Nimbus Fall Chinook Program - California Hatchery Review Project

Transcription

California Hatchery Review Project
Appendix VIII
Nimbus Fish Hatchery Fall Chinook
Program Report
June 2012
Introductory Statement from the California HSRG
This program report was developed by contractor staff tasked with providing background information to
the California HSRG on hatchery programs, natural population status and fisheries goals in California.
The resulting report is one of many sources of information used by the California HSRG in their review
process.
Information provided in this program report was developed through interviews with hatchery staff,
regional, state and tribal biologists working in the basins and a review and summarization of the
pertinent scientific literature. The draft program report was then provided to interview participants for
review and comment on multiple occasions. Comments received were incorporated into the report and
the report finalized.
Because of the review process, it is believed the report represents an accurate snapshot in time of
hatchery operations, natural salmon population status and fisheries goals in California as of 2012. This
program report may or may not be consistent with the consensus positions of the California HSRG
expressed in the main report, as their primary involvement was in the preparation of Section 4.3,
“Programmatic Strategies”, which compares existing program practices to the statewide Standards and
Guidelines developed by the California HSRG.
Table of Contents
1 Description of Current Hatchery Program ...............................................................................1 1.1 Programmatic Components ...............................................................................................1 1.2 Operational Components ...................................................................................................1 1.2.1 Facilities .....................................................................................................................2 1.2.2 Broodstock .................................................................................................................3 1.2.3 Spawning....................................................................................................................5 1.2.4 Incubation ..................................................................................................................6 1.2.5 Rearing .......................................................................................................................7 1.2.6 Release .......................................................................................................................8 2 Populations Affected by the Hatchery Program ....................................................................10 2.1 Current Conditions of Affected Natural Populations ......................................................13 2.1.1 American River Fall Chinook ..................................................................................16 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 .........................................................................20 4 Programmatic and Operational Strategies to Address Issues Affecting Achievement of
Goals .....................................................................................................................................20 4.1 Issues Affecting Achievement of Goals ..........................................................................20 4.1.1 Natural Production Issues ........................................................................................20 4.1.2 Ecological Interaction Issues ...................................................................................21 4.2 Operational Issues ...........................................................................................................21 4.3 Programmatic Strategies .................................................................................................22 4.3.1 Broodstock ...............................................................................................................22 4.3.2 Program Size and Release Strategies .......................................................................25 4.3.3 Incubation, Rearing and Fish Health .......................................................................26 4.3.4 Monitoring and Evaluation ......................................................................................32 4.3.5 Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial
Organisms. ...............................................................................................................37 5 Literature Cited ......................................................................................................................38 California Hatchery Review Project – Appendix VIII
Nimbus Fish Hatchery Fall Chinook Program / June 2012
i
List of Figures
Figure 1. Figure 2. Figure 3. Figure 4. Number of adult and grilse Chinook salmon trapped at the Nimbus Fish
Hatchery, 1955-2006...................................................................................................4 Minimum number of female Chinook salmon to be spawned by standard week
to mimic the number of fish trapped throughout the run period. ................................6 Estimated number of fall-run Chinook salmon in the American River, 1944 to
2006...........................................................................................................................12 Percent of total survival of Nimbus fall Chinook to selected fisheries and
escapement (average of 2000-2001 brood years). ....................................................20 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. Page ii
Number of fall Chinook returning to the Nimbus Fish Hatchery by sex, age,
females spawned and eggs taken. ..............................................................................4 Number of juvenile Chinook salmon released from Nimbus Hatchery, 1985 2007. ..........................................................................................................................9 Populations in the Central Valley fall-run and late fall–run Chinook ESU,
