just less than 1,000 fall Chinook
returned to Cottonwood Creek annually (Table B-3). From 2001 through 2010, an average of
only 61 spring Chinook returned to Cottonwood Creek.
June 2012
Page B 3
Table B-3.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall and spring Chinook salmon escapement in Beegum-Cottonwood Creek
(2001-2010).
Fall Chinook
Spring Chinook
245
125
73
17
47
55
1,250
34
510
0
1,055
0
1,137
15
988
61
4
Battle Creek (Spring, Fall, and Late-Fall Chinook)
Battle Creek drains the southern Cascade Range in the northern Central Valley and flows into the
Sacramento River at RM 272, approximately 2 miles east of the town of Cottonwood. Battle
Creek is comprised of two main branches, the North Fork (approximately. 29.5 miles long) and
the South Fork (approximately 28 miles long), the mainstem valley reach (approximately 15.2
miles long), and numerous tributaries. The upper 16 miles of the North Fork and the upper 10
miles of the South Fork are inaccessible to anadromous salmonids due to natural barriers (Ward
and Kier 1999). Battle Creek has the largest base flow or dry-season flow (approximately 225
cfs) of any of the tributaries to the Sacramento River between the Feather River and Keswick
Dam.
Historically, both spring and fall runs of salmon occurred in Battle Creek, and there is evidence
that a winter run was also present. The Coleman National Fish Hatchery (CNFH) began
operations in 1943 and took small numbers (<1,200) of spring-run fish from Battle Creek in
1943-1946. In 1946, CNFH also began taking fall run fish from Battle Creek (Fry 1961 as cited
in Yoshiyama et al. 2001). From 1946 to 1956, the spring run numbered about 2,000 fish in most
years, but by the late 1980s, it was close to being extirpated (Yoshiyama et al. 2001).
Currently, natural Chinook salmon spawning in Battle Creek is heavily concentrated in the reach
between the creek mouth and the CNFH weir (6 miles upstream from the mouth). The
predominant fall Chinook are blocked at the hatchery weir (Yoshiyama et al. 2001). During
recent years when stream flows were adequate, small numbers of spring and winter Chinook have
been able to ascend past the weir and spawn in upstream reaches (Yoshiyama et al. 2001). At
present, the only other population of winter Chinook outside of Battle Creek occurs in the
Sacramento River downstream of Shasta Dam. The majority of this population spawns in the
reach between Keswick Dam and Cottonwood Creek where high water temperatures periodically
threaten these fish (Ward and Kier 1999). Between 2000 and 2010, an average of 114,457 fall
Chinook and 4,762 late-fall Chinook returned to Battle Creek annually (Table B-4 and B-5).
During this same time period, an average of only 170 spring Chinook returned to Battle Creek
(Table B-6).
Page B 4
June 2012
Table B-4.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall Chinook salmon escapement in Battle Creek (2001-2010).
Downstream of
Upstream of
Coleman NFH Coleman NFH
Coleman NFH
Total
24,698
100,604
0
125,302
65,924
397,149
0
463,073
88,234
64,764
0
152,998
69,172
23,861
0
93,033
142,673
20,520
0
163,193
57,832
19,493
0
77,325
11,744
9,904
0
21,648
10,639
4,286
0
14,925
6,152
3,047
0
9,199
17,238
6,631
1
23,870
49,431
65,026
0
114,457
Table B-5.
Late-fall run Chinook salmon escapement in Battle Creek (2001-2010).
Upstream of
Year
Coleman NFH
Coleman NFH
Total
Nov2000 – Apr2001
2,439
98
2,537
Nov2001 – Apr2002
4,186
216
4,402
Nov2002 – Apr2003
3,183
57
3,240
Nov2003 – Apr2004
5,166
40
5,206
Nov2004 – Apr2005
5,562
23
5,585
Nov 2005 – Apr 2006
4,822
50
4,872
Nov2006 – Apr2007
3,360
72
3,432
Nov2007 – Apr2008
6,334
19
6,353
Nov2008 – Apr2009
6,429
32
6,461
Nov2009 – Apr2010
5,505
27
5,532
Average
4,699
63
4,762
Table B-6.
Fall Chinook salmon escapement in Battle Creek (2001-2010).
Year
Fall Chinook
2001
111
2002
222
2003
221
2004
90
2005
73
2006
221
2007
291
2008
105
2009
194
2010
172
Average
170
June 2012
Page B 5
It was reported by USFWS at the Programmatic Data Gathering Workshop on June 14, 2011 that
approximately 90% of the fall Chinook returning to Battle Creek are considered to be of hatchery
origin. The percent composition of hatchery and natural-origin fish is thought to be the same for
fish entering the hatchery as for those spawning in the wild. At the same workshop, it was
reported that the large majority of late-fall Chinook returning to Battle Creek are of hatchery
origin.
5
Antelope Creek (Spring Chinook)
Antelope Creek originates in the Lassen National Forest in Tehama County and flows southwest
to RM 235 of the Sacramento River, 9 miles southeast of Red Bluff. The 123-square-mile
Antelope Creek watershed is in various ownerships, dominated by agriculture and ranchettes
along the valley floor. Most of the canyon reach is managed by the CDFG (Tehama Wildlife
Area) and the Lassen National Forest. The Antelope Creek headwaters is in an area of corporate
timber lands.
The Antelope Creek watershed produces on average 110,800 acre feet of water per year. Average
winter flows range from 200 to 1,200 cfs in the wettest years and 50 cfs in the driest years
(NMFS 2009). Summer and early fall flows typically average from 20 to 50 cfs (NMFS 2009).
