California Hatchery Review Project Appendix VIII Nimbus Fish

Transcription

California Hatchery Review Project
Appendix VIII
Nimbus Fish Hatchery Steelhead
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 ...................................................................................................2 1.2.1 Facilities .....................................................................................................................2 1.2.2 Broodstock .................................................................................................................4 1.2.3 Spawning....................................................................................................................7 1.2.4 Incubation ..................................................................................................................7 1.2.5 Rearing .......................................................................................................................8 1.2.6 Release .......................................................................................................................9 2 Populations Affected by the Hatchery Program ....................................................................11 2.1 Current Conditions of Affected Natural Populations ......................................................13 2.1.1 American River Steelhead .......................................................................................14 2.1.2 Other Central Valley Steelhead Populations............................................................15 2.2 Long–term Goals for Natural Populations ......................................................................17 3 Fisheries Affected by the Hatchery Program .........................................................................18 3.1 Current Status of Fisheries ..............................................................................................18 3.2 Long-term Goals for Affected Fisheries .........................................................................18 4 Programmatic and Operational Strategies to Address Issues Affecting Achievement of
Goals .....................................................................................................................................18 4.1 Issues Affecting Achievement of Goals ..........................................................................18 4.1.1 Natural Production Issues ........................................................................................18 4.1.2 Ecological Interaction Issues ...................................................................................19 4.2 Operational Issues ...........................................................................................................19 4.3 Programmatic Strategies .................................................................................................19 4.3.1 Broodstock ...............................................................................................................20 4.3.2 Program Size and Release Strategies .......................................................................23 4.3.3 Incubation, Rearing and Fish Health .......................................................................25 4.3.4 Monitoring and Evaluation ......................................................................................32 4.3.5 Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial
Organisms. ...............................................................................................................36 5 Literature Cited ......................................................................................................................37 List of Figures
Figure 1. Figure 2. Number of female and male steelhead trapped at Nimbus Hatchery, 1955 to
2010. ..........................................................................................................................6 Number of fingerling and yearling size steelhead released from Nimbus Fish
Hatchery, 1956-1957 to 2007-2008.........................................................................10 California Hatchery Review Project – Appendix VIII
Nimbus Fish Hatchery Steelhead Program / June 2012
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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. Number and percentage of unmarked steelhead trapped at the Nimbus Fish
Hatchery, 2000-2001 through 2009-2010 seasons. ...................................................6 Number of female steelhead spawned and number of eggs taken 2000-2001
through 2009-2010 seasons. ......................................................................................7 Adipose clip status of adult steelhead entering Nimbus Hatchery. .........................15 Steelhead status, abundance and habitat availability in the Central Valley (NMFS
2009). .......................................................................................................................15 Broodstock Source. .................................................................................................20 Broodstock Collection. ............................................................................................20 Broodstock Composition. ........................................................................................21 Mating Protocols. ....................................................................................................22 Steelhead Spawner Disposition. ..............................................................................22 Program Size. ..........................................................................................................23 Release Strategy. .....................................................................................................24 Fish Health Policy. ..................................................................................................25 Hatchery Monitoring by Fish Health Specialists. ...................................................26 Facility Requirements..............................................................................................27 Fish Health Management Plans. ..............................................................................29 Water Quality. .........................................................................................................29 Best Management Practices.....................................................................................30 Hatchery and Genetic Management Plans...............................................................32 Hatchery Evaluation Programs. ...............................................................................32 Hatchery Coordination Teams.................................................................................32 In-Hatchery Monitoring and Record Keeping.........................................................33 Marking and Tagging Programs. .............................................................................34 Post-Release Emigration Monitoring. .....................................................................34 Adult Monitoring Programs. ...................................................................................35 Evaluation Programs. ..............................................................................................35 Direct Effects of Hatchery Operations. ...................................................................36 Appendices
Appendix A-1 Hatchery Program Review Questions
Appendix A-2 Nimbus Steelhead Program Data Tables
Appendix A-3 Hatchery Program Review Analysis Benefit-Risk Statements
Appendix B
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Central Valley Steelhead Watershed Reports
California Hatchery Review Project – Appendix VIII
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1
Description of Current Hatchery Program
The Central Valley Project (CVP) was originally conceived as a state project to protect the
Central Valley from water shortages and floods. The CVP priorities are flood control, improving
navigation on Central Valley rivers, developing hydroelectric power, irrigation, and municipal
and industrial water supply, protecting the Sacramento-San Joaquin River Delta from seawater
encroachment, and protecting and enhancing fish and wildlife.
The American River Basin Development Act of 1949 created the American River Division
(Division) of the CVP that consists of the Folsom and Auburn-Folsom South Units. Construction
of Folsom Dam was completed in May 1956 and Nimbus Dam and power plant, located 6.8 river
miles (RM) downstream from Folsom Dam, were completed in 1955. Nimbus Dam re-regulates
water released from Folsom Dam and diverts water into the Folsom South Canal.
Prior to construction of Folsom and Nimbus dams, the U.S. Fish and Wildlife Service (USFWS)
prepared “a plan of action for the conservation of salmon and steelhead affected by the
construction of Nimbus Dam on the American River” (USFWS and CDFG 1953).
Based on the recommendations contained in this plan, Nimbus Fish Hatchery (NFH) was
constructed and placed into operation in 1955 on the American River approximately 15 miles east
of Sacramento, approximately one mile downstream from Nimbus Dam, at RM 22.
The Nimbus winter steelhead program traps and artificially spawns adipose fin-marked adult
steelhead that seasonally enter the trapping facilities. Broodstock was originally derived from
several different founding populations and appears to cluster genetically with Eel River steelhead.
Nielson et al. (2005) reported that genetic analysis of the fish sampled for the American River
and NFH indicated genetic similarity in microsatellite allelic frequencies. Garza and Pearse
(2008) reported similar results for fish sampled from the lower American River and NFH.
The purpose of the program is to replace lost adult production above Nimbus Dam and below
Folsom Dam. To achieve this purpose, the program has a juvenile release goal of 430,000
yearling steelhead (4 fish per pound). It is operated as a segregated program in that no naturalorigin steelhead are used as broodstock.
Steelhead in the Central Valley were identified as a Distinct Population Segment (DPS) and listed
in 1998 as a threatened species under the US Endangered Species Act (1973). In 2006, NMFS
reaffirmed the threatened status of the Central Valley steelhead because the resident and
anadromous life forms of steelhead remain “markedly separated” as a consequence of physical,
ecological and behavioral factors (NMFS 2009). The DPS includes all naturally spawned
anadromous O. mykiss (steelhead) populations below natural and manmade impassable barriers in
the Sacramento and San Joaquin rivers and their tributaries, as well as hatchery produced
steelhead at the Coleman National Fish Hatchery and the Feather River Fish Hatchery. Naturally
spawned steelhead in the American River are included in the DPS; steelhead spawned and reared
at Nimbus Fish Hatchery are excluded (NMFS 2009).
1.1
Programmatic Components
Construction of Folsom and Nimbus dams eliminated anadromous fish access to all historical
habitats in the American River. NFH helps to fulfill mitigation requirements for construction of
Nimbus Dam as described in “Contract between the United States and the State of California for
the Operation of the Nimbus Fish Hatchery” (Reclamation 1956). Steelhead produced at Nimbus
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are not intended to enhance or benefit survival of listed steelhead populations, and program
operations are conducted to minimize adverse effects on listed fish. This is an isolated-harvest
program (i.e., does not include natural-origin steelhead in the broodstock) that propagates fish for
recreational fishing opportunities and harvest. Steelhead are not produced to spawn in the wild or
to be genetically integrated with any specific natural population. The program has no established
goals for the number of hatchery-origin fish allowed to spawn naturally.
On average, the program has released approximately 422,000 yearling steelhead since brood year
1999. The total estimated steelhead return to the river (spawning naturally and in the hatchery)
has ranged from 946 to 3,426 fish, averaging 2,184 fish from 2002 to 2010. The number of fish
harvested since the 2002-03 spawning year has averaged 474 (see Appendix A-3). Yearling to
adult survival rates have averaged 0.54% since 2002 (Appendix A-3). The proportion of the
naturally spawning population consisting of hatchery fish has been estimated to be greater than
90% from 2002 to 2010 (Appendix A-3).
1.2
Operational Components
Water for NFH comes from the American River watershed. Specifically, flows are released from
Folsom Lake into Lake Natoma, from when the hatchery is supplied by a 1,415-foot-long,
primary 60-inch concrete pipe and a secondary 42-inch-diameter parallel concrete pipe that runs
from the south abutment of Nimbus Dam. The secondary 42-inch pipeline is an emergency backup supply if the primary supply pipeline becomes unavailable. Both lines are connected through
a series of gate valves that allow water to be directed into three areas as needed, a water head box
collection structure, the American River Trout Hatchery, or directly to NFH. The volume of
water used at NFH ranges between 20 and 50 cfs. Water supplied to either hatchery is not recirculated or exchanged.
In most years, the temperature of water delivered to NFH is suitable for salmonid rearing.
However, when inflow to Folsom Lake is low or reduced, the supply of cold water in the
reservoir may be limited, resulting in marginal water temperatures to the hatchery and the
American River. This has the greatest affect on summer juvenile fish rearing (steelhead) and
results in a later fish ladder opening date.
To minimize the effects of water level fluctuations on flow in the supply line, the CDFG installed
an electronically operated gate at the head box collection structure. A series of manually operated
valves control flow from the head box to pipes leading to the rearing ponds, hatchery buildings,
and the domestic water supply.
1.2.1
Facilities
NFH facilities include a fish weir, fish ladder, gathering and holding tanks, hatchery buildings,
rearing ponds, various office, shop, and storage buildings, fish transportation equipment, and
miscellaneous equipment and supplies. A 1,600-square-foot metal building supports the NFH
office, employee break room, and public restrooms.
Weir: A weir was included as part of the original design of the hatchery (Romero et al. 1996).
Currently, the weir is installed to direct Chinook salmon into the fish ladder and is removed at the
end of the salmon run and before large rain events occur in late fall.
Ladder: A 260-foot-long concrete fish ladder provides access from the river to the NFH
spawning building. Approximately 40 cfs is directed into the fish ladder.
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The fish ladder is opened after the weir is installed and river temperatures are at or below 60° F in
early November, and remains open through late March. Once fish ascend the ladder they enter
the 60-foot-long by 12-foot-wide gathering tank at the top of the ladder. After entering the
gathering tank, a hanging bar trap prevents downstream return.
Gathering Tank and Holding Ponds: A mechanical fish crowder can be moved to the far end
of the gathering tank to push the fish through a hatch into a lift basket.
Adjacent to the fish ladder are four concrete holding ponds. Each pond is 100 feet long, 14 feet
wide and 6 feet deep and is capable of holding approximately 800 adult salmon or steelhead. The
current practice is to return sexually immature steelhead to the river after sorting, so the holding
ponds are not used for steelhead.
Sorting Area and Spawning Deck: The spawning deck provides facilities for handling,
inspecting, sorting, and spawning adult salmon and steelhead. Trapped fish are lifted from the
gathering tank to the spawning deck by a hydraulic fish lift. After the fish are electrically
narcotized, they are lifted from the gathering tank to a stainless steel sorting table where they are
inspected for marks, tags, and sorted based on sexual maturity. Fish not retained for spawning
can be returned to the holding ponds or river via one of five 15-inch-diameter stainless steel
tubes. Chinook salmon are not typically returned to the river but retained in one of the holding
ponds.
Rearing Facilities: NFH rearing facilities include two hatchery buildings and six outdoor
raceways. Hatchery building 2 is an 8,000-square-foot metal building with a concrete floor,
constructed in 1992. The building includes a small laboratory and the spawning deck for
inspecting, sorting, and spawning fish. A separate area is used for processing eggs, and egg
incubation facilities.
The egg incubation facilities in hatchery building 2 include 12 fiberglass deep tanks, each 20 feet
long, 4 feet wide, and 30 inches deep, and capable of holding 16 modified commercial Eagar
hatching jars or 16 constructed PVC egg hatching jars. Each hatching jar is capable of holding
approximately 800 ounces of eggs. The egg hatching facilities also include thirty-six 16-tray
vertical incubators with a capacity of approximately 10,000 eggs per tray. Water for the jars and
incubators is supplied through overhead PVC plumbing.
Hatchery building 1 is a 13,000-square-foot metal building. It is the original hatchery building
constructed in 1955 and houses 68 fiberglass deep tanks similar to those described in NFH
Building 2. Water is supplied to the deep tanks via overhead PVC plumbing and directed into 4foot-long by 18-inch-diameter vertically hung PVC filled with plastic Bio Barrels to remove
gases (nitrogen) and aerate the water.
Three pairs (6) of concrete rearing ponds (or raceways) are located on the east side of the
hatchery grounds. Each raceway is 400 feet long, 10 feet wide, and 42 inches deep (water depth),
and is capable of holding approximately 90,000 gallons. A flow of approximately 1.5 to 3.5 cfs
of water (depending upon the size and number of fish) is typically released from the rearing pond
head tank. Each raceway can be divided into seven individual rearing areas.
Water enters the head tank from an underground distribution conduit where the rate of flow is
adjusted with a 24-inch gate valve. Water is passed over a perforated metal plate to capture
unwanted debris prior to entering the raceway. After passing through the raceway, water enters a
collection area and is transported via an underground 10-inch diameter steel pipe to a pair of
Page 3
settling ponds located approximately 1,700 feet downstream from NFH grounds on the south side
(left bank) of the river. Water from the settling ponds percolates through a gravel and rock
substrate into the river.
A 20-foot tall chain link fence with wire mesh covering surrounds the raceways and functions as
a bird exclosure.
1.2.2
Broodstock
Broodstock for NFH has come from fish trapped in the American River as well as non-indigenous
sources. Due to the small number of eggs collected and fish reared in the early years of
operation, broodstock was subsequently collected from numerous non-indigenous sources. From
1958 through 1993, steelhead eggs were transferred from sources that included the Eel River,
Coleman Hatchery, Battle Creek, Warm Springs Hatchery, Dry Creek, Russian River; and Mad
River Hatchery. All of these stocks were described as summer, winter or late-run steelhead.
The genetic makeup of the present NFH winter steelhead has been examined. Cramer et al.
(1995) suggested that based on the transfers of eggs from the Eel River and run timing, the NFH
winter steelhead stock is similar to Eel River winter steelhead. Nielsen et al. (2005) concurred
that NFH winter steelhead were genetically most similar to Eel River stock. They examined
genetic variations at 11 microsatellite loci to describe the population genetic structure of
Oncorhynchus mykiss in the Central Valley and also indicated that the clustering of rainbow trout
populations from the upper portions of the Tuolumne, Stanislaus, American, and Yuba rivers.
These genetic similarities could be due to two factors: (1) shared ancestry among native, ancestral
populations not influenced by hatchery steelhead or other anadromous populations downstream
from the four dams found on these rivers; or (2) the influence of introduced rainbow trout from
hatchery populations that have been stocked extensively in reservoirs throughout California.
Garza and Pearse (2008) reported that in general, although structure was found, all naturally
spawned populations within the Central Valley were closely related, regardless of whether they
were sampled above or below a known barrier to anadromy.
Steelhead have been trapped at NFH as early as the first week of October; however, since 2000,
the ladder has been opened in early November. The peak of the steelhead run at NFH is generally
the later part of December, but may vary by several weeks. Steelhead have been trapped as late
as the second week of March. During the past 10 years, in an effort to ensure steelhead are
represented from throughout the run, the trap has been kept open longer and fish spawned later
during the season. Adult steelhead are artificially spawned at NFH slightly earlier than steelhead
that spawn naturally in the river. This is due to the practice of artificially spawning the fish rather
than an actual difference in spawning timing. Earlier spawning results in earlier hatching
steelhead eggs and ultimately slightly larger fry compared to fish that spawn naturally.
Prior to 2001, the percentage of naturally spawned steelhead in NFH broodstock is unknown.
Since 1999, all hatchery-origin juveniles have been marked. Information on the number of
unmarked steelhead included in the broodstock is not available prior to the 2008-2009 season;
however, since then, only marked hatchery-origin steelhead have been used as broodstock.
During the past 10 years, the majority of adult steelhead trapped at NFH appeared to be three
years of age (personal communication, T. West, CDFG, Hatchery Manager II). A small number
of half-pounder size fish are trapped each year at NFH. Half-pounders are sexually immature
steelhead that return to freshwater after only a few months in the ocean. In the 2000-2001 to
2009-2010 trapping seasons, 1,442 (annual mean of 68) half-pounder size fish were reportedly
Page 4
trapped. Many may be hatchery-origin juveniles that did not migrate to the ocean and have taken
on resident rainbow trout coloration and life history characteristics.
From 1955 to 2009, the percentage of male steelhead trapped varied from 33 to 71% (mean of all
years 54%); but only during 15 years (28% of the 53 years) has the number of females exceeded
the number of males (Figure 1).
The weir is generally installed in September and the fish ladder opened after river water
temperatures are sustained at or below 60° F. This occurs prior to the fall Chinook salmon run
and prior to steelhead entering the American River. The weir is removed in December at the
conclusion of the fall Chinook run. Some steelhead may be trapped prior to weir removal but
they are returned to the river.
The Nimbus fish ladder and trap remain open until the end of the steelhead run, typically around
the end of March. The ladder is accessible to any upstream migrating fish. All steelhead that
enter the adult gathering tank are sorted a minimum of once each week during the run, examined
for marks, and the degree of sexual maturity determined. Only marked fish greater than 16 inches
are retained for broodstock. All fish less than 16 inches are immediately returned to the river.
Steelhead adults are not held at the hatchery. All unmarked fish are returned to the river with a
caudal fin notch. All marked sexually mature adult steelhead are retained for artificial spawning
and typically are spawned a minimum of once a week. Sexually immature marked adult
steelhead are immediately returned to the river after receiving a caudal fin notch. If recaptured,
these steelhead receive a second mark and are processed as before. Experience has demonstrated
that sexually immature adult steelhead held at NFH are subject to disease, injury, and high
mortality (greater than 40% in some years). Only sexually mature adipose fin-marked steelhead
are selected for spawning. All mating and pairing of adult fish is done randomly and no attempt
is made to select fish for any morphological characteristic. After spawning, all live adult
steelhead receive a caudal fin mark and are returned immediately to the river. In some years, fish
length, scales and tissue samples are collected on natural-origin adults prior to release; however,
results are not supplied to the hatchery.
Page 5
3,000
Males
Females
Number of steelhead
2,500
2,000
1,500
1,000
500
19
55
19 195
58 6
19 195
61 9
19 196
64 2
19 196
67 5
19 196
70 8
19 197
73 1
19 197
76 4
19 197
79 7
19 198
82 0
19 198
85 3
19 198
88 6
19 198
91 9
19 199
94 2
19 199
97 5
20 199
00 8
20 200
03 1
20 200
06 4
20 200
09 7
-2
01
0
0
Season
Figure 1.
Number of female and male steelhead trapped at Nimbus Hatchery, 1955 to 2010.
Adipose fin-marked fish less than 16 inches may be non-migrant hatchery-origin fish and
unmarked sexually mature fish less than 16 inches are most likely resident trout. Since the 20002001 trapping season when all the returning hatchery-origin steelhead would have been adipose
fin-marked, 514 unmarked steelhead (2.9%) were reported trapped (Table 1).
Table 1.
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Number and percentage of unmarked steelhead trapped at the Nimbus Fish Hatchery,
2000-2001 through 2009-2010 seasons.