ordered from north to south (unlisted ESU). ...........................................................15 Populations in the Central Valley spring-run Chinook ESU, ordered from north
to south (ESA listed threatened). .............................................................................16 Fall-run Chinook salmon escapement in the American River basin (20012010). .......................................................................................................................17 Total percent smolt-to-adult survival (catch plus escapement), for Nimbus
Hatchery fall Chinook, 1982-2001 brood years. .....................................................19 Total percent survival of fingerling fall Chinook reared at Nimbus Fish
Hatchery by release location (catch plus escapement)1...........................................19 Broodstock Source. .................................................................................................22 Broodstock Collection. ............................................................................................22 Broodstock Composition. ........................................................................................23 Mating Protocols. ....................................................................................................24 Program Size. ..........................................................................................................25 Release Strategy. .....................................................................................................26 Fish Health Policy. ..................................................................................................26 Hatchery Monitoring by Fish Health Specialists. ...................................................27 Facility Requirements..............................................................................................29 Fish Health Management Plans. ..............................................................................30 Water Quality. .........................................................................................................30 Best Management Practices.....................................................................................31 Hatchery and Genetic Management Plans...............................................................32 Hatchery Evaluation Programs. ...............................................................................33 Hatchery Coordination Teams.................................................................................33 In-Hatchery Monitoring and Record Keeping.........................................................33 Marking and Tagging Programs. .............................................................................35 California Hatchery Review Project – Appendix VIII
Table 25. Table 26. Table 27. Table 28. Post-Release Emigration Monitoring. .....................................................................35 Adult Monitoring Programs. ...................................................................................36 Evaluation Programs. ..............................................................................................36 Direct Effects of Hatchery Operations. ...................................................................37 Appendices
Appendix A-1 Hatchery Program Review Questions
Appendix A-2 Nimbus Fall Chinook Program Data Tables
Appendix A-3 Hatchery Program Review Analysis Benefit-Risk Statements
Appendix B
Natural Populations Potentially Affected by the Hatchery Program
California Hatchery Review Project – Appendix 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,
improvement of navigation on Central Valley rivers, the development of hydroelectric power,
irrigation, and municipal and industrial water supply, protection of the Sacramento-San Joaquin
River Delta from seawater encroachment, and the protection and enhancement of fish and
wildlife.
The American River Basin Development Act of October 19, 1949 created the American River
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 downstream from Folsom Dam, were completed in July 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, just downstream from Nimbus Dam, at RM 22. The hatchery helps fulfill
mitigation requirements for construction of Nimbus Dam (Reclamation 1956). Mitigation is
provided for the American River reach between Nimbus and Folsom dams; it does not address
lost habitat upstream from Folsom Dam. Mitigation goals are for an annual take of 8 million fallrun Chinook salmon eggs and the release of 4 million smolts that are 60 per pound or larger.
1.1
Programmatic Components
Construction of Folsom and Nimbus dams eliminated anadromous fish access to all historical
habitats in the American River upstream of the dams. There is no evidence to indicate that
Chinook salmon presently found in the American River are not indigenous. Yoshiyama et al.
(2001) reviewed the historical distribution of Chinook salmon in the American River and reported
that most likely the American River supported both a fall and spring run. Anecdotal information
however, suggests that non-indigenous Chinook salmon from other Sacramento River sources
may have been introduced into the river after gold mining activities in the mid- to late-1800s
decimated anadromous fish runs.
The Nimbus Chinook salmon program is an integrated harvest program accomplished through the
trapping, artificial spawning, rearing, and release of Chinook salmon. All fish are trucked off-site
to release locations downstream.
1.2
Operational Components
Water for NFH comes from the American River watershed. Specifically, flows are released from
Folsom Lake into Lake Natoma, from where 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 the NFH. The volume of
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water used at NFH ranges between 20 and 50 cfs. Water supplied to either hatchery is not recirculated or exchanged in any manner.
In most years, the temperature of water delivered to NFH is suitable for salmonid rearing.
However, in years characterized by low or reduced inflows to Folsom Lake, 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 DFG installed
an electronically operated gate at the Terminal Structure. A series of manually operated valves
control flow from the Terminal Structure 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).