There are two diversions on Antelope Creek, both located at the canyon mouth. One is operated
by the Edwards Ranch, which has a water right of 50 cfs, and the other is operated by the Los
Molinos Mutual Water Company, which has a water right of 70 cfs (NMFS 2009). Unimpaired
natural flows are often less than the combined water rights of the two diverters, resulting in a total
dewatering of Antelope Creek during critical migration periods (NMFS 2009).
Both spring and fall runs, and probably a late-fall run, originally occurred in Antelope Creek
(Yoshiyama et al. 2001). Spring-run salmon ascended the creek at least to where the North and
South forks join, and they probably held there over the summer. The few spring run fish that now
enter the creek ascend the North and South forks about 5 to 6 miles, their probable historical
upper limit, beyond which there is little suitable habitat (Yoshiyama et al. 2001). Under existing
conditions, relatively few spring Chinook enter Antelope Creek each year. From 2001 through
2010, an average of only 33 spring Chinook were observed in Antelope Creek annually (Table B7).The fall run in Antelope Creek generally has been small. From 1953–1984, the fall run
numbered 50 to 4,000 fish annually (an average of about 470 fish). Population estimates have not
been made in more recent years due to the scarcity of the salmon, and the fall run may be
extirpated (Yoshiyama et al. 2001). According to ICF Jones & Stokes (2010), none of the natural
spring Chinook spawners in Antelope Creek are considered to be hatchery-origin fish.
Page B 6
June 2012
Table B-7.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Spring Chinook salmon escapement in Antelope Creek (2001-2010).
Spring Chinook
(Antelope Creek)
8
46
46
3
82
102
26
2
0
17
33
6
Mill Creek (Spring and Fall Chinook)
Mill Creek originates on the southern slopes of Lassen Peak and flows generally to the southwest
for approximately 60 miles to its confluence with the Sacramento River. The stream is confined
within a steep-sided, narrow canyon except for a few alluvial meadows at the 5,000 foot level.
Below this canyon, Mill Creek flows for 8 miles through irrigated agricultural land (mainly
pasture and orchard crops) before entering the Sacramento River near the town of Los Molinos. 2
Historically, Clough Dam, Ward Dam, and Upper Diversion Dam impeded the upstream passage
of salmonids under low‐flow conditions. Clough Dam was removed in 2003 and Ward Dam was
modified in 1997 to improve upstream passage. In recent years, stream flows have been
augmented through a water exchange program to improve upstream passage for spring‐run
Chinook. Because the upper watershed is relatively inaccessible, it is undisturbed, pristine,
salmonid spawning habitat (CH2M Hill 1998). No significant water storage impoundments in the
watershed allow for a natural hydrograph that is supported by both seasonal rainfall and
snowmelt.
Both spring and fall-run Chinook salmon are present in Mill Creek. Fry (1961) (as cited in
Yoshiyama et al. 2001) reported spring-run numbers of less than 500 to about 3,000 fish during
1947-1959, while the fall run ranged between 1,000 to 16,000 spawners. Most of the fall run
spawned below Clough Dam, while most of the spring run passed upstream beyond the dam. In
recent decades, the spring spawning escapement has varied from no fish during the severe
drought in 1977, to 3,500 fish in 1975, but the trend has been downward from an annual average
of 2,000 fish in the 1940s to about 300 in the 1980s (Yoshiyama et al. 2001). Fall-run
escapements have been zero to 16,000 spawners since 1952; generally hovering near 1,500 fish
(Yoshiyama et al. 2001; CDFG unpublished data). From 2001 through 2010, an average of 926
spring-run Chinook were observed in Mill Creek annually (Table B-8).
2
http://www.sacriver.org/documents/2010/Roadmap/Eastside_MillCreek.pdf
June 2012
Page B 7
Table B-8.
Spring and fall Chinook salmon escapement in Mill Creek (2001-2010).
Spring Chinook
Fall Chinook
Year
(Mill Creek)
(Mill Creek)
2001
1,104
2002
1,594
2,611
2003
1,426
2,426
2004
998
1,192
2005
1,150
2,426
2006
1,002
1,403
2007
920
796
2008
362
166
2009
220
102
2010
482
144
Average
926
1,252
Spring run holding pools are present in the upper canyon areas, and spawning occurs between the
Little Mill Creek confluence and the Highway 36 Bridge (CH2M Hill 1998). Armentrout et al.
(1998) noted that the amount of holding habitat is limited in the upper 7.6 miles of Mill Creek
and that holding habitat was more abundant in the section below the Mill Creek Campground.
Low flows in the lower portion of the watershed can impede upstream passage of adult salmonids
in some years (CH2M Hill 1998). No physical passage barrier limits upstream migration on Mill
Creek; however, the combined effect of high stream gradients, low flows and habitat availability
sets the upper limit for migration in the headwater reaches.
According to Yoshiyama et al. (2001), the CDFG (1993) reported an average annual fall-run
escapement in Mill Creek of 2,200 fish for the 38 years of record up to that time. In the 1990s,
the fall run numbered from about 600 to 2,100 fish but was absent in some years due to low
seasonal stream flows. Since 2001, fall-run Chinook salmon escapement to Mill Creek has
averaged approximately 1,252 fish.
As in Deer Creek (see below), the spring and fall runs in Mill Creek are separated temporally, the
fall run ascending the creek during fall flows after the spring-run fish have finished spawning.
There is also spatial separation of the spring and fall runs in both Mill and Deer creeks, with
spring-run fish spawning well upstream from the fall-run fish 3 and thus further minimizing the
possibility of hybridization (Yoshiyama et al. 2001). Recent genetic analyses by Garza et al.
(2008) show that the two seasonal runs do not appear to interact reproductively in Mill Creek.
Moreover, those analyses also indicate that Feather River hatchery-origin spring Chinook appear
not to have reproductively interacted with Mill Creek fish.