Season
Number of
Steelhead
Trapped
Number of
Marked
Steelhead
Number of
Unmarked
Steelhead
2000-2001
2001-2002
2002-2003
2003-2004
2004-2005
2005-2006
2006-2007
2007-2008
2008-2009
2009-2010
Total
Mean
2,877
1,742
887
1,862
2,772
2,308
2,684
758
1,095
987
17,972
1,797
2,813
1,692
818
1,835
2,755
2,218
2,626
711
1,037
953
17,458
1,746
64
50
69
27
17
90
58
47
58
34
514
51
Percent of
Marked
Steelhead
(2.2%)
(2.9%)
(7.8%)
(1.5%)
(0.6%)
(3.9%)
(2.2%)
(6.2%)
(5.3%)
(3.4%)
(2.9%)
(2.8%)
A steelhead broodstock goal has not been established for NFH; however, an annual release of
430,000 yearling steelhead has been the accepted mitigation for construction of Nimbus Dam.
Based on historical survival rates from green egg to juvenile fish released, hatchery personnel
take approximately 2 million green eggs. Based on a 10-year average of approximately 5,500
eggs per female, approximately 365 females and a similar number of males are required for
broodstock.
During the past 10 years, NFH has trapped an annual average of 1,797 steelhead and egg
collection has met the 2 million green egg goal. Additional steelhead have been spawned
throughout the season to ensure that sufficient eggs are taken throughout the run to meet both the
mitigation goal and to represent the entire run timing.
1.2.3
Spawning
Only sexually mature adipose fin-marked adult male steelhead (≥ 16 inches) are spawned.
Selection is done randomly (e.g., all sexually mature male fish have an equal chance of being
selected).
Air spawning described by Leitritz and Lewis (1976) is used to collect steelhead eggs. A single
male fish is randomly selected from the trapped fish and sperm expressed in to the pan with eggs.
A 1:1 male to female mating scheme is used; back-up males are not used. After eggs are
fertilized, they are washed in fresh water, drained in a colander, placed in a bucket with fresh
water and transferred to hatching jars or incubators.
All eggs taken and fertilized on a single day are identified as an egg lot and assigned a lot
number. An attempt is made to retain representative egg lots to mimic the natural spawning
period of winter steelhead from the American River. No surplus eggs are intentionally taken at
NFH; however, as part of efforts to mimic the natural run and spawning period, some eggs may
become surplus to the mitigation requirements.
No chemicals or therapeutics are used during the spawning process. Once the eggs have been
fertilized and washed, eggs are immersed for 20 minutes in a solution with PVP Iodine to help
eliminate pathogens. PVP-Iodine is effective against a broad spectrum of disease-causing
microorganisms and is used to kill bacteria, viruses, fungi, protozoa, and yeasts on contact. PVP
iodine is also applied to eggs during incubation to control fungus.
1.2.4
Incubation
During the 2000-2002 through 2009-2010 seasons, an average of 1,729,633 steelhead eggs were
taken from 320 females for an average of 5,913 eggs per female (Table 2). These eggs resulted in
an average of 1,416,061 eyed eggs with a 10-year average survival rate to the eyed stage of
82.1%.
Table 2.
Season
2000 - 2001
2001 - 2002
2002 - 2003
Number of female steelhead spawned and number of eggs taken 2000-2001 through
2009-2010 seasons.
Number of
Total
Mean
Number of
Female
Number of
Number of
Eyed Eggs
Percent
Steelhead
Eggs
Eggs per
Produced
Spawned
Collected
Female
431
2,043,545
4,741
1,696,142
83.0%
190
1,168,244
6,149
946,278
81.0%
170
1,060,490
6,238
943,836
89.0%
Page 7
Season
2003 - 2004
2004 - 2005
2005 - 2006
2006 - 2007
2007 - 2008
2008 - 2009
2009 - 2010
Total/Mean
Number of
Female
Steelhead
Spawned
163
578
422
630
145
218
248
320
Total
Number of
Eggs
Collected
1,000,120
2,580,366
2,154,768
2,891,666
1,063,649
1,680,002
1,653,479
1,729,633
Mean
Number of
Eggs per
Female
6,136
4,464
5,106
4,590
7,336
7,706
6,667
5,913
Number of
Eyed Eggs
Produced
770,092
2,327,490
1,943,601
1,937,416
811,564
1,554,002
1,230,188
1,416,061
Percent
77.0%
90.2%
90.2%
67.0%
76.3%
92.5%
74.4%
82.1%
All steelhead eggs are placed in modified hatching jars with a maximum loading density of 300
ounces of eggs per jar. Hatching jars are not used for smaller egg lots or for egg lots that would
not fill the hatching jars to a minimum of 50%. In these instances, vertical stacked tray
incubators may be used. The maximum loading density for each vertical tray is 150 ounces. All
eggs incubated in the vertical trays and hatching jars remain until 90% of the alevins have
absorbed their yolk sacks (buttoned-up). When the majority of eggs have hatched, all the
remaining eggs and alevins are carefully poured into the deep tanks.
During incubation, fresh water is circulated through the hatching jars through a hose attached to
the bottom, allowing water to travel up through the eggs and overflow out the top. Water
temperature during steelhead egg incubation can range from 46°to 55° F. Hatched fry are
allowed to escape from the hatching jars into the deep tanks.
Eggs may be culled in any given year to achieve juvenile release targets. Once the total egg take
is known, the same percentage of eggs from each lot are removed and discarded.
1.2.5
Rearing
At NFH, deep tanks are capable of holding approximately 1,500 gallons of water, although the
depth is varied from egg hatching through rearing. At maximum depth, each tank can hold
approximately 70,000-75,000 steelhead fry at a density of about 50 fish per gallon.
After hatching, steelhead alevins remain in deep tanks until they reach a weight of 30 to 80 fish
per pound at which time they are move to the concrete raceways. Fish density in the tanks varies
based on water temperature and size of fish, but due to the number of ponds and number of
juvenile steelhead, is not a limiting factor at NFH. Once the steelhead fry are free swimming and
feeding, the depth of the water in each of the deep tank is slowly increased from 10 inches to 27
inches to prevent overcrowding. Fry remain in the deep tanks for approximately 6 months until
they reach 250-300 to the pound, at which time they are moved to raceways for the remainder of
their rearing period.
Each raceway is capable of holding approximately 85,000 steelhead fry (0.95 fish per gallon) and
approximately 75,000 yearling-sized juvenile steelhead (0.8 fish per gallon). Final rearing
loadings (FI) are estimated to be 1.0 lbs/gpm/inch at 4 fpp and 3.5 cfs. Juvenile steelhead remain
in the raceways until they are released.
Page 8
After the steelhead alevins have absorbed their yolk sac, they are placed on a diet of semi-moist
fish food for five months. For the remaining 9 months, they are fed a dry, floating pellet food
with a packet of Vitamin A added. Fry are fed up to 12 times per day. Juvenile fish in the
hatchery buildings are hand fed while juvenile fish in the raceways are fed using a blowermounted feeder that is driven past the raceway. Juvenile steelhead are inventoried to determine
number and weight at least every two weeks but may be inventoried weekly, particularly if the
water is over 55° F and the fish are growing rapidly. The feed schedule is adjusted each time the
weight counts are made to minimize food waste and solid accumulation. In general, fish growth
is slowed in the summer months to prevent fish from getting too large. Fish routinely are not fed
prior to handling (i.e., moving them to another pond, loading them onto trucks for release and
tagging) to minimize stress, mortality, and expulsion of excess solids.
To help improve the health of juvenile steelhead reared in raceways, 50% (200 feet) of each
raceway was experimentally covered with shade cloth in 2007. Observations suggested that the
incidence of dorsal fin erosion and sunburn in juvenile steelhead was reduced (personal
communication, T. West, Hatchery Manager II, April 2011). Fish health is routinely monitored
by the CDFG’s Fish Health Laboratory personnel and biosecurtiy procedures followed by NFH
personnel. Disease treatments are recommended by a fish pathologists and a veterinarian
assigned to the Fish Health Laboratory.
1.2.6
Release
Presently, all juvenile steelhead are released in the American River approximately one mile
upstream from the confluence with the Sacramento River (at Jibboom Street).
Since 1955, NFH has released approximately 16 million fingerling and 17 million yearling
steelhead in anadromous waters within the Central Valley. With the exception of 2008,
fingerling-size fish have not been released since 1994 (Figure 2). Fingerling releases occurred in
2008 to reduce the number of juvenile steelhead reared at NFH in anticipation of high hatchery
water temperatures.
Page 9
1,400,000
1,200,000
Fingerling
Yearling
Number of fish
1,000,000
800,000
600,000
400,000
200,000
0
7 0 3 6 9 2 5 8 1 4 7 0 3 6 9 2 5 8
95 196 196 196 196 197 197 197 198 198 198 199 199 199 199 200 200 200
1
56 959 962 965 968 971 974 977 980 983 986 989 992 995 998 001 004 007
9
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2
Season
Figure 2.
Number of fingerling and yearling size steelhead released from Nimbus Fish Hatchery,
1956-1957 to 2007-2008.
Yearling-size steelhead are released at approximately four fpp (Appendix A-3) from January
through March at Jibboom Street below most of the fall Chinook spawning habitat. Specific
release dates depend on fish size, and equipment and personnel availability. Regardless of size,
juvenile steelhead are not held past March 30th due to increasing hatchery water temperatures and
to encourage springtime outmigration.
If releases occur during periods of low flow in the Sacramento River and possibly the American
River, some juveniles migrate back to NFH. These fish may take up residency and contribute to a
resident trout population. Anglers often report catching smaller half-pounder adipose fin-marked
steelhead in the lower American River in the fall and spring.
Additionally, juvenile fish are released in February and early March to coincide with closures of
the Delta Cross Channel Gates from February 1 through May 20. Releasing fish when the gates
are closed reduces straying into the Delta. When possible, releases of NFH-produced steelhead
coincide with higher flow releases (>30,000 cfs) in the Sacramento River to encourage outmigration and increase survival.
All juvenile steelhead are certified disease-free by CDFG fish pathologists prior to release.
Certification procedures are described in the CDFG’s operation manual. Diagnostic procedures
for pathogen detection follow American Fisheries Society standards as described in Thoesen
(1994). No acclimation procedures are conducted prior to fish release.
Page 10
2
Populations Affected by the Hatchery Program
The potential effects of the Central Valley steelhead hatchery programs, including the NFH
program, on natural populations of salmon and steelhead in the Central Valley are reviewed
below. The following summarizes the major programmatic issues, with emphasis on the NFH
steelhead program.
The California Central Valley steelhead Distinct Population Segment (DPS) is listed as threatened
under the federal Endangered Species Act and includes all naturally spawned populations of
steelhead and their progeny in the Sacramento and San Joaquin rivers and their tributaries,
excluding steelhead from San Francisco and San Pablo bays and their tributaries. Existing
naturally-produced stocks are mostly confined to the upper Sacramento River and its tributaries.
Recent monitoring in the San Joaquin River subbasin has detected steelhead presence in the
Stanislaus, Mokelumne, and Calaveras rivers at low levels (Good et al. 2005).
Steelhead can be divided into two life history types, summer run and winter run, based on their
state of sexual maturity at the time of river entry and the duration of their spawning migration.
Only winter steelhead are currently found in Central Valley rivers and streams (McEwan and
Jackson 1996), although there are indications that summer steelhead were present in the
Sacramento River system prior to large-scale dam construction in the 1940s (Interagency
Ecological Program [IEP] Steelhead Project Work Team 1999).
Central Valley steelhead exhibit flexible reproductive strategies that allow for persistence in spite
of variable flow conditions (McEwan 2001). Peak adult migration into the river historically
occurred from late September to late October (Hallock 1989 in Moyle et al. 2008). Emergent fry
migrate into shallow water areas; by late summer and fall, juveniles move into higher velocity,
deeper, mid‐channel areas (Everest and Chapman 1972, Fontaine 1988, and Hartman 1965, all in
Moyle et al. 2008). Age data from a sample of 100 fish taken in 1954 indicated that steelhead
spent one (29%), two (70%), or three (1%) years in freshwater before migrating to the ocean as
smolts (Hallock et al. 1961). This migration generally occurs from late December through the
beginning of May, with a peak in mid‐March (Moyle et al. 2008).
Central Valley steelhead habitat requirements during the freshwater residence time include cool,
clear, and well oxygenated water (Moyle 2002). Juveniles (ages 1+ and 2+) occupy deeper water
than fry and show a stronger preference for pool habitats with ample cover, as well as for rapids
and cascade habitats (Dambacher 1991). Preferred habitat for juveniles generally includes large
structures that provide feeding opportunities, segregation of territories, refuge from high water
velocities, and cover from fish and bird predators (Moyle et al. 2008).
The Central Valley steelhead DPS also includes artificially propagated steelhead stocks from
Coleman National Fish Hatchery on Battle Creek and from the Feather River Hatchery. The
Nimbus Hatchery (American River) and Mokelumne River Hatchery steelhead stocks were
excluded from the DPS. These stocks represent highly introgressed mixtures of various stocks
(McEwan and Jackson 1996). Over the period 1957 to 1993, nearly three million eggs and
juveniles were transferred to Nimbus Fish Hatchery from the Snow Mountain Egg Collection
Station and Cedar Creek Hatchery, Eel River, CA; the Coleman National Fish Hatchery, Battle
Creek, Sacramento River tributary; Warm Springs Hatchery, Dry Creek, Russian River, CA; and
Mad River Hatchery, Mad River, CA, as well as summer‐run fish from the Washougal River
(Skamania stock) in Washington and the Siletz River in Oregon (Lee and Chilton 2007; U.S.
Bureau of Reclamation 2008).
Page 11
Coleman National Fish Hatchery, Feather River Hatchery, Nimbus Hatchery, and Mokelumne
River Hatchery produce about 1.5 million yearling steelhead annually based on current
production goals (CDFG 2008). All four hatcheries were originally constructed to mitigate for
habitat lost to dam construction. In 1998, Coleman National Fish Hatchery modified its
operations to emphasize conservation (USFWS 2001). All of these hatcheries release yearling
smolts (approximately 4 fish per pound) at downstream locations in January and February during
the natural outmigration period.
In the NMFS 2005 status update for the Central Valley Steelhead DPS, the biological review
team considered the DPS in danger of extinction or likely to become endangered. Abundance,
productivity, and spatial structure were of greatest concern, although genetic and life history
diversity was also considered a risk factor (Good et al. 2005). Although abundance data for
steelhead are scarce, Central Valley steelhead have shown a negative growth rate pattern since the
late 1960s, and limited evidence suggests that this pattern has continued (Lindley et al. 2007).
Hallock et al. (1961) estimated the average population in the 1960s to be 20,540 adult steelhead
in reaches upstream of the Feather River. Steelhead counts at the Red Bluff Diversion Dam
(RBDD) declined from an average of about 8,000 in 1967 to 1977, to an average of about 2,000
in the early 1990s. The estimated total annual run size for the entire Sacramento-San Joaquin
system, based on RBDD counts, was no more than 10,000 adults (McEwan and Jackson 1996,
McEwan 2001). All of the abundance numbers above include hatchery-origin adult escapement.
A major cause of historic declines in steelhead abundance and their present status has been the
loss of access to much of their historical spawning and rearing habitat above impassable dams,
which have blocked access to more than 80% of historic steelhead spawning and rearing habitat
(Lindley et al. 2007). Other major threats include degradation of remaining habitat and threats to
the genetic integrity of wild populations from hatchery steelhead production (Moyle et al. 2008).
The genetic integrity of Central Valley steelhead is affected by past and present hatchery
practices, habitat fragmentation, and population declines that have resulted in small, isolated
populations that are subject to inbreeding, loss of rare alleles, and genetic drift (NMFS 2009).
Naturally spawning populations occur in the Feather, Yuba, American, and Mokelumne rivers,
but these populations have had substantial hatchery influence and their ancestry is unclear (Busby
et al. 1996). Steelhead runs in the American and Feather rivers are largely sustained by Nimbus
and Feather River hatcheries. Overall, hatchery-origin fish appear to comprise the majority of the
DPS (Lindley et al. 2007). Nobriga and Cadrett (2003) used Delta fish monitoring data to
estimate that the overall Central Valley spawning escapement currently is comprised of 63% to
77% hatchery‐origin fish. There is evidence that the proportion of hatchery‐origin steelhead in
the spawning escapement of the four rivers with hatchery programs is comparable (Battle Creek,
Feather River, American River, and Mokelumne River). There may, however, be a number of
populations with only minor hatchery influence. For example, no adipose‐clipped steelhead were
observed during 2003 to 2007 kayak and snorkel surveys in Clear Creek, for which mean
escapement during those five years was estimated to be 290 (U.S. Fish and Wildlife Service
2007b). Of 12 steelhead observed in a counting weir on the Stanislaus River in the 2006‐07
counting season, only one was observed to be adipose‐clipped (Anderson et al. 2007).
NMFS and CDFG (2001) concluded that the genetic integrity and population viability of natural
stocks of Central Valley steelhead have been diminished by increases in the proportion of
hatchery fish relative to naturally produced fish, the use of out-of-basin stocks for hatchery
production, and straying of hatchery produced fish. However, an accurate assessment of the
viability of the DPS is not possible with available data and is confounded by the unknown effect
of resident fish on the viability and persistence of steelhead populations (Lindley et al. 2007).
Page 12
There is still evidence of local genetic structure, but recent analyses of the genetic structure of O.
mykiss populations in the Central Valley indicate that steelhead propagation has had a significant
effect on natural stocks (Garza and Pearse 2008). Clustering of below-barrier populations with
northern California coastal stocks suggest that out-of-basin transfers of Eel River steelhead to
Nimbus Hatchery, and subsequent transfers and straying in the Central Valley, has resulted in
widespread introgression of this stock. Clustering of above-barrier populations with one another,
and their position relative to other California stocks, indicate that these populations may most
closely represent the ancestral population genetic structure of Central Valley steelhead (Garza and
Pearse 2008).
The principal mechanisms by which the hatchery stocks may affect the genetic integrity of wild
fish include the capture of native fish that might otherwise spawn in natural waters, the rearing of
fish in artificial channels and ponds that cause a preferential selection for traits beneficial in the
hatchery environment but that reduce their ability to survive in natural conditions in their streams
of origin, and the interbreeding of fish exhibiting hatchery‐selected genetic traits with the wild
fish population. These mechanisms may result in two types of genetic hazards to wild salmon and
steelhead populations: loss of genetic diversity within and among populations, and reduced
fitness of a population affecting productivity and abundance. Araki et al. (2008) summarized a
number of studies that reported a loss of reproductive success (fitness) of hatchery fish in nature.
For example, Araki et al. estimated that fitness of steelhead decreases almost 40% per generation
of hatchery culture. Some populations may be more affected than others due to a variety of
factors such as the length of exposure to the hatchery environment, the use of non‐local stocks in
the hatchery brood stock, the degree of habitat fragmentation, the degree of interbreeding, and the
reproductive success of hatchery fish in the wild population.
The potential for predation and competition between hatchery‐reared and naturally produced
salmonids depends on the degree of spatial and temporal overlap, differences in size and feeding
habitats, migration rate and duration of freshwater residence, and the distribution, habitat use, and
densities of hatchery and natural juveniles (Mobrand et al. 2005). Recently, concern has been
expressed about the potential for hatchery‐reared salmon and steelhead to prey on or compete
with wild juvenile salmonids and the impact this may have on threatened or endangered salmonid
populations (Williams 2006). Hatchery steelhead present a greater risk to natural populations
because they are relatively large at release and a relatively high portion can residualize, providing
more opportunities for them to compete for resources and prey on naturally produced salmon and
steelhead throughout the year (Kostow 2009). All Central Valley hatcheries release yearling
smolts (approximately 4 fish per pound) at downstream locations in January and February during
the natural outmigration period. The potential for these hatchery fish to prey on juvenile fall and
spring Chinook salmon exists because this period coincides with peak emergence and
downstream dispersal of salmon fry (January–March) from upstream spawning areas. The
potential for competitive interactions between hatchery steelhead produced by Feather River,
Nimbus, and Mokelumne River hatcheries and naturally produced steelhead is considered low
because all hatchery releases are made below the primary steelhead rearing areas in these
tributaries.