Under current operations, the weir is installed to direct returning salmon into the fish ladder and it
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.
The fish ladder is opened after the weir is installed and river temperatures are usually at or below
60° F and remains open between late October or early November 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 are 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,
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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 for egg
incubation.
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
settling ponds located approximately 1,700 feet downstream.
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 the fall run Chinook salmon program is obtained from fish that are redirected by
the fish weir and volitionally enter the NFH ladder and trap. The fall-run Chinook salmon
broodstock originated from American River stock and from non-indigenous Chinook salmon
stocks. Although Chinook salmon that entered NFH from the river were included as broodstock
in the past, additional eggs from other Sacramento River Chinook salmon stocks were also
transferred to NFH to help meet mitigation goals due to low number of fish trapped in some
years. More recently, neither eggs nor fish from other sources have been transferred to NFH.
No historical documents identify specific reasons why specific hatchery stocks from other rivers
were chosen for NFH, but in general, those stocks with an abundance of eggs and with similar
characteristics to NFH Chinook were usually selected. All the non-indigenous Chinook salmon
transferred to NFH were from the Sacramento River system.
Since operation began in 1955, NFH personnel reported trapping totals of 423,784 adult and
103,526 grilse Chinook salmon (Figure 1).
The size criteria for grilse salmon has changed during NFH operations. Since 1973, salmon 23.6
inches or smaller in length have been classified as grilse in NFH annual reports; however, in
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1972, the length was 23.9 inches. No length is given for grilse prior to 1972. NFH personnel
include females in the grilse salmon counts if they meet the size criterion.
The weir is installed in September and the fish ladder is opened after river temperatures stabilize
at or below 60o F. This generally occurs in late October, about six weeks after the weir is
installed. The ladder remains open to fish through approximately April 1st for the collection of
steelhead broodstock. The weir remains in place throughout the Chinook salmon run but may be
removed when flow releases are anticipated to exceed 5,000 cfs.
Number of adult Chinook salmon
35,000
30,000
Grilse
25,000
Adults
20,000
15,000
10,000
5,000
2005
2003
2001
1999
1997
1995
1993
1991
1989
1987
1985
1983
1981
1979
1977
1975
1973
1971
1969
1967
1965
1963
1961
1959
1957
1955
0
Year
Figure 1.
Number of adult and grilse Chinook salmon trapped at the Nimbus Fish Hatchery, 19552006.
During the period when the fish ladder and trap are operational, all Chinook that enter the adult
gathering tank are anesthetized and examined for marks, sorted by sex, and the degree of sexual
maturity is determined. Fish are examined and sorted a minimum of two days each week. Ripe
female and male salmon are retained for artificial spawning while unripe fish are returned to the
adult holding ponds via the stainless steel return tubes. A recent history of the number of adults
collected and spawned is provided in Table 1.
Table 1.
Brood
Year
1998
1999
2000
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Number of fall Chinook returning to the Nimbus Fish Hatchery by sex, age, females
spawned and eggs taken.
Adult
Grilse
Total
No. Eggs
No. Eggs
Season
Male
Female
Grilse
Females
Females
Adults
Taken
per Female
Spawned
Spawned
19984,980
4,961
9,941
1,853
2,701
849 12,055,059
3,396
1999
19993,923
2,280
6,203
3,557
1,787
260
7,874,238
4,406
2000
20006,211
4,108
10,319
841
3,043
47 12,561,539
4,128
2001
Brood
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
Season
20012002
20022003
20032004
20042005
20052006
20062007
20072008
20082009
20092010
Male
Female
Total
Adults
Grilse
Adult
Females
Spawned
Grilse
Females
Spawned
No. Eggs
Taken
No. Eggs
per Female
6,569
3,222
9,791
1,836
2,287
7
8,502,971
3,718
3,752
2,479
6,231
3,586
2,103
8
11,244,062
5,347
6,868
5,007
11,875
3,012
3,215
23
15,537,842
4,833
7,327
5,414
12,741
13,659
2,947
26
13,952,850
4,735
8,290
12,279
20,569
1,780
3,890
20
12,565,105
3,214
3,814
4,508
8,322
406
2,526
11
13,289,655
5,238
2,065
2,525
4,590
7
1,817
0
10,659,758
5,867
1,612
1,272
2,884
348
1,099
8
6,752,566
6,144
1,671
1,176
2,847
653
1,015
34
5,764,184
5,679
1.2.3 Spawning
In 1998, NFH and CDFG fish pathology personnel reviewed the mating protocols for Chinook
salmon with geneticists at the University of California Davis. Based on these recommendations,
no effort is made to select fish for spawning from those that enter the gathering tank except for
those with characteristics that identify them as sexually mature. Mating is accomplished using
one female and one male.