7
Deer Creek (Spring and Fall Chinook)
Deer Creek flows from its mountainous headwaters in eastern Tehama County to its confluence
with the Sacramento River near the town of Vina. As is common with neighboring watersheds,
the upper watershed is flatter with significant alluvial valleys, connected to lowland agricultural
lands via a steep and deeply incised middle reach. Timber production, cattle ranching, and
orchards are the dominant agricultural land uses. Except for three small diversions, the watershed
3
Fall-run salmon use mainly the lower 6 miles of Mill Creek.
Page B 8
June 2012
is undammed and provides important habitat for both salmon and steelhead. Land ownership is
divided equally between public (upper watershed) and private (middle and lower watersheds). 4
Historically, both spring and fall Chinook salmon occurred in Deer Creek, which is a cold,
spring-fed stream. Before the 1940s, spring Chinook ascended Deer Creek for about 40 miles
from its mouth up to 16-foot-high Lower Deer Creek Falls, located about 1 mile below the mouth
of Panther Creek (Yoshiyama et al. 2001). Salmon were never known to pass Lower Deer Creek
Falls. Fall Chinook were known to spawn from the creek mouth to about 10 miles into the
foothills (Yoshiyama et al. 2001).
To compensate for the loss of spawning habitat in the upper Sacramento drainage caused by
construction of Shasta and Keswick dams, Sacramento River spring-run salmon were caught at
Keswick and transported to Deer Creek during the 1940s to mid-1950s, but those transfers had no
noticeable effect on the spring run in Deer Creek (Fry 1961 as cited in Yoshiyama et al. 2001).
Deer Creek is currently believed to have sufficient habitat to support “sustainable populations” of
4,000 spring-run and 6,500 fall-run salmon (Reynolds et al. 1993, as cited in Yoshiyama et al.
2001).
Yoshiyama et al. (2001), citing Fry (1961), reported Deer Creek spring-run spawner estimates of
less than 500 to 4,000 fish for 1940–1956. Using DFG unpublished data, those authors reported
that the spring-run ranged between 400 and 3,500 fish annually from 1950–1979 (average of
2,200) and 80 to 2,000 fish during 1980–1998 (average of 660). More recent data show that the
run has been between 220 to 1,594 fish during 2001-2010, averaging 926 in this period (Table B9).
Fall Chinook were estimated by Fry (1961 as cited in Yoshiyama et al. 2001) to range from less
than 500 fish to 12,000 fish from 1947–1959. From the 1960s through 1980s, the number of fallrun spawners in Deer Creek ranged from 60 to 2,000 fish (average 500). From 2004 through
2010, fall Chinook have numbered 58 to 1,905 fish (average 585) (Table B-9).
Table B-9.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Spring and fall Chinook salmon escapement in Deer Creek (2001-2010).
Spring Chinook
Fall Chinook
(Deer Creek)
(Deer Creek)
1,104
1,594
1,426
998
300
1,150
963
1,002
1,905
920
508
362
194
220
58
482
166
926
585
Recent genetic analyses by Garza et al. (2008) show that the two seasonal runs do not appear to
interact reproductively in Deer Creek. Moreover, those analyses also indicate that Feather River
4
http://www.sacriver.org/documents/2010/Roadmap/Eastside_DeerlCreek.pdf
June 2012
Page B 9
hatchery-origin spring Chinook appear not to have reproductively interacted with Mill Creek fish.
It should be noted that the spring-run population in Deer Creek is one of only three or four
remaining naturally spawning spring Chinook populations in California that can be considered
genetically intact and demographically viable. Two of the other populations in the Central Valley
drainage occur in nearby Mill and Butte creeks.
8
Big Chico Creek (Spring Chinook)
Big Chico Creek is located within Butte and Tehama counties and has watershed area of
approximately 72 square miles. The headwaters of Big Chico Creek are on the southwest slope
of Colby Mountain, from where it flows approximately 45 miles to the Sacramento River west of
Chico.
Big Chico Creek contains marginally suitable habitat for salmon and probably was
opportunistically used in the past. Spring, fall and late-fall runs have occurred in this creek
(Yoshiyama et al. 2001). Fry (1961) (as cited in Yoshiyama et al. 2001) gave estimates of 50
fall-run (including late-fall-run) fish in 1957, 1,000 spring-run fish in 1958, and 200 spring-run in
1959. The average annual spring Chinook run size is believed to have been less than 500 fish
during the 1950s to 1960s and more recently has been considered to be only a remnant. Big
Chico Creek has been heavily stocked with Feather River spring-run fish, which evidently had
been genetically mixed with fall-run fish. In the last decade, an average of only 46 spring-run
Chinook returned to Big Chico Creek (Table B-10). According to ICF Jones & Stokes (2010),
none of the natural spring-run Chinook spawners in Big Chico Creek are considered to be
hatchery-origin fish.
Table B-10.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Spring Chinook salmon escapement in Big Chico Creek (2001-2010).
Spring Chinook
(Big Chico Creek)
39
0
81
0
37
299
0
0
6
2
46
9
Butte Creek (Spring and Fall Chinook)
Butte Creek is a major tributary to the Sacramento River originating in the Lassen National Forest
at an elevation of 7,087 feet. Encompassing approximately 510,000 acres, the watershed drains
the northeast portion of Butte County and enters the Sacramento Valley southeast of Chico. Butte
Creek then meanders in a southwesterly direction to its confluence with the Sacramento River at
Page B 10
June 2012
Butte Slough. 5 A second point of entry into the Sacramento River is through the Sutter Bypass
and Sacramento Slough. 6
The hydrology of the upper watershed has been modified significantly by multiple diversions for
hydroelectric power generation, while the lower watershed is managed primarily for irrigation
and flood control. Land use is dominated by agriculture in the lower portions (largely rice,
orchards, and row crops), with timber and grazing predominant in the upper watershed. 7
Historically, Butte Creek supported a relatively large run of spring Chinook salmon that that
likely ascended the creek at least as far as Centerville Head Dam near DeSabla (Yoshiyama et al.