2.1
Current Conditions of Affected Natural Populations
The Nimbus Hatchery steelhead program has the greatest potential to affect natural reproduction
of steelhead has the greatest potential to affect natural steelhead reproduction in the American
River watershed. Steelhead occurrence in the American River is described below, followed by a
summary of other Central Valley watersheds that may support steelhead.
Page 13
2.1.1
American River Steelhead
The lower American River watershed begins at Folsom Dam and flows approximately 30 miles to
its confluence with the Sacramento River near downtown Sacramento. Folsom Dam creates
Folsom Lake, which provides flood protection for the Sacramento area; irrigation, domestic,
municipal, and industrial water supply; hydropower; recreational opportunities; and flows
stipulated to protect fish and wildlife. Folsom Lake out-flow is re-regulated by Nimbus Dam
before passing through the floodplain and urbanized Sacramento area. The reach runs through
the highly urbanized Sacramento area, it is buffered by the 30-mile-long American River
Parkway, which extends 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. 1
Historically, the lower American River supported summer- and winter-run steelhead. Summer
steelhead typically entered the river between May and July, and winter-run between December
and April. Both of these populations had access to approximately 125 miles of spawning and
rearing habitat in the upper reaches of the American River. Since the early 1900s, access has
been impeded by dams constructed for mining debris containment, flood control, and water
supply diversions. Many of these dams had inadequate or no fish ladders. Construction of
Folsom and Nimbus dams in 1955 permanently blocked upstream passage at RM 23, and
reportedly blocked all of the historic steelhead spawning habitat. By 1955, it is believed that
summer-run steelhead were extirpated from the American River and only a remnant population of
the winter-run steelhead remained. Fall-run steelhead may be present in the American River, but
are likely strays from the Sacramento River.
From 1956 through the late 1980s, the Nimbus Hatchery has propagated eggs of steelhead strains
from other locations in California and Washington, planting the fry into the lower American
River. Phenotypic expression of steelhead in the lower American River most closely resembles
that of the historic winter-run strain of American River steelhead and the winter-run strain of Eel
River steelhead.
Natural production of steelhead in the American River will continue to be limited due to
inaccessibility of the headwaters. The majority of observed spawning occurs within five miles of
Folsom Dam. The proportion of hatchery-origin fish spawning in the river remains uncertain. It
is known, however, that the majority of the steelhead returning to the hatchery and river are of
hatchery origin.
The hatchery sees returns of both mature hatchery and natural-origin half-pound steelhead. The
prevalence of this life history in the natural environment is not known.
From 2001to 2007, one to eight percent of the adult steelhead entering Nimbus Hatchery were
natural-origin (unclipped) fish (Table 3). Surveys showed around 300 steelhead spawning in the
river each year compared to hatchery returns during the same years of 1,200 to 2,700 fish
(Hannon and Deason 2005, as cited in Bureau of Reclamation 2008). Many of the in-river
spawners were hatchery produced fish. Spawning density is higher in the upper seven miles of
accessible habitat, but spawning also occurs downstream in the lowest riffle in the river at
Paradise Beach (Bureau of Reclamation 2008).
1
http://www.sacriver.org/documents/2010/Roadmap/American_LowerAmerican.pdf
Page 14
Table 3.
Year
2001
2002
2003
2004
2005
2007
Adipose clip status of adult steelhead entering Nimbus Hatchery.
Number of
Number
Percent
Steelhead Entering
Unclipped
Unclipped
Nimbus Hatchery
2,877
64
2.2%
1,742
50
2.9%
887
69
7.8%
1,862
27
1.5%
2,772
17
0.6%
2,308
90
3.9%
Source: Bureau of Reclamation (2008)
The American River does not have a robust resident trout population. The steelhead model
indicates that the river should produce primarily steelhead smolts due to high growth rates (fish
can get to 300 mm in one year) (Satterthwaite et al. 2010).
2.1.2
Other Central Valley Steelhead Populations
There is evidence that Nimbus Hatchery steelhead may stray throughout the Central Valley and
spawn naturally in other streams where hatcheries are not present. Both juvenile releases and
hatchery strays from Nimbus have the potential to affect naturally spawning steelhead in other
watersheds. The status (viability), distribution, and abundance of steelhead in the Central Valley
were compiled by the NMFS (2009) in the draft Chinook and Steelhead Recovery Plan, which is
summarized in Table 4 in geographic order from north to south. In summary, steelhead
distribution and abundance data is generally lacking in the Central Valley. Out of the 25 Central
Valley watersheds ranked for their current viability potential to support local naturally
reproducing populations, only Clear, Battle, Antelope, Mill, and Deer creeks scored “High”.
Each of these streams is a tributary to the Upper Sacramento River, although steelhead adults and
progeny recently have been documented sporadically throughout the Central Valley. Overall
watershed habitat conditions and steelhead abundance and distribution are described further in
Appendix B by each major watershed where substantial recent steelhead abundance data exists or
where data are lacking, but general consensus is that significant natural steelhead production
currently occurs.
Table 4.
Steelhead status, abundance and habitat availability in the Central Valley (NMFS 2009).
Viability
Potential1
Known Steelhead Distribution
Upper
Sacramento
River
LowModerate
Mainstem Sacramento River
and accessible minor tributaries
downstream of Keswick Dam
(RM 302) to its confluence with
the Feather River.
Clear Creek
High
18.1 miles of accessible habitat
downstream of Whiskeytown
Dam (RM 18.1)
Cow Creek
Moderate
Several accessible tributaries,
but distribution unknown
Watershed
Abundance
Abundance unknown.
Steelhead spawning and rearing is known to occur and is
influenced by Coleman NFH returns, but abundance data
has not been collected since counting at Red Bluff Diversion
Dam was discontinued. Recent otolith analysis documented
that less than 50% of age 1 and 2 O. mykiss sampled were
steelhead progenyz
Abundance unknown.
Spawner abundance has been inferred from redd counts,
which varied from about 100 to 700 between 2003 and
2009.
Abundance unknown.
Surveys conducted in South Cow Creek in 2002
documented 7 adult steelhead and 2 possible redds
Page 15
Viability
Potential1
Cottonwood
/Beegum
creeks
Moderate
Several accessible tributaries,
but distribution unknown
Battle Creek
High
Dry Creek
Low
Watershed
50 miles of accessible habitat
after planned restoration
projects completed
Spawning/rearing is possible in
Secret and Miners ravines, but
distribution is unknown.
Antelope
Creek
High
20 miles of suitable spawning
habitat
Mill Creek
High
25 miles of suitable spawning
habitat
Moderate
Flashy flows and high gradient
limit distribution, which is largely
unknown.
Deer Creek
High
Accessible reaches downstream
of Deer Cr. Falls, with 25 miles
of suitable spawning habitat.
Stony Creek
Low
of Black Butte Dam (RM 24)
Thomes
Creek
Big Chico
Creek
LowModerate
Butte Creek
Moderate
Lowermost 24 miles of Big
Chico Creek are accessible
of Quartz Bowl Falls provide 53
miles of accessible habitat
Abundance
Abundance unknown.
Small steelhead runs are known to occur, but no abundance
data is available. There is widespread distribution of O.
mykiss in watershed.
Coleman NFH steelhead program present; natural-origin
adult escapement above the hatchery weir averaged 398
adults/year from 2001-2007 (min = 225, max = 593).
No steelhead conclusively documented, although O. mykiss
are present.
Abundance unknown.
Observations of 47 adults and 52 redds in 2001 in 53% of
accessible habitat; 140 adults counted in 2007 at new fish
ladder at Edwards Diversion. There is reported to be a high
density of O. mykiss throughout watershed.
Abundance unknown.
Observations of 280 adults 1980, 34 adults in 1993 (Clough
Dam counts), 15 adults and 31 redds in 2001 in 3-4% of the
accessible habitat.
Abundance unknown.
Steelhead use has not been documented; however, O.
mykiss were reported as abundant in 1982.
Abundance unknown.
Reportedly high O. mykiss density. Recent otolith analysis
documented over 75% O. mykiss sampled were steelhead
progenyz
Abundance unknown.
Spawning not been documented, although some rearing
use of the lower river may occur sporadically.
are present.
Abundance unknown.
Steelhead reported by CDFG wardens in angler catches.
Abundance unknown.
A minimum of 108 adults and 75 redds counted in 2003.
Hatchery fish are present from the Feather River Hatchery
program.
Abundance unknown.
Recent O. mykiss otolith analysis in lower Yuba R. show
most are residents, but steelhead progeny were detected
(~40% of age 2 fish)z
Feather
River
Moderate
of Oroville Project – Fish Barrier
Dam (RM 67)
Yuba River
Moderate
of Englebright Dam (RM 24)
Bear River
Low
of South Sutter Irrigation District
diversion dam (RM 15)
Steelhead may spawn in high flow years. They likely
originate from the Feather River Hatchery program.
Auburn
Ravine/
Coon Creek
Low
Distribution unknown
are present.
American
River
Low
of Nimbus/Folsom Dam
complex (RM 23)
Nimbus Hatchery steelhead program present; 1-6% of adult
returns to Nimbus Hatchery were natural-origin and ̴300
spawners/year (2001-2007).
Page 16
Watershed
Viability
Potential1
Abundance
Putah Creek
Moderate
of Putah Diversion Dam (RM
23)
Mokelumne
River
Low
of Camanche Dam (RM 29.6)
Calaveras
River
Moderate
of New Hogan Dam (RM 42)
when flows allow
Stanislaus
River
LowModerate
of Goodwin Dam (RM 58)
Tuolumne
River
LowModerate
of La Grange Dam (RM 54)
Merced
River
LowModerate
of Crocker-Huffman Dam (RM
52)
Low
Distribution unknown
Abundance unknown.
Steelhead were sporadically reported to occur downstream
of Putah Diversion Dam, but these reports are unconfirmed.
An average of 36 redds/year reported from 2001-2010
(max= 61, min = 3). Hatchery fish present from Mokelumne
Hatchery program, but excluded from upper river by
hatchery weir.
Abundance unknown.
A few steelhead carcasses and redds have been
documented, but abundance is unknown and may be
hatchery strays. O. mykiss are reportedly abundant.
Recent otolith analysis documented over 30% O. mykiss
sampled were steelhead progenyz.
Abundance unknown.
12 steelhead documented at a counting weir in 2007.
Recent otolith analysis documented about 10% O. mykiss
sampled were steelhead progenyz.
Abundance unknown.
Generally low abundance of O. mykiss downstream of La
Grange Dam. No documentation of steelhead spawning.
Recent otolith analysis documented less than 10% O.
mykiss sampled were steelhead progenyz.
Abundance unknown.
O. mykiss present, recent otolith analysis documented
about 1 of 23 O. mykiss sampled was steelhead progenyz
Abundance unknown.
Steelhead use not documented or suspected.
Upper San
Joaquin
Source: NMFS (2009) Draft Recovery Plan, Appendix A – Central Valley Watershed Profiles
Table Notes:
1 = Ranking from NMFS (2009) of potential to support self sustaining local population in watershed.
Z = Zimmerman et al. (2009)
2.2
Long–term Goals for Natural Populations
The draft recovery plan for Central Valley steelhead has a goal of maintaining a natural spawning
population of steelhead in the reach extending from approximately the Nimbus Fish Hatchery
Weir downstream to approximately Watt Avenue (NMFS 2009).
NMFS has classified American River steelhead as a Core 2 population. Core 2 populations must
meet the following moderate risk extinction criteria:

Census population size is 250 to 2,500 adults, or the effective population size is 50 to 500
adults

Productivity: Run size may have dropped below 500, but is stable

No catastrophic events occurring or apparent within the past 10 years

Hatchery influence is moderate or hatchery operates as a conservation hatchery using best
management practices
Page 17
3
Fisheries Affected by the Hatchery Program
3.1
Current Status of Fisheries
American River steelhead are primarily caught in freshwater fisheries. Data from sport catch
records indicate that from 2003 to 2005, sport fishers kept 31 wild steelhead and released 1,809,
while they kept 359 hatchery steelhead and released 1,440 (CDFG 2007). As can be seen from
these data, sport fishers tend to practice a catch-and-release strategy when fishing for steelhead.
Additionally, O. mykiss over 16 inches in length are reported as steelhead when in fact they may
be large resident rainbow trout- a size common in the American River.
An angler survey conducted in 2009-2010 reported that approximately 80,000 steelhead were
caught and released in the American River (Titus 2010). For reporting purposes, O. mykiss in the
American River were considered to be juvenile steelhead (i.e., no distinctions were made between
the anadromous or resident form).
3.2
Long-term Goals for Affected Fisheries
Long-term harvest goals for the fisheries affected by the program have not been established.
4
Programmatic and Operational Strategies to Address Issues
Affecting Achievement of Goals
This section describes programmatic and operational hatchery strategies that could be used in the
American River basin to address issues that potentially affect achieving the goals for the fish
populations.
4.1
Issues Affecting Achievement of Goals
A host of issues exist that might affect fishery, fish production, and conservation goals for the
Sacramento and San Joaquin basins. 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 American River steelhead
populations: What are the expected effects of the Nimbus steelhead hatchery program on VSP
parameters of natural steelhead populations? Can hatchery strategies be updated to enhance the
VSP parameters for the natural populations?
Hatchery stock genetic management: What is the affect of current management on the genetic
diversity of the hatchery stock and the possible affect 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?
Page 18
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
modified to ameliorate these issues?
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 were 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 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 February 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 (BMPs) and a “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 the California HSRG’s 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.
Page 19
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 5.
Broodstock Source.
Standard
Standard 1.1: Broodstock is appropriate to the basin and the
program goals and should encourage local adaptation.
Standard NOT met.
Comment: Out-of-basin broodstock has a potential to
impact the DPS.
Table 6.
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
Comment: The current broodstock for this program
should be replaced with an alternative broodstock that
is appropriate for the American River.
Guideline
Standard met.
Standard 1.3: Collection methods are appropriate for the
program goals.
Standard met.
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 met.
Standard 1.5: Hatcheries have effective facilities for the
extended holding of unripe fish and males that will be used
for multiple spawning.
Standard NOT met.
Comment: Unripe steelhead are not held at this facility.
Page 20
Guideline 1.5.1. Holding facilities in hatcheries should
provide adequate space, water flows and temperature
requirements to hold the expected number of unripe
adult fish for extended periods of time with minimal
hatchery-caused mortality (refer to Senn et al. 1984 for
specific water quality, flow and temperature
parameters).
Guideline 1.5.2. Holding facilities in hatcheries should
permit appropriate antibiotic and/or chemical
treatments when deemed necessary to control adult
mortality or prevent vertical transmission of diseases
to progeny.
Comment: With the current broodstock, all hatcheryorigin adult steelhead returns to the hatchery, whether
spawned or unspawned, should be removed from the
system. With a native broodstock, hatchery-origin
Standard
Table 7.
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.
Guideline
adult steelhead returns to the hatchery should be
treated as follows: (1) unspawned males should be
extended reconditioned and released; (2) unspawned
females should be stripped of eggs, extended
reconditioned and released; and (3) spawned fish
should be removed from the system, or extended
reconditioned and released.
Natural-origin adult steelhead returns to the hatchery,
whether spawned or unspawned, should be released.
Fish may be reconditioned prior to release.
Adult holding facilities should be upgraded and/or
expanded to provide adequate space, water flows and
temperature regimes to hold the number of adults
required for broodstock at high rates of survival (> 90
percent).
Guideline
Consistency with Standard Unknown.
Standard 1.7: The levels of natural-origin broodstock are
appropriate for program goals.
Standard met.
Comment: Although this is intended to be a segregated
program, genetic evidence confirms that Eel River genes are
throughout the Sacramento System.
Standard 1.8: Fish from different runs are not crossed.
Comment: All hatchery steelhead receive an adipose finclip. No hatchery specific marks are applied, so it is not
known if fish from other hatcheries are incorporated into the
broodstock.
Standard 1.9: Steelhead broodstock collection focuses on
the anadromous life history. Integrated steelhead programs
incorporate non-anadromous fish in a proportion not greater
than their natural (pre-disturbance) abundance in the local
Comment: Managers should investigate the feasibility
of collecting natural-origin adult fish at alternate
locations. The existing trapping location is very limited
in its 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.
Guideline 1.8.1. Hatcheries should employ effective
methods to identify fish from different runs and avoid
crossing them. Eggs produced by unintentionally
crossing types should be culled.
Page 21
Standard
population and commensurate with their reproductive
contribution in the naturally spawning population when
known. For segregated programs, only anadromous
broodstock are used.
Standard met.
Table 8.
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.
Standard NOT met.
Comment: In many years the number of females spawned
is less than 250.
Guideline
Comment: Non-anadromous (resident) or unmarked
fish should not be used as broodstock and the current
16-inch minimum length for broodstock should be
continued. This recommendation to not use unmarked
fish will no longer apply once the current broodstock is
replaced.
Guideline
Guideline 1.11.1. For broodstock numbers greater
than or equal to 250 females, matings should be 1
male x 1 female, with each 1:1 spawn in a single
spawning pan. Limit the reuse of males to
unavoidable situations (e.g., where loss of eggs might
result if males are not reused and loss of eggs
threatens program goals).
Guideline 1.11.2. For broodstock number between 50
and 250 females, female’s eggs should be split into 2
egg lots and each lot should be fertilized with a
different male in a separate pan. Limit the reuse of
males to two egg lots (or the equivalent of one
female), except for unavoidable situations (e.g., where
loss of eggs might result if males are not reused and
loss of eggs threatens program goals).
Comment: Recommend an attempt to spawn greater
than 250 females or split egg lots according to
guidelines.
Standard 1.12: Inbreeding is avoided.
Standard met.
Table 9.
Steelhead Spawner Disposition.
Standard
Standard 1.14: For steelhead hatchery programs, the postspawning disposition of mature fish that are collected as
potential broodstock are appropriate to program goals.
Standard NOT met.
Page 22
Guideline
Guideline 1.14.1. Natural-origin fish from integrated
programs will be reconditioned and released if
spawned.
Guideline 1.14.2. Hatchery-origin fish will be disposed
of in a manner consistent with identified program goals
and using methods that result in no or minimal effects
to natural-origin fish.
Comment: With the current broodstock, all hatcheryorigin adult steelhead returns to the hatchery, whether
spawned or unspawned, should be removed from the
system. With a native broodstock, hatchery-origin
adult steelhead returns to the hatchery should be
treated as follows: (1) unspawned males should be
extended reconditioned and released; (2) unspawned
Standard
4.3.2
Guideline
females should be stripped of eggs, extended
reconditioned and released; and (3) spawned fish
should be removed from the system, or extended
reconditioned and released.
Natural-origin adult steelhead returns to the hatchery,
whether spawned or unspawned, should be released.
Fish may be reconditioned prior to release.
Program Size and Release Strategies
Table 10. 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.
Standard NOT met.
Standard 2.2: Program size is measured as adult
production.
Standard NOT met.
Guideline
Guideline 2.1.1. Program purpose should be identified
and expressed in terms of measurable values such as
harvest, conservation, hatchery broodstock, education,
or research.
Guideline 2.2.1. Production goals (program size)
should be expressed in terms of number of adult
recruits just prior to harvest (age-3 ocean recruits for
Chinook salmon in California) or at freshwater entry
(age-3 adults returning to freshwater for coho;
anadromous adults returning to freshwater for
steelhead).
Standard 2.3: Annual assessments are made to determine if
adult production goals are being met.
Standard NOT met.
Comment: No adult production goals have been identified.
Comment: Clear goals should be established for the
program. Program production goals should be
expressed in terms of the number of age-3 ocean
recruits just prior to harvest (Chinook salmon), and the
number of adults returning to fresh water (steelhead).
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.