Prior to 2007, adipose fin-marked Chinook salmon (indicating they are not NFH-origin fish),
were not included in NFH broodstock. Starting with the brood year 2007, 25% of the juveniles
released were adipose fin-marked (in addition to being coded-wire tagged). As such, it has not
been possible to visually differentiate NFH-origin fish from other stocks after 2008.
Hatchery personnel attempt to take eggs from fish throughout the spawning run to ensure that all
genetic components are represented in the eggs obtained. To help improve this procedure, staff
estimate the minimum number of female Chinook salmon that are needed during a standard week
by using the average number of fish trapped during the past 10 years of operation for each week.
The number of females, normalized for a 10-week spawning period, is presented in Figure 2.
During the adult fish sorting process, only Chinook salmon that expel free flowing eggs and
demonstrate they are sexually mature and ready to spawn, are euthanized and spawned. The
incision method described by Leitritz and Lewis (1976) is used to collect Chinook salmon eggs.
The eggs from a single female are fertilized with the milt from a single male selected from the
storing table and no effort is made to select a specific male fish. The sperm is expressed into the
pan with eggs by stroking the male fish’s vent area. One grilse Chinook salmon out of 100 males
is included to ensure representation in the broodstock.
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Approximately eight ounces of a 30% saline solution (saltwater) is added to the pan to improve
fertilization. A sufficient amount of the solution is added to the empty pan to cover the eggs.
The salt solution holds the albumen from broken eggs in solution, keeps the egg micropyle from
becoming clogged, and prevents agglutination of the sperm.
400
350
Number of Fish
300
250
200
150
100
50
0
1
2
3
4
5
6
7
8
9
10
Week
Note: Blue bars represent mean number of fish trapped, maroon bars represent the estimated number of fish to be spawned.
Weeks are numbered starting with the first week when spawning typically begins.
Figure 2.
Minimum number of female Chinook salmon to be spawned by standard week to mimic
the number of fish trapped throughout the run period.
After eggs are fertilized, they are washed in fresh water and drained in a colander. The eggs are
water hardened in an iodophor solution before being 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 fall-run Chinook salmon from the American River. Eggs in excess of NFH needs are
disposed of through freezing and rendering.
1.2.4 Incubation
The incubation period or average hatching time of the eggs is not fixed for a given temperature
and the incubation period may vary as much as six days between egg lots taken from different
parent fish (Leitritz and Lewis 1976). Typically, the incubation period for Chinook salmon eggs
is about 50 days at a water temperature of 50o F, which is comparable to NFH conditions
(personal communication, T. West, Hatchery Manager II, NFH, retired).
All eggs are incubated in commercial Eagar hatching jars or PVC egg hatching jars. The
maximum loading density for Chinook salmon is 800 ounces (~55,000) eggs per hatching jar.
Hatching jars are not used for smaller experimental egg lots or for egg lots that would not fill the
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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 (~10,000) eggs. Water
temperatures during the incubation period for Chinook salmon eggs is dependent on American
River water temperatures and can vary from 48°- 58° F.