2001). However, Butte Creek reportedly had almost no fall run, setting it apart from most small
streams in the northern Sacramento Valley which had mainly, or only, a fall run. According to
Fry (1961) (as cited in Yoshiyama et al. 2001), the many removable dams on the creek blocked or
reduced flows late into the fall, and the fall Chinook could not surmount them.
Fry (1961 as cited in Yoshiyama et al. 2001) reported that the spring Chinook ranged from less
than 500 fish to 3,000 fish from 1953 to 1959. During the 1960s, at times the spring run
numbered over 4,000 fish in Butte Creek (CDFG 1998), with smaller numbers of fall and late-fall
run fish (Reynolds et al. 1993). More recently, estimated spring-run numbers were 100 to 700
fish during the 1990s, rising to 7,500 fish in 1995 and 20,000 fish in 1998. The source of the
surprisingly numerous spring-run spawners that entered Butte Creek in 1998 is not known, but
presumably they could be attributed to the strong escapement in 1995. Since 2001, spring
Chinook escapement to Butte Creek has averaged approximately 4,900 fish (Table B-11).
The Butte Creek fall run remains relatively small, numbering approximately 2,000 fish (Table B11). There are also late-fall-run salmon here, but their numbers are unknown (Reynolds et al.
1993 as cited in Yoshiyama et al. 2001).
Table B-11.
Spring and fall Chinook salmon escapement in Butte Creek (2001-2010).
Fall
Spring
Year
Butte Creek (In-River)
Butte Creek (Snorkel)
2001
4,433
9,605
2002
3,665
0
2003
3,492
4,398
2004
2,516
7,390
2005
4,255
10,625
2006
1,920
4,579
2007
1,225
4,943
2008
275
3,935
2009
306
2,059
2010
370
1,160
Average
2,246
4,869
5
Butte Creek flows are regulated into the Sacramento River by the Butte Slough outfall gates to accommodate both
flood flows and agricultural needs in the Sutter bypass area.
6
http://buttecreekwatershed.org/Watershed/ECR.pdf
7
http://www.sacriver.org/documents/2010/Roadmap/Eastside_ButteCreek.pdf
June 2012
Page B 11
Preliminary results for 2010 show that in that year, less than 3% of the natural fall-run spawners
in Butte Creek were of hatchery origin (Kormos et al. 2011). This was the first year of 4-year-old
returns from hatchery releases marked under the constant fractional marking program.
Recent genetic analysis by Garza et al. (2008) shows that Butte, Mill, and Deer creek spring
Chinook populations are genetically distinct and monophyletic (meaning that they all arose from
a common spring-run ancestor). The analysis also shows that the Butte Creek population is the
most distinct of the three. These results indicate that Feather River Hatchery-origin spring
Chinook have not reproductively interacted with Butte Creek fish.
10
Feather River (Spring and Fall Chinook)
The Upper Feather River watershed includes all tributaries to the Feather River from the
headwaters in the Sierra Nevada crest downstream to Lake Oroville. The Upper Feather is a
major source of the state’s water supply and provides virtually all the water delivered by the
California State Water Project. Most of the watershed lies in Plumas County and is roughly 65%
publicly owned, primarily by the US Forest Service. The lower Feather River watershed,
downstream of Lake Oroville (a fish migration barrier), encompasses approximately 803 square
miles. The river flows approximately 60 miles north to south before entering the Sacramento
River at Verona. There are approximately 190 miles of major creeks and rivers, 695 miles of
minor streams, and 1,266 miles of agricultural water delivery canals in the lower Feather River
watershed. Flows are regulated for water supply and flood control through releases at Oroville
Dam. The river is almost entirely contained within a series of levees as it flows through the
agricultural lands of the Sacramento Valley. Significant management issues include concerns
over growth (farmland conversion to urban uses), demands on water supply, preservation of water
quality and aquatic habitat, and potential risks from fire and floods. 8
Historically, the Feather River supported both spring and fall Chinook salmon and was renowned
as one of the major salmon-producing streams of the Sacramento Valley (Yoshiyama et al. 2001).
The major spawning areas extended from the river’s mouth to Oroville (Yoshiyama et al. 2001), a
distance of over 60 miles, with important spawning areas continuing upstream. Fry (1961 as
cited in Yoshiyama et al. 2001) reported annual fall Chinook runs of 10,000 to 86,000 fish from
1940 to1959, and about 1,000 to 4,000 spring Chinook. The fall run spawned largely in the
mainstem, while most of the spring run spawned in the Middle Fork, with a few spring run
entering the North Fork, South Fork and West Branch.
Just before the completion of Oroville Dam (in 1967), a small naturally-spawning spring Chinook
population still existed in the Feather River, but the Oroville project blocked access to the
majority of its habitat. Currently, the fall run extends to Oroville Dam and spawns from there
downstream to a point about 2 miles above the Gridley Road crossing. There is also a hatcherysustained population of “spring-run” fish that has been genetically mixed with the fall run and
that spawns in the 0.5-mile reach below the Oroville fish barrier. The hybrid spring-run fish hold
over the summer in deep pools in the “low-flow” section of the river between Thermalito
Diversion Dam (5 miles below Oroville Dam) and the downstream Thermalito Afterbay Outlet.
They are spawned artificially in the Feather River Hatchery and also spawn naturally in the river
during late September to late October. The “spring run” thus overlaps temporally as well as
spatially with the fall run, which is the cause of the hybridization between the runs (Yoshiyama et
al 2001).