Comment: Consideration of deleterious ecological effects
on other species is unclear. Few data available for
assessing ecological effects. Non-native broodstock should
not be propagated because of the potential for deleterious
genetic effects.
Guideline 2.4.1. If deleterious ecological or genetic
effects result in substantial reduction of productivity for
high-priority naturally spawning populations, and these
effects cannot be alleviated by other changes,
program size should be reduced. Under certain
circumstances, conservation-oriented programs might
increase program size to eliminate deleterious effects,
for example to reduce inbreeding.
Page 23
Standard
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).
Guideline
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
Table 11. 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 NOT met.
Standard 2.7: Juveniles are released at or in the near vicinity
of the hatchery.
Standard NOT met.
Page 24
Guideline
Guideline 2.6.1. Size and date at release should
generally mimic size and period of emigration of
naturally migrating smolts in the river system on which
a hatchery is located. Deviations from this guideline
require substantial justification that addresses both the
ecological and genetic consequences of such a
strategy, particularly when extended rearing is
proposed. Consider retaining some flexibility in
release date to take advantage of beneficial flow,
turbidity, or temperature conditions without increasing
deleterious ecological effects on natural populations.
Guideline 2.6.4. For steelhead, size (mean and
frequency distribution) and date at release should be
managed to limit residualization or extended rearing
near the release site prior to emigration.
Comment: Investigate release timing to take
advantage of good environmental conditions (flow,
temperature, turbidity, etc.).
Comment: Investigate straying rates for Jibboom
release site. We do not consider a release site 21
miles downstream of the hatchery to be an on-station
release.
Transporting and releasing juveniles to areas outside
of the American River or to the lower American River
should be discontinued. Juvenile fish should be
released at the hatchery, or if not possible, as far
upstream in the American River from the confluence of
the Sacramento River as possible to reduce adult
straying and increase the number of adults returning to
the hatchery. Consider necessary facility
modifications or equipment purchases that will
facilitate on-site releases. Release locations for
steelhead may take into consideration ecological and
predation effects on other fish populations but should
not compromise homing of adults to the hatchery.
4.3.3
Incubation, Rearing and Fish Health
Table 12. 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).
Standard NOT met.
Comment: Current “working” CDFG fish health policy is
inadequate.
Guideline
Guideline 3.1.1. Develop and promulgate a formal,
written fish health policy for operation of DFG
anadromous fish hatcheries through the Fish and
Game Commission policy review process. Such a
policy may be formally identified in regulatory code,
Fish and Game Commission policy, or in the
Department of Fish and Game Operations Manual.
Comment: CDFG should develop and promulgate a
formal, written fish health policy for operation of its
anadromous hatcheries through the Fish and Game
Commission policy review process. Hatchery
compliance with this policy should be documented
annually as part of a Fish Health Management Plan.
The current CDFG fish health policy is inadequate to
protect native stocks.
CDFG should develop an updated Hatchery
Procedure Manual which includes performance criteria
and culture techniques presented in IHOT (1995), Fish
Hatchery Management (Wedemeyer 2001) or
comparable publications. The fish culture manual
(Leitritz and Lewis 1976) is outdated and does not
reflect current research and advancements in fish
culture.
Page 25
Table 13. Hatchery Monitoring by Fish Health Specialists.
Standard
Guideline
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.
Standard met.
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 NOT met.
Comment: Diagnostic exams alone do not meet the
standard.
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.
Comment: Unknown due to lack of fish health
documentation.
Standard 3.5: Examinations of fish are conducted prior to
release or transfer to ensure fish are in optimum health
Page 26
Guideline 3.3.1. The frequency of monitoring should
depend on the disease history of the facility, the
importance of the species being reared, and the
variable environmental conditions that occur in a
particular rearing cycle (e.g., elevated water
temperatures in spring and summer months).
Guideline 3.3.2. Review fish culture practices with
manager including nutrition, water flow and chemistry,
loading and density indices, handling methods,
disinfection procedures, and preventative treatments.
Guideline 3.3.3. The number of fish examined is at
the discretion of the fish health specialist.
Guideline 3.4.1. Re-occurring mortality, or repeated
use of antibiotics or chemicals to control mortality,
generally indicates that underlying fish culture,
nutritional or environmental problems are not being
fully remediated and should be further investigated.
Guideline 3.5.1. Review transportation protocols with
appropriate hatchery staff to ensure fish are handled
Standard
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.
documentation.
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 NOT met.
Comment: Current annual report information is inadequate.
Standard 3.7: Fish health status of stock is summarized prior
to release or transfer to another facility.
documentation.
Table 14. Facility Requirements.
Standard
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 NOT met.
Comment: In some years, elevated summertime water
temperatures limit production capabilities due to limited
Guideline
and hauled in a manner that minimizes stress and
provides the best opportunity for survival.
Comment: For state hatcheries, a more thorough
assessment of smoltification is recommended prior to
release.
Guideline 3.6.1. Include an annual fish disease
assessment for each program in the hatchery annual
report (see Standard 3.14).
Guideline 3.7.1. Written reports should include
findings of monitoring and laboratory results. For fish
transfers, feeding regime and current growth rate, and
any other information necessary to assist fish culturists
at the receiving station, should be provided.
Comment: For state hatcheries a more thorough
assessment of smoltification is recommended prior to
release.
Guideline
Guideline 3.8.1. Facilities and equipment should
allow: effective capture and holding of adults,
appropriate incubation and rearing units with adequate
capacity to meet program size, equipment and/or
methods for effective predator control, and release of
fish without undue stress or harm. (see Section 4.1.1,
Broodstock Management for additional adult holding
requirements).
Guideline 3.8.2. Hatchery managers, fish health
specialists, biologists and fish culturists should identify
facility/equipment deficiencies that constrain hatchery
operations and/or prevent the facility from meeting
program goals. Such facility deficiencies or
constraints should be communicated to resource
managers for remedy or redress.
Guideline 3.8.3. When physical facility and/or
equipment needs exist, resource managers and
appropriate funding source(s) should actively pursue
facility maintenance, upgrades or equipment needs
Page 27
Standard
rearing facilities.
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 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 NOT met.
Comment: Fish spawning, egg incubation, and early
rearing areas are not adequately separated.
Standard 3.10: All hatchery water intake systems follow
federal and state fish screening policies.
Guideline
through a prioritized budget process. In the interim,
modifications should be made to program goals to
minimize adverse impacts to fish culture and/or fish
health.
Comment: An alternative cold-water source should
be developed to reduce summer rearing water
temperatures.
Guideline 3.9.1. Use dedicated equipment and rain
gear that is not moved between adult spawning,
incubation and rearing areas of the hatchery;
otherwise, thoroughly scrub and disinfect gear when
moving between these areas.
Guideline 3.9.2. A critical control point is defined as
the physical location where pathogen containment
occurs from a "dirty" to a "clean" area (i.e., between
functional areas such as spawning and incubation). In
addition to egg disinfection, ensure that spawning
buckets/trays are surface-disinfected before entering
incubation area.
Comment: Develop the hatchery operational plan
(specific Fish Culture Procedures), a Fish Health
Management Plan, the hatchery coordination team
process, and/or in annual written reports. Install
physical barriers and follow biosecurity measures.
Guideline 3.10.1. Follow existing statutes, including
NEPA, CEQA, ESA, CESA, and current court
decisions.
Standard NOT met.
Comment: CDFG statewide fish screening policy provides
that under the provisions of the USFWS Coordination Act,
the CDFG shall require the installation of fish screens on all
Page 28
Standard
unscreened diversions where fish are present (i.e., hatchery
intake).
Table 15. 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
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 16. 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
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: Elevated summer temperatures constrain
production and lead to early fish release.
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,
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.
Comment: Explore options for reducing summertime
water temperatures instead of addressing through
reduced rearing densities.
Page 29
Table 17. Best Management Practices.
Standard
Standard 3.14: The rationale, benefits, risks, and expected
outcomes of any deviations from established best
management practices 2 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.
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.
Standard NOT met.
Guideline
Guideline 3.14.1. Develop required plans.
Comment: Develop the hatchery operational plan
(specific Fish Culture Procedures), a Fish Health
Management Plan, the hatchery coordination team
process, and/or in annual reports.
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.
Guideline 3.16.1. Culling should be done to minimize
unintentional selection.
Guideline 3.16.2. Excess eggs are culled in a manner
that does not eliminate representative families or any
temporal segment of the run; and culled in portions
that are representative of the entire run. Culling may
be done to change the variance in family size.
Guideline 3.16.3. Non-representative culling may
occur to achieve specific program goals, but must be
justified based on genetic considerations of
maintaining or rebuilding desired characteristics of the
spawning stock.
Guideline 3.16.4. Eggs, fry, or juvenile fish in excess
of production needs are disposed of in a manner that
is consistent with agency policies on egg culling and
fish disposal and will not be released, and should have
no effects on natural populations.
Guideline 3.16.5. For conservation-oriented
programs, individual reproductive output should be as
close to equivalent as possible, while avoiding
selection for egg size and age at maturity, and not
unduly reducing overall production. These stipulations
generally require that families are kept separate until
staff can move eyed eggs for separate rearing for
specific program types. Avoid loss of within population
2
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 30
Standard
Comment: The lack of an egg inventory prevents
assessment of survival by life stage.
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 NOT met.
Guideline
diversity resulting from reduced effective population
size in the hatchery stock.
Comment: Guideline 3.16.2 not always followed.
The cause of the low egg-to-juvenile release survival
rate (24.5 percent) should be determined. It is
suspected that the low value is a result of egg-culling
practices; however, this cannot be confirmed because
of the way data are collected and reported.
Guideline 3.17.1. Feeding practices should supply
feed at a rate that is quickly consumed by juvenile fish,
and does not permit excess feed to accumulate in
rearing units. Excess or uneaten food has a high
potential to increase organic loads in the rearing unit
that can lead to fish pathogen amplification and
disease outbreaks.
Guideline 3.17.2. Fish Health specialists should be
promptly contacted when fish feeding behavior
appears abnormal or when fish stop feeding.
Guideline 3.17.3. Stress induced infections or
diseases, related to crowding or high rearing densities,
should be minimized to promote optimal growth, and
to avoid excessive use of therapeutics (antibiotic
medicated feed or chemical treatments).
Guideline 3.17.4. Rearing strategies will optimize the
physical layout and use of rearing units at the facility to
minimize handling of juvenile fish for inventory,
transfer between rearing units, or tagging purposes.
Preferably, fish are placed in units that allow adequate
space and flows to permit extended periods of growth
with no handling.
Guideline 3.17.5. Steelhead size at release should
follow guidelines established in IHOT 1995 (Table 16,
Chapter 4-Hatchery Performance Standards Policy),
or guidelines established through program-specific
experimental management strategies, but should not
substantially alter the natural maturation schedule of
the population from which broodstock originate.
Comment: Guideline 3.17.4 is not always followed.
Feeding strategy should not include maintenance
feeding rates. It is desirable to have an accelerated
growth strategy prior to release to promote
smoltification.
Performance standards for each phase of the fish
culture process should be established and tracked
annually. Summaries of data collected with
comparisons to established targets must be included
in annual hatchery reports.
Page 31
4.3.4
Monitoring and Evaluation
Table 18. 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: There is a completed older draft. An updated
HGMP is under development.
Table 19. 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.
Standard NOT met.
Comment: Hatchery lacks a Monitoring and Evaluation
Program.
Table 20. Hatchery Coordination Teams.
Standard
Standard 4.3. A Hatchery Coordination Team has been
created for each hatchery.
Standard NOT met.
Comment: Hatchery lacks a Hatchery Coordination Team.
Page 32
Guideline
Guideline 4.2.1. Hatchery Monitoring and Evaluation
programs should be outside the direct hatchery line-ofcommand so they have a large degree of
independence and autonomy from decisions made at
the hatchery level. Program member expertise should
include fish biology, population ecology, genetics, field
sampling methods, experimental design and survey
sampling strategies, database creation and
management, and statistical analysis. Descriptions of
specific monitoring and evaluation programs may be
included as part of HGMPs.
Comment: A Monitoring and Evaluation Program
should be developed and implemented and a Hatchery
Coordination Team formed for the program.
Implementation of these processes will inform
hatchery decisions and document compliance with
best management practices defined in this report.
Guideline
Guideline 4.3.1. Hatchery Coordination Teams should
be comprised of hatchery managers, hatchery
biologists/fish culturists, monitoring and evaluation
biologists, fish health specialists, regional fish
biologists, and fishery managers.
Table 21. 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
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,
Page 33
Standard
including monitoring of treatment efficacy.
k) Report CWT releases and recoveries to relevant
databases (i.e., RMIS) on a timely annual basis.
Standard NOT met.
Comment: In-hatchery data are generally lacking for a
number of important biological criteria. Program does not
assess rate of anadromy used in steelhead broodstock.
Table 22. Marking and Tagging Programs.
Standard
Standard 4.7: Steelhead marking and tagging programs
allow for:
a) Estimation of freshwater fishery impacts and natural area
and hatchery escapements,
b) Estimation of the proportion of hatchery-origin fish in
natural spawning areas,
c) Real-time visual identification of hatchery-origin juveniles
and adults (i.e., hatchery vs. non-hatchery origin),
d) Real-time identification of Nimbus hatchery-origin adults
from other hatchery-origin steelhead as long as broodstock
derived from out-of-basin sources is used,
e) Identification of stock of origin for hatchery fish.
Guideline
Comment: Performance standards for each phase of
the fish culture process should be established and
tracked annually. Summaries of data collected with
comparisons to established targets must be included
in annual hatchery reports.
Guideline
Guideline 4.7.1. All broodstock should be genotyped
as part of a parentage-based tagging (PBT) program.
Guideline 4.7.3. All Nimbus Hatchery juvenile fish
released should receive an additional distinguishing
external mark (non-adipose fin clip) or CWT until a
native broodstock is established.
Standard NOT met.
Comment: There is no genetic monitoring program and no
coded wire tag data to identify stock of origin for hatcheryorigin returns.
Comment: Because Nimbus steelhead currently are
not part of the Central Valley steelhead Distinct
Population Segment, all fish should be uniquely
identifiable through application of a unique external
mark (in addition to an adipose fin clip) or tag, until a
native broodstock is established. This additional mark
will ensure that if these fish return to another hatchery,
they can be excluded from its broodstock.
Table 23. Post-Release Emigration Monitoring.
Standard
Guideline
Standard 4.9: The quantities listed below are monitored in
the freshwater environment following release of juvenile
steelhead. Summaries of collected data and associated
estimates, along with comparisons to established targets,
are included in periodic (every 5 to 10 years) reports
produced by the monitoring agencies/entities.
Page 34
Standard
a) Assess residualization (permanent freshwater residence).
b) Assess extended rearing (following release) prior to
ocean entrance.
Guideline
Standard NOT met.
Comment: Information on juvenile NORs and HORs, post
release, is unavailable.
Table 24. Adult Monitoring Programs.
Standard
Standard 4.12: Monitoring programs for steelhead allow
estimation of the following on an annual or periodic (every 5
to 10 years) basis:
a) Annual: Freshwater recreational and tribal catch, ideally
by hatchery and brood year,
b) Annual: Hatchery returns by age and stock,
c) Annual: Total escapement to individual tributaries
important for natural production,
d) Annual: Proportion of hatchery-origin fish among natural
area spawners (pHOS), at the stock-specific level, in
individual tributaries important for natural production,
e) Periodic: Proportion of adult hatchery returns that have
exhibited an anadromous life history.
Guideline
Standard NOT met.
Comment: An estimated percent of first generation
hatchery and natural fish on the spawning grounds is not
known. Catch in the Sacramento River cannot be separated
between other Central Valley steelhead programs.
Table 25. Evaluation Programs.
Standard
Standard 4.15: Evaluation programs for steelhead estimate
the following attributes on an annual basis:
a) Age-specific freshwater adult returns (and half-pounders
in the Klamath/Trinity Basin), in order of the following
preference:
• River catch and catch-and-release adult mortality
plus tributary returns of adults plus hatchery returns
of adults,
• Tributary returns of adults plus hatchery returns of
adults,
• River catch and catch-and-release adult mortality
plus hatchery returns of adults,
• Hatchery returns of adults.
b) At facilities where kelts are reconditioned and released,
determine the survival (return for subsequent spawning) of
Guideline
Page 35
Standard
Guideline
reconditioned and released kelts.
Evaluation programs for steelhead assess the following
fundamental issues on a periodic basis (i.e., every 5 to 10
years):
c) The relationship of life history patterns (age at return,
tendency to exhibit half-pounder life history pattern in the
Klamath/Trinity Basin, residualization) to hatchery rearing
and release practices with a focus on size and age at
release.
d) 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.
e) Spatial and temporal overlap and relative sizes of
emigrating juvenile hatchery and natural-origin fish (including
juvenile salmon) and total (hatchery- plus natural-origin)
spawner distribution and densities to assess the likelihood or
magnitude of deleterious effects of hatchery-origin fish on
naturally spawning fish due to competition, predation, or
behavioral effects.
Standard NOT met.
4.3.5
Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial
Organisms.
Table 26. 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.
Comment: The relationship between the hatchery and
restoration efforts in the American River is unknown.
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 NOT met.
Page 36
Guideline 5.2.2. Consider screening needs of facility
water supply intakes in non-anadromous waters to
protect other ESA or CESA listed organisms. Design
and operation of facility water diversion/supply
structures also needs to consider operational flexibility
to avoid catastrophic facility water loss due to debris
loading or other failure.
Standard
Guideline
Guideline 5.2.3. Barrier weirs should effectively block
adult passage either for broodstock
congregation/collection or as required for in-river
fishery management.
Comment: The requirements for screening of the water
supply for the protection of species in the reservoir is
unknown.
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 NOT met.
Comment: Working conditions during weir installation,
operations, and removal are dangerous.
5
Literature Cited
Anderson, J., C. Watry, and A. Gray. 2007. Upstream Fish Passage at a Resistance Board Weir Using
Infrared and Digital Technology in the Lower Stanislaus River, California 2006−2007 Annual
Data Report. Cramer Fish Sciences. Prepared for: U.S. Fish and Wildlife Service Anadromous
Fish Restoration Program Grant No. 813326G004.
Araki, H., B. Cooper, and M. S. Blouin. 2007. Genetic Effects of Captive Breeding Cause a Rapid,
Cumulative Fitness Decline in the Wild. Science 318(5847): 100.
California Department of Fish and Game (CDFG). 2007. California Steelhead Fishing ReportRestoration Card. A Report to the Legislature.
Cramer, S.P., D.W. Alley, K. Baldridge, D.B. Demko, B. Farrell, J. Hagar, T.P. Keegan, A. Laird, W.T.
Mitchell, R.C. Nuzum, R. Orton, J.J. Smith, T.L. Taylor, P.A. Unger, and E.S. Van Dyke. 1995.
The status of steelhead populations in California in regards to the Endangered Species Act. Final
report submitted for the Association of California water agencies, submitted to the National
Marine Fisheries Service on behalf. Portland, OR. 190 p.
Garza, J.C. and D. E. Pearse. 2008. Population genetic structure of Oncorhynchus mykiss in the
California Central Valley. Final report for California Department of Fish and Game Contract #
PO485303. University of California, Santa Cruz and NOAA Southwest Fisheries Science Center.
California Department of Fish and Game, Sacramento CA. 54 p.
Page 37
Good, T.P., R.S. Waples, and P. Adams (editors). 2005. Updated status of federally listed ESUs of West
Coast salmon and steelhead. U.S. Dept. Commerce, NOAA Tech Memo., NMFS-NWFSC-66,
598 p.
Hatchery Scientific Review Group (HSRG). 2010. Columbia River Hatchery Reform System-Wide
Report. Prepared by the Hatchery Scientific Review Group.
Kostow, K. 2008. Factors that contribute to the ecological risks of salmon and steelhead hatchery
programs and some mitigating strategies. Rev. Fish. Biol. Fisheries. 2008.