All eggs incubated in the vertical trays and hatching jars remain until nearly all the alevins have
buttoned-up. When the majority of eggs have hatched, all the remaining eggs and alevins are
carefully poured into the deep tanks.
Surplus eggs are not intentionally taken at NFH. However, as part of efforts to mimic the natural
run and spawning period of Chinook salmon, some egg lots may not be needed to meet the
mitigation requirements of NFH. Egg lots or portions of egg lots subsequently are disposed of
through a rendering company. No formal method is used to determine which eggs lots or
portions of egg lots to cull.
Total number of fish spawned and number of eggs taken are summarized in NFH annual reports.
From 1996 to 2005, a total of 126,276,714 Chinook salmon eggs were taken from 27,785 female
Chinook for an average of 4,545 eggs per female. These eggs resulted in a total of 101,107,544
eyed eggs for a 10-year average survival rate to the eyed stage of 80%.
1.2.5 Rearing
Chinook salmon fry remain in the deep tanks until they reach a size of 250 to 300 per pound, at
which time they are moved to the raceways. Juvenile Chinook salmon remain in the raceways
until they are released.
Deep tanks are capable of holding approximately 1,500 gallons of water, although the depth is
varied from egg hatching through rearing. Each tank at maximum depth is capable of holding
approximately 70,000-75,000 Chinook salmon fry at a density of approximately 50 fish per
gallon of water.
The volume and flow rate of raceways can be varied by adjusting the flow rate and dam boards
and the end of each raceway section. At maximum depth and flow rate, each raceway is capable
of holding between 900,000-950,000 fry and fingerlings. (2.6 - 2.7 lb/gpm/inch of fish at 60 fpp
and 3.5 cfs).
Once Chinook salmon fry are free swimming and feeding, the depth of the water in each deep
tank is increased (at the discretion of the hatchery manager), from 10 inches to 27 inches to
prevent overcrowding. Fry remain in the deep tanks until they reach 250-300 to the pound, at
which time they are transported to raceways for the remainder of their six month rearing period.
Juvenile salmon remain the concrete raceways until they are released.
Data on fish size are routinely collected by NFH personnel (weight samples) to help adjust feed
size and amount during rearing; however, this information is not included in the annual reports or
summarized annually.
Once the Chinook salmon fry have absorbed their yolk sac, they are placed on a semi-moist food
manufactured by Bio-Oregon for the remainder of the six month rearing period. Fry are fed up to
12 times per day. The ideal amount of food per fish is 3% of their total body weight. Juvenile
fish in the hatchery buildings are hand fed while juvenile fish in the raceways are fed using a
blower-mounted feeder that is driven past the raceway. The amount of food fed through the
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rearing period depends on their body weight and fish appetite, i.e., they are given as much as they
will eat without wasting food.
Health inspection data for infectious hematopoietic necrosis virus (IHNV) and the bacteria
Renibacterium salmoninarum are collected from ovarian fluid of returning adult females during
spawning each season.
During the eyed egg incubation period, eggs are stirred two times a day and after hatching, the
alevins are stirred up to 8 times daily to prevent suffocation. Dead eggs and alevins are removed
daily from each of the deep tanks to minimize fungal growth and transmission. The deep tanks,
screens, and overflow sections are scrubbed daily. Salt is added to each tank on a weekly basis
after the fry absorb the yolk sac and begin feeding. The salt treatment is continued once the fish
are in the raceways until they are released.
Fish health is routinely monitored by the CDFG’s Fish Health Laboratory personnel. In addition,
specific protocols for biosecurity at NFH have been provided by the CDFG Fish Health
Laboratory. Diagnostic procedures for pathogen detection follow American Fisheries Society
professional standards as described in Thoesen (1994). Appropriate treatments are recommended
or prescribed by a CDFG Fish Pathologist/Veterinarian as appropriate, and follow-up
examinations are performed as needed.