8
http://www.sacriver.org/
Page B 12
June 2012
The Feather River Hatchery, located at the town of Oroville, was completed in 1967 by the
California Department of Water Resources (DWR) to mitigate for the loss of upstream spawning
habitat of salmon and steelhead due to the building of Oroville Dam. The Feather River Hatchery
is the only source of eggs from “spring-run” Chinook salmon in the Central Valley and is viewed
as a key component in plans to restore spring Chinook populations (Yoshiyama et al. 2001).
In recent decades, the majority of Chinook salmon production in the Feather River has been
heavily supported by hatchery production. Since 2001, both spring and fall Chinook salmon
escapement to the Feather River Hatchery has averaged approximately 15,000 fish (Table B-12).
During this same period, river returns (natural spawners) averaged approximately 79,000 fish.
According to DWR (2005), approximately two-thirds of natural fall Chinook spawning occurs
between the Fish Barrier Dam and the Thermalito Afterbay Outlet (RM 67 - RM 59), and onethird of the spawning occurs between the Thermalito Afterbay Outlet and Honcut Creek (RM 59 RM 44).
Carcass surveys in 2010 show that essentially 100% of the Chinook spawning in the low flow
channel of Feather River (RM 67 - RM 59) are of hatchery origin and at least 60% of those in the
high flow channel (RM 59 - RM 44) are of hatchery origin (inferred from Hartwigsen 2011).
Table B-12.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Chinook salmon escapement in the Feather River basin (2001-2010).
Feather River1
Feather River
Percent In-River
Hatchery
In-River
Total
(Feather)
24,870
178,645
203,515
87.8%
20,507
105,163
125,670
83.7%
14,976
89,946
104,922
85.7%
21,297
54,171
75,468
71.8%
22,405
49,160
71,565
68.7%
14,034
76,414
90,448
84.5%
5,341
21,886
27,227
80.4%
5,082
5,939
11,021
53.9%
9,963
4,847
14,810
32.7%
19,972
44,914
64,886
69.2%
15,845
63,109
78,953
71.8%
Note: Feather River survey data does not provide separate estimates for fall and spring escapement. Spring run
estimates are included with fall-run estimates.
11
Yuba River (Fall Chinook)
The Yuba River watershed drains approximately 1,340 square miles and extends from the crest of
the Sierra Nevada to the confluence of the Feather River near Marysville and Yuba City. The
principal tributaries include the North Yuba River, with a drainage area of approximately 490
square miles; the Middle Yuba River, with a drainage area of about 210 square miles; and the
South Yuba River, with a drainage area of about 350 square miles. The North Yuba and the
Middle Yuba rivers join below New Bullards Bar Reservoir to form the Yuba River. Farther
downstream, the South Yuba River flows into Englebright Lake (DWR 2007).
Englebright Dam was completed in 1941 to capture gold-rush era hydraulic mining debris
(sediment) that posed a flood threat to downstream residents. Located at RM 25, the 260-foot-
June 2012
Page B 13
high dam marks the division between the upper and lower Yuba River and defines the upper
extent of the anadromous fishery. Consequently, anadromous fish do not have access to the
North, South and Middle Yuba rivers (DWR 2007). An additional influence on both the
hydraulics of the lower Yuba River and fish passage is Daguerre Point Dam. Located
approximately 11.4 miles upstream from the confluence with the Feather River, Daguerre Point
Dam stores sediment and creates head for irrigation diversions, but is also an impediment to the
movement of anadromous fish. The Daguerre Point Dam Fish Passage Improvement Project was
recently initiated with a goal of improving fish passage at the dam. 9
The lower Yuba River is used by spring and fall Chinook salmon. Although late fall-run Chinook
populations occur primarily in the Sacramento River (CDFG Website 2007), incidental
observations of late fall-run Chinook have been reported in the lower Yuba River.
Historically, the Yuba River contained about 80 miles of potentially accessible Chinook salmon
habitat. The California Fish Commission reported that in 1850 “the salmon resorted in vast
numbers to the Feather, Yuba, American, Mokelumne, and Tuolumne Rivers,” and on the Yuba
River as late as 1853 “the miners obtained a large supply of food from this source”; however, by
1876 the salmon no longer entered those streams (CFC 1877 as cited in Yoshiyama et al. 2001).
By the late 1950s, Fry (1961 as cited in Yoshiyama et al. 2001) noted that the spring salmon run
had “virtually disappeared.” Fall Chinook escapements from 1953 to 1989 ranged from 1,000 to
39,000 fish, averaging 13,050 annually (Yoshiyama et al. 2001). More recently (2001-2010), the
annual number of fall Chinook returning to the Yuba River has ranged from 2,604 to 28,316
spawners (Table B-13). Under existing conditions, most of the salmon spawning habitat is in the
7.8-mile reach of river on the open valley floodplain downstream of Daguerre Point Dam;
however, the greater part of the run generally spawns above Daguerre Point (Yoshiyama et al.
2001).
Table B-13.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall Chinook salmon escapement in the Yuba River basin (2001-2010).
Fall Chinook Escapement
(Yuba River)
23,392
24,051
28,316
15,269
17,630
8,121
2,604
3,508
4,635
14,375
14,190
9
http://www.water.ca.gov/pubs/environment/fish/daguerre_point_dam_fish_passage_improvement_project__2002_water_resources_studies/daguerre_fish_passage.pdf
Page B 14
June 2012
Preliminary results for 2010 show that in that year, nearly 75% of the natural fall run spawners in
the Yuba River were of hatchery origin (Kormos et al. 2011). This was the first year of 4-year-old
returns from hatchery releases marked under the constant fractional marking program.
It was reported by DWR staff at the Programmatic Data Gathering Workshop on June 16, 2011
that upwards to 65% of the spring-run Chinook passing Daguerre Point Dam have been finclipped. All spring Chinook produced at Feather River Hatchery are fin-clipped.