Lee, D.P. and J. Chilton. 2007. Hatchery and Genetic Management Plan for Nimbus Fish Hatchery
Winter-Run Steelhead Program. California Department of Fish and Game.
Leitritz, E. and E. Lewis. 1976. Trout and Salmon Culture (Hatchery Methods). California Department
of Fish and Game Fish Bulleting 164. 197 p.
Lindley, S., A. Low, D. McEwan, B. MacFarlane, T. Swanson, J. Anderson, B. May, J.
Williams, S. Greene, C. Hanson (Central Valley Technical Recovery Team). 2007.
Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and
Steelhead in the Sacramento-San Joaquin Basin. San Francisco Estuary & Watershed
Science 5(1) February 2007. 26 pages.
McElhany, P., M. H. Ruckelshaus, M. J. Ford, T. C. Wainwright, and E. P. Bjorkstedt. 2000. Viable
Salmonid Populations and the Recovery of Evolutionarily Significant Units. NOAA Tech. Memo.
NMFS-NWFSC-42. U.S. Dept. of Commerce. NOAA-National Marine Fisheries Service.156 p.
McEwan, D., and T.A. Jackson. 1996. Steelhead restoration and management plan for California.
Report of the California Department of Fish and Game.
Mobrand, L.E., J. Barr, L. Blankenship, D.E. Campton, T.T.P. Evelyn, T.A. Flagg, C.V.W. Mahnken,
L.W. Seeb, P.R. Seidel, and W.W. Smoker. 2005. Hatchery reform in Washington state:
principles and emerging issues. Fisheries 30(6): 11-23.
Moyle, P. B. 2002. Inland Fishes of California. Berkeley, CA: University of California Press.
Moyle, P.B., J.A. Israel, and S.E. Purdy. 2008. Salmon, Steelhead and Trout in California: Status of an
Emblematic Fauna. University of California, Davis, Center for Watershed Sciences.
National Marine Fisheries Service. 2009. Public draft recovery plan for the evolutionarily significant
units of Sacramento River winter‐run Chinook salmon and Central Valley spring‐run Chinook
salmon and the distinct population segment of Central Valley steelhead.
Nielsen, J.L., S.A. Pavey, T. Wiacek, and I. Williams. 2005. Genetics of Central Valley O. mykiss
populations: drainage and watershed scale analyses. San Francisco Estuary and Watershed
Science 3(2): 31 p.
Nobriga and Cadrett. 2003. Differences among hatchery and wild steelhead: evidence from Delta fish
monitoring programs. Interagency Ecological Program for the San Francisco Estuary Newsletter
14:3:30-38.
Page 38
Romero, J., A. Glickman, and R. Christensen. 1996. Nimbus Fish Hatchery fish rack structure –
modifications. Concept study prepared for the U.S. Bureau of Reclamation. Folsom,
California.65 p.
Satterthwaite, W.H., M.P. Beakes, E.M. Collins, D.R. Swank, J.E. Merz, R.G. Titus, S.M. Sogard and M.
Mangel. 2010. State-dependent life history models in a changing (and regulated) environment:
steelhead in the California Central Valley. Evolutionary Applications ISSN 1752-4571.
Thoesen, J.C. 1994. Bluebook: Suggested Procedures for the Detection and Identification of Certain
Finfish and Shellfish Pathogens, Fourth Edition. American Fisheries Society, Bethesda.
Titus, R. 2010. F-119-R, Central Valley Angler Survey. July 1, 2009 to June 30, 2010.
US Bureau of Reclamation. 1956. Contract between the United States and the State of California for
operation of the Nimbus Fish Hatchery. 3 pages.
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the Central Valley Project and the State Water Project. U.S. Department of the interior, Bureau
of Reclamation, Mid-Pacific Region, Sacramento, California. August 2008.
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plan for the protection and maintenance of salmon and steelhead in the American River,
California, together with recommendations for action. Prepared jointly by U.S. Fish and Wildlife
Service and the California Department of Fish and Game, June 30, 1953. 47 p.
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Page 39
Appendix VIII
Program Report
Appendix A-1
June 2012
APPENDIX A-1
HATCHERY PROGRAM REVIEW QUESTIONS
NIMBUS FISH HATCHERY STEELHEAD
BACKGROUND INFORMATION
1
Name of Hatchery and Program
Hatchery:
Nimbus Hatchery
Program:
Steelhead
2
Species and Population (or stock) under Propagation and ESA Status
Species:
Winter Steelhead
ESA Status:
Not listed
3
Responsible Organization and Individuals
Lead Contact:
David B. Robinson, Environmental Specialist
Bureau of Reclamation Central California Area Office
7794 Folsom Dam Road (CC-413)
Folsom, CA 95630-1799,
(916) 989-7179
FAX (916) 989-7208
drobinson@usbr.gov
Kent Smith, Regional Manager
1701 Nimbus Road
Rancho Cordova, CA 95670
(916) 358-2900
FAX: (916) 358-2912
ksmith@dfg.ca.gov
Nimbus Fish Hatchery Steelhead Program /Appendix A-1 / June 2012
Page A-1 1
Hatchery Manager:
Paula Hoover, Hatchery Manager II
2001 Nimbus Road
(916) 358-2820
FAX: (916) 358-1466
phoover@dfg.ca.gov
Bob Burks, Hatchery Manager I
2001 Nimbus Road
(916) 358-2820
FAX: (916) 358-1466
bburks@dfg.ca.gov
Other Contacts:
4
Funding Source, Staffing Level, and Annual Hatchery Program
Operational Costs
Nimbus Fish Hatchery (NFH) is operated by the CDFG and funding is provided by the US
Bureau of Reclamation to meet mitigation goals for the American River downstream from
Folsom Dam (mitigation requirements as part of the American River Basin Development Act of
October 14, 1949).
NFH staff includes 11.5 permanent employees and the annual operating costs are approximately
$1.4 million. Staff and operating costs are for both the winter steelhead and fall-run Chinook
salmon programs at NFH.
5
Location(s) of Hatchery and Associated Facilities (weirs, etc.)
NFH is located adjacent to the American River approximately 15 miles east of the town of
Sacramento, California, approximately 1 mile downstream from Nimbus Dam, at river kilometer
35.4 (mile 22). Longitude 121.225.4000 W, Latitude 38.633.6000 N.
6
Type of Program
Segregated Harvest Program.
7
Purpose (Goal) of Program
Replace lost adult production above Nimbus Dam (and below Folsom Dam). To do that, the
Nimbus Hatchery produces 430,000 yearling steelhead (4 fpp).
Page A-1 2
8
Justification for the Program
Prior to construction of Folsom and Nimbus dams, the U.S. Fish and Wildlife Service (USFWS)
had the responsibility of “preparing a plan of action for the conservation of salmon and steelhead
affected by the construction of Nimbus Dam on the American River” (USFWS and DFG 1953).
The plan concluded, “The need for a hatchery to mitigate for the construction of Folsom and
Nimbus dams has been recognized for a long time” and the following eight recommendations
were made:
1. A hatchery site be acquired,
2. A permanent fish rack be constructed,
3. Suitable initial water supply be developed,
4. A permanent water supply be provided,
5. An initial hatchery to handle fish eggs is constructed,
6. Consideration be given to testing an artificial spawning channel and stream
improvements,
7. Reclamation construct a permanent hatchery, and
8. Reclamation and DFG enter into an agreement whereby DFG will operate the
hatchery and Reclamation will pay for annual operating costs.
Based on these recommendations, NFH was constructed and placed into operation in 1955.
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.
Page A-1 3
Answer:
No. C. The broodstock is a mixture of several stocks of which the Eel River winter steelhead
genome is predominate.
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.
Choice of a broodstock with a similar life history and evolutionary history to the extirpated stock
improves the likelihood of successful reintroduction.
Answer:
Yes, the stock used was the best available to survive in the re-engineered system. There is
question from NMFS about changing the stock for conservation reasons.
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:
No. There is little to no self sustaining population spawning below the dam. However, TRT
determined American River to have an extant population of steelhead.
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.
Page A-1 4
Answer:
Yes. A history of pathogen incidence is available in Appendix A-3.
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.
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:
Yes.
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, they are enumerated, but natural origin fish are not used in the broodstock.
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:
0.
Page A-1 5
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.
Answer:
N/A. (Dropped due to answer to number 6.)
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. Steelhead are not held at the hatchery. All NORs are returned to the river with a caudal fin
notch. Unripe hatchery origin steelhead are given a notch and returned to the river. All post
spawn steelhead are returned to the river with a caudal notch.
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:
Page A-1 6
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.
Answer:
Hatchery Fish: Yes, number used, m/f ratio, every ripe steelhead that arrives at the hatchery is
spawned. Run time from late November, peak in January, tends to fall off in late February
(winter run).
Wild Fish: Lengths, scales, and tissue samples are taken from natural origin fish (Rob Titus –
Central Valley Surveying) but results are not returned to the hatchery.
No fish less than 16 inches are used as broodstock.
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:
N/A.
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:
No, but numbers are collected for number trapped, number spawned, and eggs produced.
Page A-1 7
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.
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. Eggs have been shipped out, but none brought in. Transplants out go to Mokelumne River
Fish Hatchery.
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:
No. Historically, holding broodstock has resulted in approximately 40% broodstock loss, so all
green fish are returned to the river with a caudal notch. If adult holding is required in the future,
it will likely require facility upgrades.
17
Does the program have guidelines for acceptable contribution of
hatchery-origin fish to natural spawning?
Clarification:
If YES, describe your guidelines.
Page A-1 8
Having established guidelines for acceptable contribution of hatchery-origin fish to natural
spawning provides a clear performance standard for evaluating the program.
Answer:
No.
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:
N/a.
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 are two pipelines from Nimbus Dam that run to the hatchery. Ambient river water.
Most common pathogens are ectobacteria. See pathogen reports and annual health certifications.
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 9
Use of water resulting in natural water temperature profiles for adult holding ensures maturation
and gamete development synchronous with natural stocks.
Answer:
Yes, ambient water. Hatchery water is similar to re-engineered river water. Nimbus does not
provide opportunity for temperature control.
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:
No. There are alarms on the intake pipe that feeds the hatchery, but no alarm specific to adult
holding.
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. There is a second 46 inch pipeline that can be used as a backup.
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.
Page A-1 10
Answer:
Yes, 1:1 mating. There is no selection process. No fish under 16 inches are spawned.
Unmarked steelhead are not used in broodstock.
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.
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.
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).
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:
N/A.
Page A-1 11
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:
N/A.
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. See pathogen reports.
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.
Page A-1 12
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:
No.
31
Is the incubation water supply protected by flow alarms?
Clarification:
Security during incubation is maintained by flow alarms at the incubation units.
Answer:
No. There is an alarm on the hatchery intake, but no alarm specific to incubation flow.
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.
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.
Page A-1 13
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.
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:
No. Families are combined after water hardening. No culling for BKD due to rarity of
occurrence, but would occur if BKD became a problem.
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. Upwelling jars are used, not Heath trays. Flow rates to jars are based on site-specific
successes and best professional judgment.
Page A-1 14
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 – jars are used, not Heath trays.
38
followed for density parameters?
Clarification:
Request information about density recommendations or protocols. What density index is
targeted? Is the facility able to maintain the prescribed Density Index 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, site-specific successes and best professional judgment are used. Jars are 6 inch diameter.
Approximately 40,000 eggs per jar, 20,000-30,000 steelhead/tank.
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, iodophor at water hardening.
Page A-1 15
40
Are eggs culled and if so, how is culling done?
Clarification:
Are eggs from Reni bacterium 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:
Yes, eggs are culled to decrease the number of eggs to exactly what is needed (615,000). All
fish that enter the hatchery are spawned, regardless of egg take target. The total number of eggs
is calculated and the reduction to 615,000 is taken with the same percentage from each jar (if a
general reduction of 48% is needed, 48% is taken from each jar).
40A Additional Question: Would the program benefit by having an ability
to chill or heat incubation water supply?
Answer:
No.
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, see pathogen reports.
Page A-1 16
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, ambient river water.
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.
Answer:
N/A. There is a small amount (1200 ft) of habitat between the weir and the dam.
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:
No. There is an alarm on the hatchery intake, but no alarm specific to rearing.
45
Is the water supply [for rearing] protected by back-up power
Clarification:
Page A-1 17
Security during rearing is maintained by back-up power generation for the pumped water supply.
Answer:
Yes, the 46 inch pipeline.
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.
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. Eggs are culled, no juveniles.
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?
Page A-1 18
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, target size is 4 fpp by February 1. This target changed recently from January to February
due to the Delta CC opening/closing dates.
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?
Feeding to achieve the desired condition factor is an indicator of proper fish health and
physiological smolt quality.
Answer:
No, there is a condition factor calculated during pre-release exam to document, but there is no
standard to be met.
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:
No. Steelhead are slowed down in the summer compared to natural growth patterns.
Page A-1 19
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.
Answer:
No. Predation is managed by bird wire.
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.
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, based on site-specific successes and best professional judgment.
Page A-1 20
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.
Answer:
Yes, based on site-specific successes and best professional judgment.
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. Only one release type, only one release location – Jibboom Street, below most of fall
Chinook spawning area.
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.
Page A-1 21
Answer:
Yes, 4 fpp. Yes, based on site-specific successes and best professional judgment. Historical
research was used to set release size.
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)?
Producing fish that are qualitatively similar to natural fish in morphology may improve
performance and reduce adverse ecological interactions.
Answer:
No. There is a qualitative snapshot done with the pre-release assessment, but no defined
standard.
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, size at time and operational constraints (i.e. water temperature) are the controlling factors in
release timing. The on station release must be released prior to Delta Cross Canal project
opening. There is a qualitative snapshot done with the pre-release assessment, but no defined
standard.
62
Are there protocols for fish growth rates up to release?
Clarification:
Page A-1 22
Answer:
Yes, manage growth to reach size at release. Growth is decreased in the summer to meet 4 fpp in
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?
Answer:
No. There is a qualitative snapshot done with the pre-release assessment, but no defined
standard.
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, 4 fpp yearling smolt. American River natural production is most likely a 1 year old smolt
due to accelerated growth rate.
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.
Page A-1 23
Answer:
No. Fish are trucked to release location (Jibboom Street). There is no way to direct release fish
to river except fish ladder, which would still be forced/pumped.
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?
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. Fish size, water temperature, and water diversions regulate release timing.
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. No releases adjacent to the hatchery. In river plants are released approximately 22 miles
downstream (Jibboom Street).
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?
Page A-1 24
Answer:
Yes, size, type, release methods, number, purpose, and mark groups, but no length frequency is
collected. Data is collected by truck load. Pre-release pathology samples are done on a raceway
basis.
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 impacts to naturally produced fish are considered through selection of appropriate
release sites. Release sites are below the natural spawning areas.
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. All fish are trucked.
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.
Page A-1 25
69B 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, 100% of steelhead are clipped. Half are hand clipped, half are clipped in trailer (with hand
clip for those that are rejected at the trailer). No QA/QC on the hand clipping.
Counts are done at clipping, mortalities are subtracted between clipping 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:
Yes. There are no standards for this area. No standards for non-anadromous fish.
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 26
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:
N/A.
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, autodialer, and/or pagers?
Clarification:
Notification to staff of emergency situations using alarms, autodialers, and/or pagers reduces the
likelihood of catastrophic loss.
Answer:
Yes. Autodialers in the intake structure at the dam.
Page A-1 27
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. Some staff live on site.
76A Additional Question:
procedures manual?
Does the hatchery have an emergency
Clarification:
How are fish handled under emergency scenarios?
Answer:
Yes.
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.
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 28
Answer:
Yes, complete covering with bird wire.
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. The hatchery manager will call pathologists when there is a problem. There is also annual
certification of production and broodstock monitoring to assess presence or absence of
pathogens.
M&E2
Additional Question: Does the program monitor stock
characteristics in relation to the population traits of the ESU?
Clarification:
Answer:
No.
Page A-1 29
M&E3
Additional Question:
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, the HGMP is draft completed, currently being updated. There is an administrative draft.
By June 2011 HGMP should be complete.
M&E4
Additional Question: Is there an ongoing genetic monitoring
program? If so, please describe.
Clarification:
Answer:
Yes. Genetic samples are taken on unmarked fish, but have not been analyzed. Data is not
collected on marked fish or fish used in the hatchery broodstock.
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:
No, no biologist dedicated to M&E. Central Valley Angler Program monitors catch in the
Central Valley.
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, 100% adipose fin clip. Funded by BOR since 1999.
Page A-1 30
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, all fish are marked.
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, 100% of ripe fish are spawned. Run timing is collected at hatchery, as well as scales and
size from unmarked fish.
M&E9
Additional Question: Is there coordination in tagging and
recovery of marks/tags among watersheds, hatcheries and/or other
programs?
Answer:
Marked fish are recorded in the Central Valley Angler Survey. Anecdotal information on high
stray rate.
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
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.
Page A-1 31
This question is used to evaluate the level of hatchery influence on the population.
Answer:
Unknown, no attempt to collect HOR data on spawning grounds.
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:
No – no information.
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.
Explicit standards for survival, size, condition, etc., make it easier to detect culture problems
before they become impossible to rectify.
Answer:
Yes, goals for broodstock collections, egg take and smolt release. Other in hatchery goals are
based site specific past performance.
Page A-1 32
87
Are in-culture performance standards met? How often?
Meeting these standards is assumed to be the best management practice.
Answer:
Yes, more often than not.
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, historical size at release survival studies showed that 4 fpp was more successful than larger
or smaller.
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?
Answer:
Yes. The only post release performance standard specified is adult return to hatchery to achieve
egg take. Using this standard, Nimbus has never not met the standard in the last 10 years.
Page A-1 33
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:
No.
Page A-1 34
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
Nimbus Fish Hatchery, April 11-12, 2011.
Attendee
Affiliation
Dave Robinson
Paula M Hoover
Bob Burks
William Smith
Donovan Ward
Dennis P. Lee
Robyn Redekopp
Andy Appleby
Kevin Malone
USBOR
CDFG
CDFG
CDFG
CDFG
California HSRG/CDFG
Meridian Environmental, Inc.
DJ Warren & Associates
Malone Environmental
Page A-1 35
Appendix VIII
Program Report
Appendix A-2
June 2012
Appendix A‐2 Nimbus Hatchery Steelhead Program Data Tables Table 1. Results of fish pathologist reports for Nimbus Hatchery steelhead, 2007-2010.
Date
Purpose
3/1/2007
Annual
Disease
Certification
Weight Length
(g)
(mm)
6/23/2008
6/23/2008
Condition
Hematocrit Mesenteric
Factor
(%)
Fat Score
(average)
Fingerlings
100/lb
7/1/2008
7/18/2008
Internal
Assessment
44/lb
8/13/2008
External
Assessment
Pathogens
Flavobacterium
columnare
Aeromonad/
Pseudomonad
Flavobacterium
columnare
Aeromonad/
Pseudomonad/
Flavobacterium
columnare
Flavobacterium
columnare
Aeromonad/
Pseudomonad/
Flavobacterium
columnare
Treatment
All tests
negativebacteriology,
WD, BKD,
virology,
ectoparasites
tetramycin
feed/KMnO4
treatments
tetramycin feed
tetramycin feed
tetramycin feed
tetramycin feed
Page A-2 1
Date
Purpose
8/28/2008
Weight Length
(g)
(mm)
Condition
Hematocrit Mesenteric
Factor
(%)
Fat Score
(average)
Internal
Assessment
External
Assessment
34/lb
Flavobacterium
columnare
9/15/2008
6/26/2009
Aeromonad/
Pseudomonad/
Flavobacterium
columnare
pre-release
21.23
6/29/2009
46.2
1.9
Fingerlings
7/20/2009
ulceration
due to
sunburn
4-5 in
8/31/2009
2/16/2010
pre-release
123.3
240.2
0.90
48.7
1.1
6/12/2010
Fingerlings
6/29/2010
unremarkable
6/22/2010
Page A-2 2
Pathogens
Fingerlings
black tail
mortalities
Treatment
tetramycin
feed/KMnO4
treatments
tetramycin
feed/KMnO4
treatments
approved for
release
Flavobacterium
tetramycin
columnare/Costia feed/KMnO4
treatments
tetramycin
Flavobacterium
feed/screen
psychrophilum
covers
Flavobacterium
psychrophilum
Approved for
release
oxytetracycline
Flavobacterium
bath w/ pre salt
psychrophilum
treatments
Aeromonad/
Pseudomonad
KMnO4
Flavobacterium
100 ppm
columnare
oxytetracycline
Nimbus Fish Hatchery Steelhead Program /Appendix A-2 / June 2012 Table 2. Egg to release survival of steelhead reared at Nimbus Hatchery. 2000 - 2009.