Hatchery management practices (including early detection and treatment of sick fish) minimize
the release of fish infected with pathogens. A random sampling of fish is assessed for general
health prior to release, and transfer of fish to saltwater as a control measure for any freshwater
parasites that may remain when the fish are released.
1.2.6 Release
Mitigation requirements are for the annual release of four million fall-run Chinook salmon smolts
at 60 per pound or larger. The majority of juvenile Chinook salmon produced at NFH are
released in the Carquinez Straits, downstream from the Carquinez Bridge. The first priority
release site is a south shore access point near the City of Crockett using an offshore net pen
release system. The second priority site is the Conoco Phillips deepwater pier at Davis Point. If
access to the deepwater pier is not available, fish are released directly into the straits from the
hauling tank at the first priority release site.
During 2009 and 2010, small groups of 100% uniquely coded-wire tagged juvenile Chinook
salmon were released in the American River at the Sunrise Avenue Boat Ramp. The purpose of
these releases was to compare smolt-to-adult returns, and the incidence of straying for in-river
and bay releases.
Since 1985, NFH has released approximately 149 million juvenile Chinook salmon in the
American, Sacramento, and Cosumnes rivers, San Francisco Bay, and other locations including
several tributaries to the Sacramento River in Placer County (Table 2).
Page 8
Table 2.
Release
Year
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
Totals
Brood
Year
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
Number of juvenile Chinook salmon released from Nimbus Hatchery, 1985 - 2007.
American
River
4,600
1,685,480
410,710
5,530,901
7,631,691
Release Locations
San
Other
NonSacramento Francisco Anadromous Anadromous
River
Bay
Waters
Waters
5,272,100
5,290,290
4,681,725
216,000
5,331,360
5,240,390
366,700
4,900,100
1,170,300
6,995,625
438,140
9,963,840
939,652
9,540,285
602,705
8,795,300
638,000
8,578,437 3,314,750
601,120
5,733,951 2,363,400
646,440
9,209,896
310,800
1,253,570 3,970,450
377,760
4,538,008
732,670
3,851,700
4,131,750
142,200
101,856
81,576,973
4,361,300
4,578,400
4,570,000
3,002,600
5,045,900
52,938,154
115,066
7,182,487
216,922
Total
5,272,100
5,294,890
6,583,205
5,742,070
5,607,090
11,601,301
7,433,765
10,903,492
10,142,990
9,433,300
12,494,307
8,743,791
9,520,696
5,601,780
5,270,678
3,851,700
4,375,806
0
4,361,300
4,693,466
4,570,000
3,002,600
5,045,900
149,546,227
Source: CDFG Hatchery Information System
Juveniles are released as soon as they average 60 fish per pound. Depending on water
temperatures and growth rates, the release period is generally from mid-May through mid-June.
Fish are not held at NFH past June 30. In addition to fresh water from the NFH water system, ice
and kiln-dried salt are added to the transportation tank.
Acclimation Procedures: Since 1996, efforts have been made to release as many of the
program’s juvenile Chinook salmon as possible using a net pen system at the bay release site.
The purpose is to reduce predation by allowing the transported fish the opportunity to acclimate
prior to release. Fish are transferred from the fish-hauling tank into one of three net pens that are
hung from a floating framework which are then towed towards the center of the straits, the net
pen opened, and the fish are allowed to escape.
Juveniles released in the America River are directly released into the river. Since the hatchery
and river water supplies are the same, no effort is made to acclimate the fish prior to release.
Marking Procedures: Prior to 2007, juvenile Chinook salmon were not routinely marked to
identify NFH adult fish. Various groups of fish have been fin-marked and coded-wire tagged as
Page 9
part of various experiments and studies during the operation of NFH. As such, it has not been
possible to differentiate between naturally produced and unmarked hatchery-origin Chinook
salmon.