12
American River (Fall Chinook)
The lower American River watershed begins at Folsom Dam and flows 30 miles to its confluence
with the Sacramento River near downtown Sacramento. Folsom Dam creates Folsom Lake which
is operated for multiple purposes. Flows from Folsom Lake are re-regulated by Nimbus Dam,
from where the American River flows the floodplain and the urbanized Sacramento area. The
river is buffered by the 30-mile-long American River Parkway, extending from Folsom to the
Sacramento River confluence near Old Sacramento. Water quality in the lower American River
is considered to be very good and it has been designated a “Recreational River” under both the
California Wild and Scenic Rivers Act and the National Wild and Scenic Rivers Act. 10
Historically, Chinook salmon and steelhead had access to approximately 125 miles of spawning
and rearing habitat in the upper reaches of the American River. According to Yoshiyama et al.
(2001), spring, fall and possibly late-fall runs of salmon, as well as steelhead, ascended the
American River and its major tributaries, impeded to varying degrees by a number of natural
barriers. Clark (1929) as cited in Yoshiyama et al.(2001) described the 1927-1928 salmon run as
“very good” and noted spawning occurred from the river mouth to Old Folsom Dam, about one
mile above the city of Folsom.
In the 1940s, both the spring and fall runs began to reestablish themselves in the American River
above Old Folsom Dam. Counts at the fishway at Old Folsom Dam showed that the spring run
reached a maximum of 1,138 fish in 1944 and the fall run reached 2,246 fish in 1945. The
spring-run count dropped to 42 fish in 1945, 16 in 1946, and three fish in 1947; both the spring
and fall runs reportedly were decimated after the fish ladder on Old Folsom Dam was destroyed
by flood waters in 1950. The spring-run was finally extirpated during construction of present-day
Folsom Dam and Nimbus Dam (Gerstung 1971 unpublished report as cited in Yoshiyama et al.
2001).
From 1944–1959, combined Chinook run sizes were 6,000 to 39,000 spawners annually; these
fish were mainly fall Chinook (Fry 1961 as cited in Yoshiyama et al. 2001). From 1944–1955, an
estimated average of 26,500 salmon (range 12,000 to 38,652) spawned annually in the mainstem
American River below the City of Folsom (Gerstung 1971 unpublished report as cited Yoshiyama
et al. 2001).
When the Folsom-Nimbus project was completed in 1958, access to about 70% of the spawning
habitat historically used by Chinook salmon and 100% of the spawning habitat used by steelhead
was blocked. As a result, the Nimbus Salmon and Steelhead Hatchery was constructed to replace
the affected runs. The fish weir and ladder now direct these fish to the Nimbus Fish Hatchery.
In recent decades, fall Chinook spawning escapements have ranged from about 5,700 (in 2008) to
178,000 (in 2003) fish annually. From 2001 through 2010, Chinook salmon escapement to the
10
http://www.sacriver.org/documents/2010/Roadmap/American_LowerAmerican.pdf
June 2012
Page B 15
Nimbus Hatchery has averaged approximately 11,500 fish (Table B-14). During this same
period, natural spawners averaged 75,800 fish, or approximately 73% of the total run.
Preliminary results for 2010 show that in that year, approximately 30-35% of the natural fall-run
spawners in the American River were of hatchery origin (Kormos et al. 2011).This was the first
year of 4-year-old returns from hatchery releases marked under the constant fractional marking
program. However, views expressed by individuals knowledgeable of the American River at the
Programmatic Data Gathering Workshop on April 25, 2011 suggested the percentage is likely
higher.
Table B-14.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall Chinook salmon escapement in the American River basin (2001-2010).
Nimbus
In-River
Percent In-River
Hatchery
(American)
Total
(American)
11,750
135,384
147,134
92.0%
9,817
124,252
134,069
92.7%
14,887
163,742
178,629
91.7%
26,400
99,230
125,630
79.0%
22,349
62,679
85,028
73.7%
8,728
24,540
33,268
73.8%
4,597
10,073
14,670
68.7%
3,184
2,514
5,698
44.1%
4,789
5,297
10,086
52.5%
9,095
14,688
23,783
61.8%
11,560
64,240
75,800
73.0%
13
Mokelumne River (Fall Chinook)
The Mokelumne River originates in the Sierra Nevada Mountains and flows through the Central
Valley before entering the Delta forks of the Mokelumne just downstream of the Delta Cross
Channel. The watershed drains some 627 square miles and contains a number of dams and
reservoirs. Pardee Dam and Reservoir (at RM 73) serves multiple purposes that include water
supply and maintenance of the Camanche Reservoir hypolimnion. Camanche Dam and
Reservoir, completed by EBMUD in 1964 at RM 64, is the upstream limit of anadromous
salmonid migration.
Historically, the Mokelumne River supported both spring and fall Chinook salmon. Some
evidence suggests that a late-fall run also entered the river at one time (Yoshiyama et al. 2001).
Salmon ascended the river at least as far as the vicinity of present-day Pardee Dam. A large
waterfall 1 mile downstream of the Pardee Dam site posed a significant barrier to the fall run;
however, spring Chinook likely ascended the falls to reach elevations where water temperatures
were suitable for over-summering (FERC 1993). While historical abundance data are limited,
Fry (1961 as cited in Yoshiyama et al. 2001) reported that counts of fall run spawners passing
Woodbridge Dam (RM 39) ranged from less than 500 (in two separate years) to 7,000 fish from
1945 to1958, with partial counts of 12,000 fish each in 1941 and 1942. Fry also stated that the
spring run appeared to be “practically extinct”. During the period 1940–1990, total annual run
sizes ranged between 100 and 15,900 fish (Yoshiyama et al. 2001).
Under current conditions, fall Chinook are stopped at the lower end of Camanche Reservoir,
about 9 miles below Pardee Dam. They spawn in the reach from Camanche Dam (RM 29.6)
Page B 16
June 2012
downstream to Elliott Road, and 95% of the suitable spawning habitat is within 3.5 miles of
Camanche Dam.