Brood
Year
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
Total
Average
Females
Spawned
431
190
170
163
578
422
630
145
218
248
3,195
320
Egg Take
2,043,545
1,168,244
1,060,490
1,000,120
2,580,366
2,154,768
2,891,666
1,063,649
1,680,002
1,653,479
17,296,329
1,729,633
Average
Fecundity
Eyed Eggs
Juveniles
Released1
4,741
6,149
6,238
6,136
4,464
5,106
4,590
7,336
7,706
6,667
59,133
5,913
1,696,142
946,278
943,836
770,092
2,327,490
1,943,601
1,937,416
811,564
1,554,002
1,230,188
14,160,610
1,416,061
599,114
281,705
419,160
455,140
410,330
454,570
394,292
483,290
483,357
439,490
3,821,334
424,593
Egg to
Release
Survival2
29.3%
24.1%
39.5%
45.5%
15.9%
21.1%
13.6%
45.4%
28.8%
26.6%
24.5%
1 Eggs
may have been culled before hatch. Number of eggs culled annually is not available.
2 This percentage includes mortality from culling eggs, and may be lower than hatchery survival in years when culling occurs.
Page A-2 3
Table 3. Actual number, release location and average size of steelhead releases from the Nimbus
Hatchery, 2000-2009.
Brood
Year
Date
Location1
Size
2000
Jan, Feb, and Mar
2001
Sacramento River
yearling
2001
Jun-01
Sacramento River
2001
Jun-01
2002
Fish
Released
Weight
(fpp)
147,500
466,00
3.2
yearling
89,584
281,705
3.1
Sacramento River
fingerlings
3,102
133,114
42.9
Jan and Feb 2003
Sacramento River
yearling
419,160
419,160
4.1
2003
Jan and Feb 2004
Sacramento River
yearling
95,497
455,140
4.8
2004
Jan and Feb 2005
Sacramento River
yearling
97,650
410,330
4.2
2005
Jan, Feb, and Mar
2006
Sacramento River
yearling
96,300
454,570
4.2
2006
Feb and Mar 2007
Sacramento River
yearling
69,230
394,292
5.7
2007
Feb and Mar 2008
Sacramento River
yearling
73,500
483,290
6.6
2008
Jul 2008 and Feb
2009
Sacramento River
yearling
73,392
250,240
3.4
2008
Jul-08
Sacramento River
fingerling
7,193
233,117
32.4
2009
Feb-10
Sacramento/American
Rivers
yearling
119,300
439,490
3.7
yearling
964,653
4,054,217
yearling
96,465
405,422
fingerling
10,295
366,231
fingerling
5,148
183,116
Total
yearling
Average
yearling
Total
fingerling
Average
fingerling
1
Total
Pounds
Marks
Applied
Ad clip Ad clip Ad clip Ad clip
Ad clip Ad clip Ad clip Ad clip Ad clip Ad clip Ad clip Ad clip 4.2
38
All fish are trucked to release sites. There are no releases (volitional or forced) at the hatchery.
Page A-2 4
Nimbus Fish Hatchery Steelhead Program /Appendix A-2 / June 2012 Table 4. Number of steelhead returns to Nimbus Hatchery by sex and age, 2000-2010.
Season
2000 - 2001
2001 - 2002
2002 - 2003
2003 - 2004
2004 - 2005
2005 - 2006
2006 - 2007
2007 - 2008
2008 - 2009
2009 - 2010
Total
Mean
Male
1,412
982
488
999
1,444
1,243
1,396
432
597
514
41,894
762
Female
1,465
760
399
863
1,328
1,065
1,277
326
498
473
37,905
689
Adult
2,877
1,742
887
1,862
2,772
2,308
2,684
758
1,095
987
79,810
1,451
Half
Pounder
17
10
0
25
101
115
11
248
96
9
1,442
69
Half Pounder
Criteria
<22"
<22"
<22"
<22"
<22"
<16"
<16"
<16"
<16"
<16"
Total Fish
Trapped
2,894
1,752
887
1,887
2,873
2,423
2,695
1,006
1,191
996
81,252
1,477
Page A-2 5
Table 5. Annual return of steelhead to the American River, 2002-2010.
Adult
Spawning
Year 1
Yearling
Brood
Year
2002-03
2003-04
2004-05
2005-06
2006-07
2007-08
2008-09
2009-2010
1999
2000
2001
2002
2003
2004
2005
2006
Average
Yearlings
Released
Estimated
In-river
Spawning
Population2
402,300
599,114
281,705
419,160
455,140
410,330
454,570
394,292
427,076
300
343
330
266
300
150
47
46
223
Estimated
Number of
NORs in Inriver
Spawning
Population3
Estimated
Number of
HORs in
In-river
Spawning
Population
25
5
2
14
7
10
3
2
8
275
338
328
252
293
140
45
44
214
Total
HORs
Trapped
818
1,835
2,755
2,190
2,626
711
1,037
953
1,616
Total
NORs
Trapped
69
27
17
118
58
47
58
34
54
Total
Spawning
Escapement
1,093
2,173
3,083
2,442
2,919
851
1,082
997
1,830
Total
Total
Estimated
Estimated
In-river
Harvest 4
Run
122
241
343
271
324
95
731
706
354
1,215
2,414
3,426
2,713
3,243
946
1,813
1,703
2,184
Percent
Return5
0.30%
0.40%
1.22%
0.65%
0.71%
0.23%
0.40%
0.43%
0.54%
Assumes all fish return as 3-year old adult fish.
2 USBR unpublished data.
3 Assumes same ratio of hatchery and naturally produced steelhead in river as trapped at NFH.
4 Assumes 10% harvest rate (Jackson 2007) and steelhead harvest from Titus (2008 and 2009).
5 Number of marked adult/number of yearling fish released 2 years prior.
1
Page A-2 6
Nimbus Fish Hatchery Steelhead Program /Appendix A-2 / June 2012 Table 6. Number of steelhead returns to Nimbus Hatchery by mark, 2000-2010.
Season
2000-2001
2001-2002
2002-2003
2003-2004
2004-2005
2005-2006
2006-2007
2007-2008
2008-2009
2009-2010
Total
Mean
Number of
Steelhead
Trapped
2,877
1,742
887
1,862
2,772
2,308
2,684
758
1,095
987
17,972
1,797
Number of
Marked
Steelhead
(HOR)
2,813
1,692
818
1,835
2,755
2,218
2,626
711
1,037
953
17,458
1,746
Number of
Unmarked
Steelhead
(NOR)
64
50
69
27
17
90
58
47
58
34
514
51
Percentage of
Marked
Steelhead
97.8%
97.1%
92.2%
98.5%
99.4%
96.1%
97.8%
93.8%
94.7%
96.6%
97.2%
Page A-2 7
Appendix VIII
Program Report
Appendix A-3
June 2012
Appendix A‐3 Hatchery Program Review Analysis Nimbus Hatchery Winter Steelhead Benefit‐Risk Statements Question
ID
1
Category
Broodstock
Choice
Question
Does the broodstock chosen
represent natural populations native
or adapted to the watersheds in
which hatchery fish will be released?
2
Broodstock
Choice
Was the best available broodstock
selected for this program?
3
Broodstock
Choice
Does the broodstock chosen display
morphological and life history traits
similar to the natural population?
4
Broodstock
Choice
Does the broodstock chosen have a
pathogen history that indicates no
threat to other populations in the
watershed?
Correct
Answer
Y
Y
Y
Y
Answer
Provided
by
Managers
Benefit
Risk
N
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 non-target stocks.
Y
Choice of a broodstock with a similar
life history and evolutionary history to
the extirpated stock improves the
likelihood of successful reintroduction.
N
Choice of a broodstock with similar
morphological and life history traits
improves the likelihood of the stock's
adaptation to the natural environment.
Y
The broodstock chosen poses no
threat to other populations in the
watershed from pathogen
transmission
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.
The broodstock chosen poses a risk
to other populations in the
watershed from pathogen
transmission
Page A-3 1
Question
ID
Correct
Answer
Answer
Provided
by
Managers
Category
Question
5
Broodstock
Choice
Does the broodstock chosen have
the desired life history traits to meet
harvest goals? (e.g. timing and
migration patterns that result in full
recruitment to target fisheries)?
Y
Y
7
Broodstock
Choice
Do natural origin fish make up less
than 5% of the broodstock for this
program?
NA
Y
10
11
12
Page A-3 2
Broodstock
Choice
Is the percent natural origin fish
used as broodstock for this program
estimated?
Broodstock
Collection
Are adults returned to the river?
Broodstock
Collection
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?
Y
N
Y
Benefit
Risk
The broodstock chosen is likely to
have the life history traits to meet
harvest goals for the target stocks
without adversely impacting other
stocks.
Maintaining a hatchery population
composed of less than 5% natural fish
reduces the risk of loss of among
population diversity.
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
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
Y
Collection of representative samples
of both the natural and hatchery
populations reduces the risk of
domestication and loss of within
Failure to collect representative
samples of both the natural and
hatchery populations poses a risk of
loss of within population diversity
and viability.
Nimbus Fish Hatchery Steelhead Program /Appendix A-3 / June 2012 Question
ID
Correct
Answer
Answer
Provided
by
Managers
Category
Question
13
Broodstock
Collection
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)?
Y
NA
14
Broodstock
Collection
Is the effective population size being
estimated each year?
Y
N
15
Broodstock
Collection
Within the last 10 years, has the
program used only eggs or fish from
within the watershed?
Y
Y
16
Broodstock
Collection
Is the broodstock collected and held
in a manner that results in less than
10% prespawning mortality?
Y
N
17
Broodstock
Collection
Do you have guidelines for
acceptable contribution of hatchery
origin fish to natural spawning?
18
Broodstock
Collection
Are guidelines for hatchery
contribution to natural spawning met
for all affected naturally spawning
populations?
Y
NA
19
Adult Holding
Is the water source [for adult
holding] pathogen free?
Y
N
Adult Holding
Does the water used [for adult
holding] result in natural water
temperature profiles that provide
optimum maturation and gamete
development?
20
Y
Y
N
Y
Benefit
Risk
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.
Maintaining pre-spawning survival
higher than 90% maintains effective
population size and reduces
domestication selection.
Having established guidelines for
origin fish to natural spawning
provides a clear performance standard
for evaluating the program.
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.
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
origin fish to natural spawning
makes program evaluation difficult.
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.
Page A-3 3
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Benefit
Risk
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.
Adult Holding
Is the water supply [for adult holding]
protected by flow alarms?
Y
N
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 singlefamily pairing prior to fertilization?
Y
Y
Single family pairing increases the
effective population size of the
hatchery stock.
25
Spawning
Are multiple males used in the
spawning protocol?
Y
N
Use of back-up males in the spawning
protocol increases the likelihood of
fertilization of eggs from each female.
26
Spawning
Are precocious fish (jacks and jills)
used for spawning according to a set
protocol?
Y
NA
Use of precocious males for spawning
as a set percentage or in proportion to
their contribution to the adult run
promotes within population diversity.
27
Incubation
Is the water source [for incubation]
pathogen-free?
Y
N
Fish health is promoted by the use of
pathogen-free water during incubation.
28
Incubation
Y
NA
incubation.
Y
temperature profiles for incubation
ensures hatching and emergence
timing similar to naturally produced
stocks with attendant survival benefits.
21
29
Page A-3 4
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
Non-random mating increases the
risk of loss of within population
diversity.
Pooling of gametes poses a risk to
maintaining genetic diversity in the
hatchery population.
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.
the lack of pathogen-free water for
incubation.
water for incubation.
profiles may contribute to
domestication selection during
incubation.
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
N
N
Security during incubation is
maintained by flow alarms at the
incubation units.
Y
Security during incubation is
maintained by back-up power
generation for the pumped water
supply.
Incubation
Can incubation water temperature
be modified?
Incubation
Is the water supply [for incubation]
Incubation
Is the water supply [for incubation]
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
N
Incubation
Are agency or tribal species-specific
incubation recommendations
followed for flow rates?
Incubation
followed for substrate?
30
31
32
36
37
Y
Y
Y
Y
Y
Benefit
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.
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.
Risk
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 to
the security of incubating eggs and
alevin.
Absence of back-up power
supply may pose a risk to the
security of incubating eggs and
alevin.
Incubation conditions that result in
unequal survival of all segments of
the population pose a risk of
Not incubating families individually
poses a risk of loss of genetic
variability.
Failing to meet IHOT flow
recommendations during 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.
Page A-3 5
Question
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Y
Proper disinfection procedures
increase the likelihood of preventing
dissemination and amplification of
pathogens in the hatchery.
Lack of proper disinfection
procedures increase the risk of
dissemination and amplification of
pathogens in the hatchery.
Random culling of eggs over all
segments of the egg-take maintains
genetic variability during incubation.
rearing.
temperature profiles for rearing
promotes growth of fish and
smoltification synchronous with
naturally produced stocks.
Providing upstream and downstream
passage of juveniles and adults
supports natural distribution and
productivity of naturally produced
stocks.
Security during rearing is maintained
by flow and/or level alarms at the
rearing ponds.
Non-random culling of eggs
increases the risk of loss of genetic
variability during incubation.
water for rearing.
followed for density parameters?
39
Incubation
Are disinfection procedures
implemented during spawning
and/or incubation that prevent
pathogen transmission within or
between stocks of fish on site?
Y
Y
40
Incubation
Are eggs culled and if so, how is
culling done?
Y
Y
41
Rearing
Is the water source [for rearing]
pathogen free?
Y
N
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?
Y
Y
43
Rearing
Does the hatchery operate to allow
all migrating species of all ages to
by-pass or pass through hatchery
related structures?
Y
NA
44
Rearing
Is the water supply [for rearing]
Y
N
Rearing
Is the water supply [for rearing]
water supply?
Y
Y
42
45
Page A-3 6
Y
Risk
Failing to meet IHOT density
poses a risk to the survival of eggs
and alevin and may not allow for
optimum fry development.
Incubation
38
Benefit
Use of IHOT density
promote survival of eggs and alevin
and allow for optimum fry
development.
Security during rearing is maintained
by back-up power generation for the
pumped water supply.
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.
Absence of back-up power
supply may pose a risk to the
security of the cultured fish.
ID
Category
46
Rearing
47
Rearing
Question
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.
Correct
Answer
Answer
Provided
by
Managers
Risk
Rearing conditions that result in
unequal survival of all segments of
the population pose a risk of
Non-random culling of juveniles
increases the risk of loss of genetic
variability during rearing.
Y
Y
Rearing conditions that result in equal
survival of all segments of the
population reduce the likelihood of
Y
Y
Random culling of juveniles over all
segments of the population maintains
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.
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?
Y
N
50
Rearing
Does the program use a diet and
growth regime that mimics natural
seasonal growth patterns?
Y
N
48
Benefit
Y
Feeding to achieve the desired
condition factor is an indicator of
proper fish health and physiological
smolt quality.
Use of diet and growth regimes that
mimic natural seasonal growth
patterns promote proper smolitification
and should produce adults that
maintain the age structure of the
natural population.
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 quality.
Use of diet and growth regimes that
do not mimic natural seasonal
growth patterns pose a risk to
proper smolitification and may alter
the age structure of the hatchery
population.
Page A-3 7
Question
ID
51
52
53
Category
Question
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?
Rearing
Are fish reared in multiple facilities
or with redundant systems to reduce
the risk of catastrophic loss?
Rearing
54
Rearing
55
Rearing
56
Rearing
57
Rearing
Page A-3 8
Are agency or tribal juvenile rearing
standards followed for flow rates?
Are agency or tribal juvenile rearing
standards followed for density?
For captive broodstocks, are fish
maintained on natural photoperiod to
ensure normal maturation?
For captive broodstocks, are fish
maintained reared at 12C to
minimize disease?
For captive broodstocks, are diets
and growth regimes selected that
produce potent, fertile gametes and
reduce excessive early maturation of
fish?
Correct
Answer
Answer
Provided
by
Managers
Benefit
N
Providing artificial cover increases the
development of appropriate body
camouflage and may improve
behavioral fitness.
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
Y
Following IHOT standards for juvenile
density maintain fish health, growth,
and survival, and increases the
likelihood of preventing dissemination
and amplification of fish pathogens.
Y
NA
Y
NA
Y
NA
Y
Y
Y
Maintaining captive broodstock on
natural photoperiods ensures normal
maturation.
rearing water below 12oC reduces the
risk of loss from disease.
Producing viable gametes and
maintaining age structure of the
population in captive breeding
increases the likelihood of meeting
conservation goals.
Risk
Lack of overhead and in-pond
structure does not produce fish with
the same cryptic coloration or
behavior as do using enhanced
environments.
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 dissemination and
amplification of fish pathogens.
Not following IHOT standards for
juvenile density poses a risk to
maintaining fish health, growth, and
survival, and increases the
likelihood of dissemination and
amplification of fish pathogens.
unnatural photoperiods poses a risk
to normal maturation.
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.
ID
58
59
60
61
62
63
64
Category
Question
Rearing
For captive broodstocks, are families
reared individually to maintain
pedigrees?
Release
Is there a protocol to produce fish to
a set size at release (fpp and
length)?
Release
Are there protocols for fish
morphology at release?
Release
Are there protocols for fish behavior
characteristics at release?
Release
Are there protocols for fish growth
rates up to release?
Release
Release
Are there protocols for physiological
status of fish at release?
Are there protocols for fish size and
life history stage at release?
Correct
Answer
Y
Y
Y
Y
Y
Y
Y
Answer
Provided
by
Managers
Benefit
Risk
NA
Rearing families separately for captive
broodstock programs maintains
pedigrees to reduce the risk of
inbreeding depression.
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
N
similar to natural fish in behavior may
improve performance and reduce
Y
similar to natural fish in growth rate
may improve performance and reduce
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 may improve
performance and reduce adverse
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 adverse
morphology may adversely affect
performance.
behavior may adversely affect
growth rate may adversely affect
physiological status may adversely
affect performance and increase
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.
Page A-3 9
Question
ID
65
66
67
68
69
Page A-3 10
Category
Release
Release
Question
Are volitional releases during natural
out-migration timing practiced?
Are there protocols for fish release
timing?
Release
Are all hatchery fish released at or
adjacent to the hatchery facility (onsite)?
Release
Are data routinely collected for
released fish?
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?
Correct
Answer
Y
Y
Y
Y
Y
Answer
Provided
by
Managers
Benefit
N
Volitionally releasing smolts during the
natural outmigration timing may
improve homing, survival, and reduce
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.
Y
Releasing fish in the same subbasin
as the rearing facility reduces the risk
of dissemination of fish pathogens to
the receiving watershed.
N
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
Failure to volitionally release smolts
during the natural outmigration
timing may adversely affect homing,
survival, and increase risk of
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.
ID
70
71
72
Category
Question
Correct
Answer
Answer
Provided
by
Managers
Release
Are 100% of the hatchery fish
marked so that they can be
distinguished from the natural
populations?