Starting with the 2007 brood year, 25% of all juvenile Chinook salmon produced at NFH have
been marked with an adipose fin clip and have also been coded-wire tagged. In 2009 and 2010,
smaller groups of approximately 270,000 juveniles that were released in the American River were
100% adipose fin clipped and coded-wire tagged with unique codes.
2
Populations Affected by the Hatchery Program
This section presents information about natural populations that could be affected to some extent
by the Nimbus fall Chinook hatchery program. The section begins with an identification of major
issues of concern, and then follows with a description of the relevant populations (Section 2.1),
and finally a summary of natural production goals (Section 2.2). Appendix B contains
descriptions of other populations potentially affected by this program.
The potential effects of the Central Valley fall Chinook hatchery programs, including the NFH
program, on natural or wild populations of salmon in the Central Valley have been reviewed by a
number of authors in recent years. The following summarizes the major programmatic issues
identified in these reviews, with emphasis on the NFH fall Chinook program where relevant
information is available.
In their review of the factors associated with the recent collapse of the Sacramento fall Chinook
salmon, Lindley et al. (2009) concluded that anthropogenic effects, including hatchery
production, likely played a significant role in increasing the susceptibility of this stock to collapse
during the recent period of unfavorable ocean conditions. 1 They hypothesize that the historical
loss and simplification of habitat in combination with the increasing dominance of hatchery fish
have substantially reduced the life history diversity that once buffered the stock from the effects
of environmental variation. These factors may explain the lack of significant genetic variation
among Central Valley fall Chinook stocks, which is atypical for a basin of this size (Garza et al.
2008, Banks et al. 2000, Williamson and May 2005). Lindley et al. (2009) suggested two
plausible explanations. One is that Central Valley fall Chinook never had significant
geographical structuring because of frequent migration among populations in response to highly
variable hydrological conditions. The other is that extensive straying and interbreeding of
hatchery fish has genetically homogenized the ESU. Historic losses and degradation of habitat as
a result of mining, dams, altered hydrology, levee construction, agricultural conversion, and other
land uses may have also contributed to the loss of genetic diversity (Moyle et al. 2010,
Yoshiyama et al. 1998, 2001, Williams 2006, Lindley et al. 2009).
Concerns regarding the effects of hatchery fish on natural populations focus largely on the loss of
genetic diversity and fitness of naturally spawning fish. For Central Valley fall Chinook stocks,
the practice of releasing large numbers of fall Chinook into the bay and associated high straying
rates is a major concern (CDFG and NMFS 2001). Transporting hatchery fish downstream to
either the Sacramento-San Joaquin Delta or west of there to the bay has gone on for many years
to improve survival and contribution to fisheries. Survival has been found to be enhanced
1
Marine survival rates can fluctuate widely for all natural salmon stocks and can be particularly variable for
Chinook salmon, especially in the southern parts of the species’ range (Pearcy 1992). The hypothesis put forth by
Lindley et al. (2009) is that variability in ocean survival for the aggregate of all Central Valley runs has increased
substantially due to significant loss of life history within the aggregate runs for the reasons summarized in the text.
If this is true, years of low survival can be expected to have an even lower survival than occurred historically.
Page 10
significantly by releasing fish either downstream of the delta or within the delta (CDFG and
NMFS 2001; Lindley et al. 2009; personal communication, Alice Low, CDFG, April 2011).
Garza et al. (2008) stated that the lack of genetic structure of fall-run Central Valley Chinook is
likely at least partly due to the trucking of juvenile fish to the San Francisco Bay estuary by
several hatcheries and the consequent migration pattern (straying) upon return, thereby increasing
gene flow between stocks. Annual releases of hatchery fall Chinook generally exceed 30 million,
and over half of these fish are released at locations downstream from their natal hatchery (mostly
in San Francisco and San Pablo Bay). The Joint Hatchery Review Committee examined the level
of straying of hatchery fish in the Central Valley and found that off-site releases result in straying
indices as high as 90%, with higher indices as the distance from release point to hatchery
increases (CDFG and NMFS 2001). On-site releases typically resulted in stray indices of 5-10%.