The Mokelumne River Fish Hatchery was constructed in 1964 to produce both fall-run Chinook
salmon and steelhead trout. Average production from the facility since the early 1990s has been
approximately 3.0 to 5.0 million fall-run Chinook smolts, 500,000 yearling Chinook, and 100,000
yearling steelhead. Approximately 2.0 million salmon are raised to post-smolt stage each year for
an ocean enhancement program. These fish are trucked downstream to San Pablo Bay or reared
in net pens on the coast. Remaining salmon smolts that were Mokelumne-origin fish were
planted below Woodbridge Dam (ICF Jones & Stokes 2010, Miyamoto and Hartwell 2001).
Since 2001, fall-run Chinook salmon escapement to the Mokelumne River Hatchery has averaged
fewer than 5,000 fish (Table B-15). During this same period, natural spawners averaged
approximately 2,400 fish (about 31% of the total return).
Preliminary results for 2010 show that in that year, approximately 75% of the natural fall-run
spawners in the Mokelumne River were of hatchery origin (Kormos et al. 2011).This was the first
program. Views expressed by individuals knowledgeable of the Mokelumne River spawning
patterns at the Programmatic Data Gathering Workshop on April 25, 2011 suggested the
percentage is likely much higher.
Table B-15.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall Chinook salmon escapement in the Mokelumne River Basin (2001-2010).
Mokelumne River
Cosumnes Mokelumne River
Percent In-River
River
Hatchery
In-River
Total
(Mokelumne)
5,728
2,307
8,035
28.7%
1,350
7,913
2,840
10,753
26.4%
122
8,117
2,122
10,239
20.7%
1,208
10,356
1,588
11,944
13.3%
370
5,563
10,406
15,969
65.2%
530
4,139
1,732
5,871
29.5%
77
1,051
470
1,521
30.9%
15
239
173
412
42.0%
0
1,553
680
2,233
30.5%
740
5,275
1,912
7,187
26.6%
490
4,993
2,423
7,416
31.4%
14
Stanislaus River (Fall Chinook)
The Stanislaus River watershed is bordered by the Mokelumne watershed to the north and the
Tuolumne watershed to the south. The river is 95.9 miles long and has north, middle and south
forks. The headwaters of the Stanislaus River are in the Emigrant Wilderness area at elevations
above 9,000 feet, and it flows in a general southwesterly direction to its confluence with the San
Joaquin River 23 miles above Stockton. The watershed has been heavily dammed and diverted
and currently contains 13 large reservoirs. Goodwin Dam, located at RM 52 on the Stanislaus
River is a barrier to anadromous fish migration.
June 2012
Page B 17
Both spring and fall-run Chinook salmon historically occurred throughout the Stanislaus River
basin (Yoshiyama et al. 2001). Spring-run and likely some fall-run salmon migrated considerable
distances up the forks because there were few natural obstacles. The spring run was said to have
been the primary salmon run in the Stanislaus River, but after the construction of dams which
regulated the stream flows (namely, Goodwin Dam and, later, New Melones and Tulloch dams),
the fall run became predominant. Fry (1961 as cited in Yoshiyama et al. 2001) described the
Stanislaus River as “a good fall run stream for its size” but it had “almost no remaining spring
run.”
The Stanislaus River fall run has contributed up to 7% of the total salmon spawning escapement
in the Central Valley (Yoshiyama et al. 2001). From 1946 through 1959 (before construction of
Tulloch Dam), annual escapements of fall-run Chinook were estimated at 4,000 to 35,000
spawners (averaging about 11,100 spawners) (Fry 1961 as cited in Yoshiyama et al. 2001). In the
following 12-year period (1960–1971), the average run size was about 6,000 fish. Fall-run
abundances during the 1970s and 1980s ranged up to 13,600 (averaging about 4,300) spawners
annually; however, the numbers of spawners returning to the Stanislaus River were very low
during most of the 1990s (less than 500 fish annually in 1990–1992, 600 to 1,000 fish in 1994–
1995, and less than 200 fish in 1996). Since 2001, fall Chinook escapement to the Stanislaus
River has averaged approximately 3,100 fish (Table B-16). Only the fall run has sustained itself
in the Stanislaus River, although small numbers of late-fall Chinook have been reported to enter
the river. As in the Tuolumne River, the recent occurrence of late-fall Chinook in the Stanislaus
River could be due to strays from the Sacramento River system (Yoshiyama et al. 2001).
spawners in the Stanislaus River were of hatchery origin (Kormos et al. 2011).This was the first
program.
Table B-16. Fall Chinook salmon escapement in the Stanislaus River basin (2001-2010).
Year
In-River (Stanislaus)
2001
7,033
2002
7,787
2003
5,902
2004
4,015
2005
1,427
2006
1,923
2007
443
2008
1,392
2009
595
2010
1,086
Average
3,160
15
Tuolumne River Fall Chinook
The 150-mile-longTuolumne River is the largest of three major tributaries to the San Joaquin
River. Originating in Yosemite National Park, it flows west between the Merced River and
Stanislaus River to its confluence with the San Joaquin River at the tailrace of the Don Pedro
powerhouse. The 1,960-square-mile watershed can be subdivided into three river reaches: the
upper Tuolumne River above roughly RM 80, the foothills reach between RM 54 and 80, and the
Page B 18
June 2012
valley reach from the mouth to RM 54. Upstream fish passage is blocked at RM 54 by La Grange
Dam.