Y
Y
Facilities
Does hatchery intake screening
comply with California State,
National Marine Fisheries Service,
and/or other agency facility
standards?
Y
NA
Y
Y
Facilities
73
Facilities
74
Facilities
75
Facilities
76
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 the
use of alarms, autodialer, and
pagers?
Is the facility continuously staffed to
ensure the security of fish stocks onsite?
Y
NA
Y
Y
Y
Y
Y
Y
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
Compliance with NDPES discharge
limitations maintain water quality in
downstream receiving habitat
Hatchery discharge may pose a risk
to water quality in downstream
receiving habitat
For facilities that fall below the
minimum production requirement for
an NPDES permit, compliance with
these discharge limitations maintain
water quality in downstream receiving
habitat
Siting the facility where it is not
susceptible to flooding decreases the
Notification to staff of emergency
situations using alarms, autodialers,
and pagers reduces the likelihood of
catastrophic loss.
For facilities that fall below the
minimum production requirement
for an NPDES permit, hatchery
discharge may pose a risk to water
quality in downstream receiving
habitat
Siting the facility where it is
susceptible to flooding increases
the likelihood of catastrophic loss.
Inability to notify staff of emergency
situations using alarms, autodialers,
and pagers increases the likelihood
of catastrophic loss.
Lack of continuous facility staffing
increases the likelihood of
catastrophic loss.
Continuous facility staffing reduces the
Page A-3 11
Question
ID
77
78
79
80
82
85
Page A-3 12
Category
Question
Correct
Answer
Answer
Provided
by
Managers
M&E
Question was dropped - Do you
have a numerical goal for total catch
in all fisheries?
M&E
have a goal for broodstock
composition (hatchery vs. natural) in
the hatchery?
Y
NA
M&E
have a goal for spawning
escapement composition (hatchery
vs. natural) in the wild?
Y
NA
M&E
have a goal for smolt-to-adult return
survival?
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?
Effectiveness
Is the percent hatchery-origin fish
(first generation) in natural spawning
areas estimated?
Y
Y
Y
Y
NA
NA
Benefit
This program has a numerical goal for
total catch in all fisheries, which
makes it possible to evaluate its
success and implement information
responsive management.
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.
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.
This program has an explicit goal
smolt to adult survival, which makes it
possible to evaluate success and
implement information responsive
management.
NA
Maintaining a natural spawning
population composed of less than 5%
hatchery fish reduces the risk of loss
of among population diversity.
N
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.
Risk
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
composition (hatchery vs 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 composition
(hatchery vs 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.
Maintaining a natural spawning
population composed of greater
than 5% hatchery fish increases the
risk of loss of among population
diversity.
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.
ID
Category
Question
Correct
Answer
Answer
Provided
by
Managers
86
Accountability
Are standards specified for in-culture
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 postrelease performance standards of
hatchery fish and their offspring?
89
Accountability
90
Accountability
Are post-release performance
standards met?
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.
Y
Y
Y
Y
Y
N
Benefit
Risk
Having in-culture performance goals
provides clear performance standards
for evaluating the program.
The program lacks standards for inculture performance. Of hatchery
fish, making it difficult to determine
causes for program successes and
failures.
Having post release performance
goals provides clear performance
standards for evaluating the program.
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.
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.
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 13
Appendix VIII
Program Report
Appendix B
June 2012
Nimbus Hatchery Steelhead Program
Appendix B
Central Valley Steelhead Watershed Reports
This appendix summarizes relevant available information on steelhead distribution and
abundance in the Central Valley by major watershed, and provides brief overviews of the
conditions of the watersheds to support natural steelhead production. Information is summarized
from the NMFS Draft Recovery Plan (2009), Appendix A – Central Valley Watershed Profiles.
While it is recognized that there is a general scarcity of long-term abundance data for Central
Valley streams, there is no doubt that run sizes have declined sharply over time. Still, it is
believed that significant natural production of steelhead remains in some streams. The summaries
are presented in geographic order from north to south.
1
Upper Sacramento River
The Sacramento River is approximately 384 miles long from its headwaters near Mount Shasta to
its mouth at the Delta. The watershed covers approximately 27,000 square miles and has an
annual runoff of 22,000,000 acre-feet; approximately one-third of the total runoff in the state.
The upper watershed of the Sacramento River region includes the drainages above Lake Shasta
and Lake Oroville. The valley 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
of the valley. It is geographically continuous with the San Joaquin Valley to the south, but is
defined by its distinct drainage basin.
Land use in the mountainous regions of the basin is principally forest with largely mixed forest
and rangeland at lower elevations upslope from the Central Valley. One of the world’s most
productive agricultural regions is spread through the Central Valle, but the region also supports
urban centers and diverse land uses.. Beginning near the town of Red Bluff at its northern
terminus, the Sacramento Valley stretches about 150 miles to the southeast where it merges into
the Sacramento-San Joaquin River Delta south of the Sacramento metropolitan area. Like the
larger Central Valley, the Sacramento Valley supports a diverse agricultural economy, much of
which depends on the availability of irrigation water. Water is collected in reservoirs at several
locations within the mountains surrounding the Sacramento Valley and is released according to
allocations for agricultural, urban, and environmental needs. The reservoirs also are managed for
flood control 1 . The current limit of potential steelhead migration is at Keswick Dam (RM 302),
which is an upstream migration barrier.
According to Hallock (1989) adult steelhead migrate into the Upper Sacramento River system
(upstream of the Feather River confluence) from July through the middle of March. The peak of
the run passes the mouth of the Feather River near the end of September. Steelhead spawn in
most tributaries to the Upper Sacramento and appear to do so in proportion to creek size as
measured by the amount of runoff (Hallock 1989). Actual numbers of steelhead that spawn in the
mainstem of the Sacramento (if any) and in each tributary are unknown. Based on Chinook
monitoring data collected by CDFG and USFWS, steelhead natural production is still found in
several Upper Sacramento tributaries, including Clear, Cottonwood/Beegum, Antelope, Deer,
Mill, and Battle creeks, and possibly other streams to a lesser degree. Of the 25 Central Valley
1
http://ca.water.usgs.gov/sac_nawqa/study_description.html
Nimbus Fish Hatchery Steelhead Program /Appendix B / June 2012
Page B 1
watersheds ranked for current viability potential to support local naturally reproducing
populations, only Clear, Battle, Antelope, Mill, and Deer creeks scored “High”. Each of these is
a tributary to the Upper Sacramento River. Steelhead use of these principal major tributaries of
the Upper Sacramento River system is discussed in the sections that follow.
Recent steelhead monitoring data is scare for the Upper Sacramento River system. Hallock
(1989) reported that steelhead have declined drastically above the mouth of the Feather River. In
the 1950s, the average estimated spawning population size above the mouth of the Feather River
was 20,540 fish (SAIC 2007). In 1991-1992, the annual run size for the total Sacramento River
system was likely less than 10,000 adult fish (SAIC 2007). From 1967 to 1993, the estimated
number of steelhead passing Red Bluff Diversion Dam ranged from a low of 470 to a high of
19,615. Recent otolith sampling of O. mykiss in the Upper Sacramento River system documented
that less than 50% of age 0 to 4 fish sampled were progeny of an anadromous (steelhead) mother
(Zimmerman et al. 2009).
All of these abundance data are likely influenced by hatchery fish presence. Coleman National
Fish Hatchery (CNFH), located on Battle Creek, a tributary to the Upper Sacramento River, has
been producing steelhead since 1947. The current CNFH long-term goal is to release 600,000
steelhead in the Sacramento River system annually, which may contribute substantially to the
abundance of natural spawners in the Upper Sacramento River system.
2
Clear Creek
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 Clear Creek and lower Clear Creek, with Whiskeytown Reservoir
forming the boundary between them. Lower Clear Creek flows southeast from Whiskeytown
Reservoir approximately 18.1 river miles to the Sacramento River. Whiskeytown Dam is a
complete barrier to fish passage and is the uppermost boundary of habitat available to steelhead.
The lower Clear Creek watershed is approximately 48.9 square miles and receives supplemental
water from a cross-basin transfer between Lewiston Lake in the Trinity River watershed and
Whiskeytown Reservoir in the Sacramento watershed. Most of the lower Clear Creek watershed
is undeveloped, with scattered private residences, gravel mining operations, light industrial and
commercial uses.
Historically, steelhead probably ascended Clear Creek past the French Gulch area, but access to
the upper basin was blocked by Whiskeytown Dam in 1964. Removal of McCormick‐ Saeltzer
Dam in 2000 provided access to an additional 12 miles of habitat; steelhead may have
recolonized this area and taken advantage of newly added spawning gravels. Redd surveys
conducted since 2001 indicate an increasing trend of natural spawning in Clear Creek (Figure
B-1), with the highest density in the first mile below Whiskeytown Dam. A recent review of
habitat potential on Clear Creek indicates carrying capacity estimates of 7,292 steelhead 2 .
2
Whether the carrying capacity refers to adult spawners or juveniles was not reported in NMFS (2009).
Page B 2
Source: NMFS (2009)
Figure B-1.
3
Estimated abundance of steelhead spawners in Clear Creek based on annual redd
counts 2003‐2009.
Cottonwood/Beegum Creek
Cottonwood Creek is the third largest watershed (938 square miles) tributary west of the
Sacramento River and the largest undammed tributary in the Upper Sacramento River Basin. The
lower two-thirds of the watershed is in Central Valley uplands, and the upstream portion includes
the slopes of several mountain ranges. Cottonwood Creek flows eastward for 68 miles to the
Sacramento River and has three main tributaries: North Fork, Middle Fork, and South Fork. With
an annual runoff of 586,000 acre-feet, Cottonwood Creek has a natural pattern of high flows and
peak runoff events in winter and low flows in the summer and fall.
Beegum Creek is a major tributary to the Middle Fork Cottonwood Creek. The North, Middle,
and South forks of Beegum Creek originate in the easternmost portion of the Shasta‐Trinity
National Forests and converge to form the mainstem of Beegum Creek before entering a remote,
steep‐sided canyon known as Beegum Gorge. Beegum Creek is thought to contain the majority
of steelhead spawning habitat in the Cottonwood Creek watershed.
The Cottonwood Creek watershed remains relatively undeveloped, and is generally characterized
by tracts of harvestable timber in the upper reaches, irrigated pastureland in the middle reaches,
and ranches, residential housing, and gravel mining operations in the lower reaches.
Approximately 70% of land within the watershed is privately owned. The Beegum Creek
watershed is generally forest covered and has not been significantly modified.
Cottonwood Creek has moderate potential to support viable steelhead reproduction. Although
comprehensive population abundance data are not available, there is a widespread presence of
O. mykiss throughout the watershed. Small runs of adult steelhead have been observed to migrate
in the mainstem and lower reaches of the North, Middle, and South forks of Cottonwood Creek.
Page B 3
4
Battle Creek
Battle Creek drains the southern Cascade Range in the northern Central Valley and enters the
Sacramento River at river mile 272. The watershed is about 360 square miles and includes two
main branches, North Fork Battle Creek (about 29.5 miles long), South Fork Battle Creek (about
28 miles long), the mainstem valley reach (about 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 not accessible to
anadromous salmonids due to natural barriers.
The geology and hydrology of Battle Creek are unique among the tributaries to the upper
Sacramento River downstream of Shasta Dam but quite similar to tributaries upstream of Shasta
Dam. Battle Creek has the largest base flow (approximately 225 cfs) of any of the tributaries to
the Sacramento River between the Feather River and Keswick Dam on the Sacramento River.
Land use in Battle Creek ranges from rural residential development to undeveloped wilderness in
Lassen National Park, and is predominated by industrial timber harvesting, livestock ranching,
grape growing, and other agricultural development. Above the valley reach, Battle Creek has
been extensively developed to produce hydroelectric power.
Currently, the Battle Creek watershed has five dams blocking upstream migration of salmonids to
much of the suitable and historic habitat; however, there is a major restoration project planned.
The Battle Creek Salmon and Steelhead Restoration Project (Restoration Project), was scheduled
to begin implementation in 2009. The Restoration Project, once complete, will open 21 miles of
historical habitat and will restore and enhance nearly 50 miles of habitat.
CNFH is located in the valley reach of Battle Creek. The abundance and distribution of salmon
and steelhead in Battle Creek has been artificially managed by the operation of a permanent fish
barrier dam at CNFH since 1952. Prior to that time, adult salmon were collected from Battle
Creek at seasonally installed racks at the hatchery. The existing dam has a fish ladder that is
closed to create a migration barrier during certain seasons, except during high runoff events.
Propagation of steelhead at the CNFH was initiated in 1947 using natural-origin steelhead adults
collected at the Keswick Dam fish trap. In 1953, hatchery-origin adults began to return to Battle
Creek and steelhead broodstock were collected from Battle Creek for the first time.
During the 1990s, an average of 1,836 steelhead were trapped. Escapement estimates of Battle
Creek clipped and unclipped rainbow trout/steelhead passing upstream through the CNFH barrier
weir between March and August from 1995 through 2007 is presented in Table B-1.
Table B-1.
Year
1995
1996
1997
1998
1999
2000
2001
2002
Page B 4
Escapement of adult steelhead upstream of CNFH barrier weir, 1995-2007.
Hatchery Origin
(marked)
------1,382
1,442
Natural Origin
(unmarked)
------225
593
Total
161a
317a
344a
469a
1,263a
1,520a
1,607
2,035
Year
2003
2004
2005
2006
2007
Hatchery Origin
(marked)
772
329
0
1
3
Natural Origin
(unmarked)
534
304
344
438
346
Total
1,306
633
344
439
349
Source: NMFS (2009)
a
Marking was not used to differentiate hatchery- and natural-origin adult steelhead returns until 2001 (marking started in 1998).
5
Antelope Creek
Antelope Creek originates in the Lassen National Forest and flows southwest from the foothills of
the Cascade Range to RM 235 of the Sacramento River near Red Bluff. The Antelope Creek
watershed encompasses approximately 123 square miles that are in various ownerships, with
agriculture and ranchettes dominating the valley floor. Most of the canyon reach is managed by
the CDFG (Tehama Wildlife Area) and the Lassen National Forest. Corporate timber lands
surround the Antelope Creek headwaters.
The Antelope Creek watershed produces an average of 110,800 acre feet of water per year. In
wettest years, average winter flows range from 200 to 1,200 cfs. In the driest years, winter flows
average 50 cfs. In all but the wettest years, summer and early fall flows average from 20 to 50
cfs. There are two diversions on Antelope Creek, both located at the canyon mouth. 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.
Historically, Antelope Creek was reported to support a few hundred adult steelhead. Currently
the stream is estimated to contain about 20 miles of suitable steelhead spawning habitat. No
annual monitoring is conducted on Antelope Creek for steelhead, although recently some
monitoring was performed. Pedestrian and snorkel surveys in 2001 from March through May
counted adult steelhead and steelhead redds in Antelope Creek. These surveys observed 47
steelhead and 52 redds in about 53% of the accessible anadromous habitat. These numbers do not
represent a population estimate because the entire amount of habitat was not surveyed and
surveys may have missed the peak spawning period. In 2007/2008, CDFG installed a video
camera and observed 140 adult steelhead moving through the newly constructed fish ladder at the
Edwards Diversion (USFWS 2011).
6
Mill Creek
Mill Creek is an eastside tributary to the Sacramento River that flows in a southwesterly direction
for approximately 60 miles and drains 134 square miles. The creek originates near a thermal
spring area in Lassen Volcanic National Park, flows through meadows and dense forests before
descending rapidly through a steep rock canyon into the Sacramento Valley. The creek then
flows eight miles across the Sacramento Valley floor, entering the Sacramento River north of
Tehama.
There are three diversions on Mill Creek and during low flows, their allowable water rights are
sufficient to dewater the stream. Late spring and early summer withdrawals have resulted in
flows low enough to block access for late‐migrating adult salmonids. Low flows may also
prevent outmigrating smolts from reaching the Sacramento River (McEwan and Jackson 1996).
Evaluations of Central Valley anadromous fishery resources (Reynolds et. al. 1993; McEwan and
Page B 5
Jackson 1996) have consistently identified insufficient instream flows as one factor limiting
anadromous fish production in the Mill Creek watershed. This has led to cooperative programs
between agencies and water users to develop and operate wells, or to obtain water rights (lease or
purchase) to provide flows for spring Chinook and steelhead.
Steelhead are reported to begin migrating into Mill Creek in the late‐fall and winter, primarily
when storms increase flows. Ladder counts at Clough Dam, on Mill Creek, between 1953 and
1963 showed that adult steelhead migrate upstream from September through June. Two distinct
migration peaks were observed in this monitoring data. The largest peak occurred from
late‐October to mid‐November, and accounted for 30% of the run. A smaller peak occurred in
the first two weeks of February, accounting for 11% of the run. Based on observations using a
video weir in Mill Creek from March 6 through June 18, 2007, peak upstream and downstream
steelhead passage occurred from May 8‐10, 2007. This may represent the presence of two runs of
steelhead in Mill Creek, with one run exiting the system while another is entering the system.
Steelhead counts in Mill Creek are available from 1953 to 1963, 1980, 1993, and 1994, for adult
fish that passed Clough Dam (which was removed in 2003). From 1953 to 1963, between 417
and 2,269 steelhead (annual average of 911 steelhead) were counted at Clough Dam. In 1980,
280 steelhead were counted, and in the 1993 to 1994 migration season, 34 steelhead were
estimated. Surveys conducted in 2001 used snorkel and foot methods in January, March, and
April to count adult steelhead and steelhead redds in Mill Creek. These surveys observed 15
adult steelhead and 31 redds in about 3 to 4% of the accessible anadromous habitat. Mill Creek is
estimated to currently contain about 25 miles of suitable steelhead spawning habitat.
7
Deer Creek
Deer Creek is an eastside tributary to the Sacramento River that flows in a southwesterly
direction for approximately 60 miles and drains 134 square miles. Deer Creek flows through
meadows and dense forests and then descends rapidly through a steep rock canyon into the
Sacramento Valley. The creek flows 11 miles across the Sacramento Valley floor before joining
the Sacramento River. Timber production, cattle ranching, and orchards are the dominant
agricultural land uses. Except for three small diversions, the watershed 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). 3
There are three diversion dams and four diversion ditches on the 10 miles of stream between the
canyon mouth of Deer Creek and the Sacramento River. During low flows, the existing water
rights are sufficient to dewater the stream. Late spring and early summer diversions have resulted
in flows low enough to block fish migration (NMFS 2009). It is thought that relatively few
actions would be needed to restore ecosystem function to support steelhead freshwater life stages
in Deer Creek (NMFS 2009). With the exception of impaired stream flows and fish passage
conditions on the valley floor below the agricultural diversions, habitat in the upper watershed in
good condition (NMFS 2009).
Although comprehensive population abundance data are not available, Deer Creek is believed to
support a population of steelhead. Steelhead have access to about 25 miles of suitable spawning
habitat downstream of Deer Creek Falls. With the exception of some limited data on juvenile
outmigration, steelhead population monitoring data in Deer Creek are lacking. Recent otolith
sampling of O. mykiss in the Deer Creek watershed documented that over 75% of age 0 to 2, and
3
http://www.sacriver.org/documents/2010/Roadmap/Eastside_DeerlCreek.pdf
Page B 6
100% of age 3 fish sampled were progeny of an anadromous (steelhead) mother (Zimmerman et
al. 2009).
8
Feather River
The tributaries of the Upper Feather River flow from the northern Sierra Nevadas, eventually into
Lake Oroville, a major reservoir of the California State Water Project. 4 The lower Feather River
watershed (downstream of Lake Oroville) encompasses about 803 square miles. Steelhead
distribution is limited to accessible reaches below the Oroville Project Fish Barrier Dam at RM
67.