The lower Tuolumne River watershed (RM 0 to 54), covers approximately 430 square miles and
contains one major tributary, Dry Creek. Other tributaries include Peaslee Creek and McDonald
Creek (via Turlock Lake). The lower Tuolumne River watershed is long and narrow and is
dominated by irrigated farmland and the urban/suburban areas associated with the cities of
Modesto, Waterford, and Ceres. Flows in the lower Tuolumne River are significantly controlled
by La Grange Dam, a diversion dam constructed in 1893 that diverts water from the Tuolumne
River for irrigation, municipal and industrial supply purposes.
While both spring and fall-run Chinook salmon were once abundant in the Tuolumne River, only
the fall run presently occurs in appreciable numbers. In the past, the number of fall-run Chinook
returning to the Tuolumne River was sometimes larger than in any other Central Valley streams
except for the mainstem Sacramento River, reaching as high as 122,000 spawners in 1940 and
130,000 in 1944 (Fry 1961 as cited in Yoshiyama et al. 2001). At times, Tuolumne River fall run
Chinook comprised up to 12% of the total fall-run spawning escapement in the Central Valley,
but run sizes during the early 1990s fell to extremely low levels (i.e., less than 500 spawners).
The fall run rebounded in the late-1990s, approaching 9,000 spawners in 1998; however, from
2001 through 2010, the fall run has averaged only 2,259 fish (Table B-17). Since 2005, the
number of Chinook retuning to the Tuolumne River has averaged less than 500 fish.
The fall run historically has been a naturally sustained population because there is no hatchery on
the Tuolumne River. Increasing numbers of hatchery-derived spawners have ascended the
Tuolumne River in recent years, mainly due to large releases of hatchery juveniles (from Merced
River Hatchery) for study purposes into this stream and elsewhere in the San Joaquin River Basin
and Sacramento-San Joaquin Delta (Yoshiyama et al. 2001).
Table B-17.
Fall Chinook salmon escapement in the Tuolumne River basin (2001-2010).
In-River Escapement
Year
(Tuolumne)
2001
8,782
2002
7,173
2003
2,163
2004
1,984
2005
668
2006
562
2007
224
2008
372
2009
124
2010
540
Average
2,259
Preliminary results for 2010 show that in that year, nearly 50% of the natural fall-run spawners in
the Tuolumne River were of hatchery origin (Kormos et al. 2011). This was the first year of 4year-old returns from hatchery releases marked under the constant fractional marking program.
June 2012
Page B 19
16 Merced River (Fall Chinook)
The Merced River is a tributary to the San Joaquin River in the southern portion of the Central
Valley. The river, which drains a 1,276-square-mile watershed, originates in Yosemite National
Park and flows southwest through the Sierra Nevada range before joining the San Joaquin River
87 miles south of Sacramento. Elevations in the watershed range from 13,000 feet at its crest to
49 feet at the confluence with the San Joaquin River (Stillwater Sciences 2006).
Similar to other rivers in the Central Valley, the Merced River has been affected by numerous
human activities, including water storage and diversion, land use conservation, introduction of
exotic plant and animal species, gold and aggregate mining, and bank protection. Alteration to
the flow and sediment supply within the lower Merced River began with construction of the
original Exchequer Dam in 1926. Currently, flow is controlled by four dams on the mainstem
Merced River, New Exchequer Dam, McSwain Dam, Merced Falls Dam, and the
Crocker‐Huffman Dam (Stillwater Sciences 2006).
Historically, both spring and fall-run Chinook salmon occurred in the Merced River, but only the
fall run has survived and is now the southernmost native Chinook salmon run in existence
(Yoshiyama et al. 2001). Fry (1961 as cited in Yoshiyama et al. 2001) considered the Merced
River to be “a marginal salmon stream” due to the removal of water by irrigation diversions, and
he stated that there was “a poor fall run and poor spring run.”
The CDFG has been conducting escapement surveys in the Merced River since 1953. Data
collected from the surveys allow CDFG to estimate fall Chinook escapement; evaluate the
distribution of redds in the study area; collect length and sex data; collect scale and otoliths for
age determination and cohort analyses; and collect and analyze coded-wire tag data. The
escapement surveys cover a 24.7-mile reach extending from Crocker-Huffman Dam at the
Merced River Hatchery (RM 51.9) to Santa Fe Road (RM 27.1).
During the 1950s and 1960s, Merced River fall Chinook escapement averaged less than 500 fish
in most years. Escapement began to increase substantially in 1970 following flow increases from
the New Exchequer Dam and releases of hatchery-reared fish into the river. However, spawning
escapements in the Merced River, including returns to the Merced River Hatchery, dropped
significantly in the early 1990s to less than 100 fish in 1990 and less than 200 in 1991
(Yoshiyama et al. 2001). From 2001 through 2010, the fall Chinook run in the Merced River,
including fish returning to the Merced River Hatchery, has averaged just over 3,500 fish, with
total escapement experiencing another dramatic decline beginning in 2007 (Table B-18).
spawners in the Merced River were of hatchery origin (Kormos et al. 2011).This was the first
year of 4-yearold returns from hatchery releases marked under the constant fractional marking
program. Over the past 20 years, Mesick (2010) estimates that the percent of hatchery-origin fish
in the total Merced system (includes to the hatchery) escapement has rangedfrom about 40-95%.
Page B 20
June 2012
Table B-18. Fall Chinook salmon escapement in the Merced River Basin (2001-2010).
Merced River Fish
In-River
Percent In-River
Year
Facility
(Merced)
Total
(Merced)
2001
1,663
9,181
10,844
84.7%
2002
1,840
8,866
10,706
82.8%
2003
549
2,530
3,079
82.2%
2004
1,050
3,270
4,320
75.7%
2005
421
1,942
2,363
82.2%
2006
150
1,429
1,579
90.5%
2007
79
495
574
86.2%
2008
76
389
465
83.7%
2009
246
358
604
59.3%
2010
146
651
797
81.7%
Average
622
2,911
3,533
80.9%
17
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