Flows are regulated for water supply and flood control at Oroville Dam. Under normal
operations, the majority of water released is directed into the Thermalito Complex. Except for
local water diversions, the rest is returned to the Feather River through the Thermalito Afterbay
Outlet. The river then flows southward through the valley to the confluence with the Sacramento
River at Verona. The remainder of releases from Lake Oroville, typically 600 cfs, runs through
the historic river channel locally known as the Low Flow Channel.
The river is almost entirely contained within a series of levees as it flows through the fertile
agricultural lands of the Sacramento Valley. 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. Significant management issues include concerns over growth
(farmland conversion to urbanization), demands on water supply, preservation of water quality
and aquatic habitat, and potential risks from fire and floods. 5
Historically, the Feather River supported a large steelhead population. Today the run is supported
almost entirely by the Feather River Hatchery, which produces about 400,000 yearling steelhead
annually to mitigate for Oroville Dam and losses at the State Water Project Delta facilities.
Steelhead passage to the upper watershed has been blocked since 1967 after the completion of
Oroville Dam.
The Feather River Hatchery was built by the California Department of Water Resources to
mitigate for the loss of salmon and steelhead spawning habitat from Oroville Dam. CDFG
operates the hatchery. In recent decades, most steelhead returning to the Feather River are
thought to be hatchery returns, although abundance of natural-origin returns as well as the
abundance of natural spawners is uncertain (Mills et al. 2003). Hatchery returns have averaged
1,019, with a minimum of 78 in 1971 and a maximum of 2,999 in 2003 (Table B-2).
Table B-2.
Feather River Hatchery adult steelhead returns, 1990 to 2003.
Year
1990
1991
1992
1993
1994
1995
Adult Steelhead Count
1,193
1,025
1,028
297
1,594
877
4
The Oroville Reservoir is the principal water storage facility of the State Water Project, which conserves and
delivers water to over two-thirds of California’s population.
5
http://www.sacriver.org/
Page B 7
Year
1996
1997
1998
1999
2000
2001
2002
2003
Adult Steelhead Count
1,058
2,113
1,023
633
1,742
2,161
1,431
2,999
Source: Mills et al. (2003)
Little information is known about natural steelhead spawning in the Feather River, as limited
surveys have been completed. Based on surveys conducted in 2003, most natural steelhead
spawning is thought to occur in the Low Flow Channel, particularly between RM 66 and 67
(FERC 2007). Adult steelhead peak immigration probably occurs from September through
January. Spawning surveys conducted in 2003 indicated that redd formation probably began in
late December, peaked in late January, and was essentially complete by the end of March.
Surveys counted 75 steelhead redds and 108 steelhead, and revealed that 48% of all redds were in
the upper mile of the accessible reach of the Feather River (Mills et al. 2003). No attempt was
made to estimate the total number of adult steelhead spawning. Weir counts of adult steelhead
have occurred since 2007, but reports are not readily available
(http://weir.fishsciences.net/case_study_feather.php).
Juvenile steelhead are thought to primarily emigrate at Age 1 or younger based on studies
conducted from 1999 to 2001; Age 1 and Age 2 steelhead were relatively rare during surveys
(Cavallo et al. 2003). Most juveniles were found in side/secondary channels to the Low Flow
Channel, habitat that makes up less than one percent of the available habitat (FERC 2007). The
lack of side/secondary channels may be an important limitation on natural production (Cavallo et
al. 2003).
9
Yuba River
The Yuba River watershed drains approximately 1,340 square miles and extends from the crest of
the Sierra Nevadas to the confluence with the Feather River near Marysville and Yuba City. The
principal tributaries include the North Yuba River (490 square mile watershed), the Middle Yuba
River (210 square mile watershed), and the South Yuba River (350 square mile watershed). The
North and Middle Yuba rivers converge below New Bullards Bar Reservoir to form the Yuba
River. Farther downstream, the South Yuba River flows into Englebright Lake.
Englebright Dam, completed in 1941, is at RM 24 and marks the division between the upper and
lower Yuba River. Anadromous fish access to the North, South and Middle Yuba rivers is
completely blocked by Englebright Dam. 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, the 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 initiated to improve fish passage at
the dam.
Although there are no available data describing the historical or current abundance of
steelhead/rainbow trout in the lower Yuba River, the reach downstream of Englebright Dam is
Page B 8
known to support a relatively large population of O. mykiss. CDFG estimated that only about 200
steelhead spawned in the lower Yuba River annually before New Bullards Bar Reservoir was
completed in 1969. From 1970 to 1979, CDFG annually stocked between 27,270 and 217,378
fingerlings, yearlings, and sub‐catchables from Coleman National Fish Hatchery into the lower
Yuba River. Based on angling data, CDFG estimated a run size of 2,000 steelhead in the lower
Yuba River in 1975. The current status of this population is unknown, but it appears to be stable
and able to support a significant sport fishery. The immigration of adult O. mykiss into the lower
Yuba River has been reported from August through March, with peak immigration occurring
from October through February. Steelhead spawning is thought to generally extend from January
through April. The majority of steelhead spawning and juvenile rearing has been documented
between Daguerre Point Dam and Englebright Dam. Recent otolith sampling of O. mykiss in the
Yuba River system shows that over 10% of 0-, 2-, 3-, and 4-year-olds, and nearly 50% of 1-yearold fish sampled were progeny of an anadromous (steelhead) mother (Zimmerman et al. 2009).
10
American River
The American River watershed is approximately 1,895 square miles and is a major tributary
entering the Sacramento River at RM 60. Historically, the American River provided over 125
miles of riverine habitat to anadromous and resident fishes. Presently, anadromous salmonid use
is limited to the 23 miles of river below Nimbus Dam (i.e., the lower American River), which was
finished in 1955.
The lower American River flow is highly regulated by Folsom Dam. Folsom Lake outflows are
re-regulated by Nimbus Dam before passing through the floodplain and urbanized Sacramento
area. The reach through the highly urbanized Sacramento area is buffered by the 30-mile-long
American River Parkway, which extends 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. Completion and operation of Folsom and Nimbus
dams resulted in higher flows during fall, significantly lower flows during winter and spring, and
significantly higher flows during summer.
Historically, the lower American River may have supported summer-, fall-, and winter-run
steelhead. Summer steelhead typically entered the river between May and July, fall-run between
September and November, and winter-run between December and April. Each of these
populations had access to approximately 125 miles of spawning and rearing habitat in the upper
reaches of the American River. Since the early 1900s, access has been impeded to varying
degrees by mining debris containment, flood control, and water supply diversions. By 1955, it is
believed that summer-run steelhead were extirpated from the American River and only remnant
populations of the fall and winter-run steelhead remained.
From 1956 through the late 1980s, Nimbus Hatchery propagated eggs of steelhead strains from
other locations in California and Washington, planting the fry into the lower American River.
Phenotypic expression of steelhead in the lower American River most closely resembles that of
the historic winter-run strain of American River steelhead and the winter-run strain of Eel River
steelhead.
Natural production of steelhead in the American River will continue to be limited by
inaccessibility of the headwaters. The proportion of hatchery-origin fish spawning in the river
remains uncertain. It is known, however, that the majority of the steelhead returning to the
hatchery are of hatchery origin.
Page B 9
From 2001to 2007, one to six percent of the adult steelhead entering Nimbus Hatchery were
natural-origin (unclipped) fish (Table B-3). Surveys showed around 300 steelhead spawning in
the river each year compared to hatchery returns during the same years of 1,200 to 2,700 fish
(Hannon and Deason 2005, as cited in Bureau of Reclamation 2008). Many of the in-river
spawners were hatchery produced fish. Spawning density is higher in the upper seven miles of
accessible habitat, but spawning also occurs downstream in the lowest riffle in the river at
Paradise Beach (Bureau of Reclamation 2008).
Table B-3. Adipose clip status of adult steelhead entering Nimbus Hatchery.
Year
2001
2002
2003
2004
2005
2007
Number of Steelhead
Entering Nimbus Hatchery
2,877
1,742
887
1,862
2,772
2,308
Number Unclipped
64
50
69
27
17
90
Percent Unclipped
2.2%
2.9%
7.8%
1.5%
0.6%
3.9%
Source: Bureau of Reclamation (2008)
The American River does not have a robust resident trout population. The steelhead model
indicates that the river should produce primarily steelhead smolts due to high growth rates (fish
can get to 300 mm in one year) (Satterthwaite et al. 2010).
11
Mokelumne River
The Mokelumne River originates in the Sierra Nevada Mountains and has a watershed area of
661 square miles that contains a number of dams and reservoirs. It is a major tributary to the
Sacramento‐San Joaquin Delta, entering the lower San Joaquin River northwest of Stockton.
Almost 90% of precipitation occurs as rainfall from November through April; snowfall within the
watershed is rare. The landscape of the Mokelumne River watershed is typical of the lower
Sierra foothills, with rolling terrain interrupted by scattered rock outcrops and moderate to steep
hillsides. The vegetation is predominantly grasslands and oak woodlands.
The Mokelumne River watershed is a significant source of water for both consumption and
energy production. The major land use in the upper watershed, owned both privately and
publicly, is timber management. Much of the privately held land is undeveloped open space or is
used for grazing. Additionally, the Mokelumne River has a long history of water development.
East Bay Municipal Utility District owns about 44% of the watershed. Existing developments on
the Mokelumne River upstream of Camanche Reservoir include facilities for hydroelectric,
irrigation, and municipal use. Downstream of Camanche Reservoir, developments include both
hydroelectric and irrigation facilities.
No information exists on the size of historic runs of steelhead in the Mokelumne. The river once
produced a significant number of natural steelhead, although there is debate about whether there
was an indigenous steelhead stock prior to releases of out-of-basin hatchery stocks. The
Mokelumne River Fish Hatchery, operating since 1964, has a steelhead production goal of
250,000 yearlings annually. According to creel census data, steelhead were the most sought after
fish in the lower Mokelumne River prior to the completion of Camanche Dam in 1963, after
which the steelhead run declined significantly.
Page B 10
According to NMFS (2009), Camanche Dam, the Woodbridge diversion, and other structures
caused a loss of over 85% of the historical habitat. Currently, steelhead distribution is limited to
accessible reaches downstream of Camanche Dam (RM 29.6). Dams, sedimentation from gold
mining and loss of habitat access are the primary reasons that steelhead and Chinook runs have
severely declined since the early 1900s. Current efforts to improve conditions for fish passage
and flows include the recent improvement of passage at the Woodbridge diversion structure.
Currently the O. mykiss population in the Mokelumne River likely consists of both resident and
anadromous life histories, with the resident form likely dominating. Natural-origin juveniles
tagged with acoustic tags in 2007 and 2008 showed little migrational movement out of the
system. In these two years, only 5% (6 of 119) of the natural-origin tagged fish migrated to the
ocean.
Since 2002, annual winter steelhead escapement to the Mokelumne River Hatchery has averaged
99 fish. During this same period, approximately 32% of the total return was unmarked naturalorigin steelhead (Table B-4).
Table B-4.
Return Season
2002-2003
2003-2004
2004-2005
2005-2006
2006-2007
2007-2008
2008-2009
2009-2010
Average
Number and percent of adipose fin-marked steelhead trapped at the Mokelumne
River Fish Hatchery, 2002-2010.
Year
2003
2004
2005
2006
2007
2008
2009
2010
Unmarked
Adults
27
22
14
26
47
27
Marked Adults
25
36
33
114
198
81
Total Adults
52
58
47
140
245
51
99
Percent Adults
Unmarked
52%
38%
30%
19%
19%
32%
The annual number of adult steelhead/rainbow trout redds observed in the lower Mokelumne
River since 2001 has ranged from 3 to 61 fish and averaged 36 fish (Table B-5). Data describing
the percent natural verses hatchery-origin fish on the spawning grounds are not available.
Table B-5.
The number of steelhead redds observed in the Mokelumne River, 2001-2010.
Year
2001
2002
2003
2004
2007
2008
Number of
Steelhead Redds
36
26
50
18
3
41
Page B 11
Year
2009
2010
Average
12
Number of
Steelhead Redds
55
61
36
Calaveras River
The Calaveras River, a tributary to the San Joaquin River, is a relatively small, low elevation
Central Valley drainage that receives runoff mainly from winter rainfall (Stillwater Sciences
2004). The Calaveras River is not a direct tributary to the mainstem San Joaquin River, rather it
enters a network of sloughs and channels in the Delta east of the mainstem of the San Joaquin
River. The watershed of the Calaveras River is about 400 square miles with headwater elevations
of about 5,000 feet. The watershed has changed from an uncontrolled floodplain of sloughs and
oak groves of the 1860s to today’s system of controlled channels, dams, and levees. Flow in the
Calaveras River is regulated by New Hogan Dam (a fish passage barrier), at approximately RM
42. New Hogan Reservoir is operated by the Corps of Engineers for flood control, water supply,
and recreation.
The Lower Calaveras River system consists of two constructed channels, Mormon Slough and the
Old Calaveras River Channel, that separate flow below the Bellota Weir. Mormon Slough is a
flood control channel that carries most floodwater. The Old River Channel carries local runoff
and some irrigation flow. The Bellota Weir complex on the Lower Calaveras River is
approximately 25 miles from the mouth on the San Joaquin River and 20 miles below New
Hogan Dam.
The flow regime of the Calaveras River has been fundamentally altered since the 1930s, first by
construction of Hogan Dam and subsequently by New Hogan Dam. Historically, the river’s
hydrology was characterized as highly variable during winter months, with rapid flow attenuation
in the summer. Under current flow management, the variability and magnitude of winter flows is
strongly reduced, while the magnitude and consistency of summer flows has increased
dramatically. Water supplies stored in New Hogan Reservoir are transferred, via the Calaveras
River, to downstream locations as far as Bellota. The effect has been to transform the lower river
from a system with high intra-year variability, to one that behaves like a typical snowmelt system,
with fall and winter precipitation stored and released gradually in the summer months (Stillwater
Sciences 2004).
Because of highly variable seasonal stream flow patterns and elevated stream temperatures, it is
thought that this river was historically marginal for anadromous fish production (Stillwater
Sciences 2004). Steelhead were known to be present historically, but it is unknown to what
degree and whether annual production occurred. While little is known of the historical
anadromous runs in the Calaveras River, currently steelhead enter the river when suitable fall
flows occur. The Calaveras River also supports a popular resident rainbow trout fishery
(Stillwater Sciences 2004). Recent otolith sampling of O. mykiss in the Calaveras River system
documented that over 30% of fish sampled were progeny of an anadromous (steelhead) mother
Currently, adult steelhead have two potential migration routes into the Calaveras River upstream
of Bellota Weir: 1) the Old Calaveras River channel downstream of the town of Bellota, and 2)
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Mormon Slough via the Stockton Diverting Canal). Most steelhead are thought to migrate
through the Stockton Diverting Canal and Mormon Slough to access the mainstem Calaveras
River, because this route typically has higher flows than the Old Calaveras River channel
(Stillwater Sciences 2004). However, in many years, the timing and magnitude of flows below
Bellota Weir are not sufficient for steelhead to migrate upstream into the high quality spawning
and rearing habitat between Bellota and New Hogan Dam (Stillwater Sciences 2004).
Additionally, numerous in-channel structures, natural hydraulic barriers, and dry reaches along
these migration routes create partial or complete migration barriers to steelhead.
Only winter steelhead are believed to have occurred in the San Joaquin River Basin and
Calaveras River (Marsh 2006). Winter run enter spawning streams in fall or winter, spawning a
few months later in winter or late spring. While very few studies of the fishery resources in the
Calaveras River have been conducted, recent monitoring indicates that steelhead opportunistically
use the watershed when sufficient rainfall produces passage flows in the system (Stillwater
Sciences 2004). In April 2002, the Fishery Foundation of California (FFC) found a spawned-out
female steelhead downstream of Bellota Weir, several live and dead adult steelhead in Mormon
Slough, and steelhead redds in riffles downstream of Bellota Weir. FFC snorkel surveys of the
lower river downstream of New Hogan Dam in 2002 indicate a large population of rainbow trout
exists and naturally reproduces in the reach (Stillwater Sciences 2004). While conducting
passage surveys in Mormon Slough from November 2003 to March 2004, FFC documented live
outmigrating O. mykiss smolts (smolt index 3 to 5) in the pool downstream of Bellota Weir and
further downstream. Biologists have documented smolt-size fish (smolt index size ≥5) for several
years, with 146 smolts in 2002, 103 in 2003, 194 in 2004, and 34 in 2005 (data are numbers of
captured fish, not expanded data) (Marsh 2006).
13
Stanislaus River
The Stanislaus River watershed, located between the Mokelumne River and the Tuolumne River
watersheds, extends 96 miles with north, middle and south forks. The headwaters of the
Stanislaus River is in the Emigrant Wilderness from where it flows in a general southwesterly
direction to its confluence with the San Joaquin River, 23 miles above Stockton. The heavily
dammed and diverted watershed currently contains 13 large reservoirs that have highly modified
the hydrograph. Spring and summer flows are capped at 1,500 cfs (barring flood releases), while
summer flows are increased to maintain downstream water quality. Goodwin Dam, located at
RM 52, is the lowermost barrier to anadromous fish migration.
The lower Stanislaus River has been extensively developed to provide water, hydropower, gravel,
and habitat for agricultural and residential uses. The river floodplain below Knights Ferry (with
the exception of a narrow riparian border) has been converted to urban and rural uses. By 1994, it
was estimated that about 50% of the riparian corridor along the lower Stanislaus River had been
converted for agricultural, mining, and urban uses.
Historically, steelhead distribution was thought to have extended into the headwaters of the
Stanislaus River. Dams and water diversion for mining and irrigation began in the Gold Rush
era. The original Melones Dam, completed in 1926, permanently blocked anadromous salmonid
access to the upper watershed. Today steelhead can ascend over 58 miles up the Stanislaus River
to Goodwin Dam (RM 52). Although steelhead spawning locations are unknown in the
Stanislaus, most are thought to be upstream of the City of Oakdale where gradients are slightly
higher and more riffle habitat is available.
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The FFC has monitored habitat use by juvenile steelhead/rainbow trout since 2000 by snorkeling
seven sites in the Stanislaus River from Oakdale to Goodwin Dam. Data collected during these
surveys documented of the presence of steelhead fry in late March and April at the upstream sites,
with densities increasing into June and distribution becoming more even between upstream and
downstream sites through July. Beginning in August and continuing through the winter months,
densities appeared highest at upstream sites (Goodwin to Knights Ferry). Age 1-plus fish were
observed throughout the year, with densities generally higher at upstream sites (Goodwin to
Knights Ferry). Low densities were observed from late December until April (Bureau of
Reclamation 2008).
Since 1993, juvenile steelhead/rainbow trout catches in rotary screw traps indicate a small
percentage of the Stanislaus River steelhead/rainbow trout population displays downstream
migratory characteristics at a time that is typical of steelhead migrants. The advanced smolt-like
characteristics exhibited by many of these fish indicate that some juveniles may migrate to the
ocean during the spring. It is not known whether the parents of these fish were anadromous or
fluvial; however, recent otolith sampling of O. mykiss in the Stanislaus system documented that
about 10% of Age 1 to 4 fish sampled were progeny of an anadromous (steelhead) mother
A weir has been operated annually at RM 31.4 since 2003. The primary purpose of the weir is to
monitor the escapement of fall-run Chinook salmon, so it is installed from September through
June each year. From 2003 through 2007, O. mykiss have been observed passing the weir a total
of 16 times. Scale analysis of one individual indicated that it was a steelhead. Genetic analysis
of rainbow trout captured below Goodwin Dam shows that this population has closest genetic
affinities to upper Sacramento River steelhead.
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14
References
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Facilities Relicensing, FERC Project No. 2100, California Department of Water Resources.
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Hallock, R.J. 1989. Upper Sacramento River steelhead, Oncorhynchus mykiss, 1952-1988, a Report to the
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