This general pattern was also evident from a recent analysis of CWT recovery data associated
with different hatcheries and release locations (ICF Jones & Stokes 2010).
Since 1985, NFH has released up to 12.4 million juveniles annually into the American and
Sacramento rivers, San Francisco Bay and a number of tributaries to the Sacramento River and
Delta. Mitigation requirements are for the annual release of 4 million fall Chinook salmon smolts
(60 per pound or larger). The current practice is to release all juveniles from net pens or a
deepwater pier in the Carquinez Strait. Recovery data for NFH fall Chinook released into the bay
during the period 1987-2007 indicate that most adults were recovered in the lower American
River (97%) with the remainder being recovered in Battle Creek, Butte Creek, Feather River,
Merced River, Mokelumne River, Sacramento River, Stanislaus River, Tuolumne River, and
Yuba River (ICF Jones & Stokes 2010) . Of the 97% of tagged hatchery fish that were recovered
in the lower American River, only 17% of these fish were recovered at the hatchery.
Hatchery fish that spawn in the wild appear to be a large and increasing fraction of the spawning
escapement in the Central Valley (Barnett-Johnson et al. 2007) but evaluation of the contributions
of hatchery fish to naturally spawning population has been limited by the lack of an adequate
marking and recovery program. Otoliths of salmon captured in the California coastal fishery in
2005 indicated that wild fish comprised only 10% (plus or minus 6%) of the catch
(Barnett‐Johnson et al. 2007). Assuming roughly equivalent survival of hatchery and wild fish
from the fishery to the spawning grounds, these results imply that currently about 90% of the
return could consist of hatchery fish. A limited study in the Mokelumne River in 2004 confirmed
this high rate of hatchery-origin fish spawning naturally in the river. Microchemistry analysis
revealed that 90% of the in-river spawners were hatchery fish, based on a sample of 100 spawners
(Weber et al. 2009 as cited in Mesick et al. 2010). Using different methods, Mesick (2010)
estimated that a very high proportion of the naturally spawning Chinook in the Merced River are
likely of hatchery origin (based on CWT recoveries combined with regression modeling).
Figure 3 shows a pattern of increasing total escapement to the American River, even though the
number of adult Chinook trapped at the hatchery has not changed much over time. The studies
cited above suggest that the pattern of increasing escapements to the river is due to an increasing
abundance of hatchery fish in combination with a growing fraction of the number spawning in
nature being composed of hatchery-origin fish.
Page 11
200,000
Number of Chinook salmon
180,000
160,000
NFH trapped Chinook salmon
In-river Chinook salmon estimate
140,000
120,000
100,000
80,000
60,000
40,000
20,000
19
1944
1946
1948
1950
1952
1954
1956
1958
1960
1962
1964
1966
1968
1970
1972
1974
1976
1978
1980
1982
1984
1986
1988
1990
1992
1994
1996
2098
2 00 0
2002
2004
06
0
Year
Source: CDFG Grand Tab database.
Figure 3.
Estimated number of fall-run Chinook salmon in the American River, 1944 to 2006.
The studies cited above, while telling, may not be representative of hatchery composition in all
years or seasons. As a component of current federal and state monitoring and evaluation
programs, a constant fractional marking program has recently been implemented to improve the
estimation of hatchery contributions to ocean and inland harvest, in-river spawning escapement,
and hatchery returns (personal communication, Alice Low, CDFG, April 2011).
Ecological interactions between hatchery and naturally produced fish has also been identified as a
concern, and such interactions may be magnified by straying and the limited capacity and
diversity of habitats currently available to natural Central Valley stocks. Competition is probably
most significant in streams with hatcheries (Battle Creek, Feather River, American River,
Mokelumne River, and Merced River) where relatively large numbers of hatchery-origin fish may
compete with naturally produced fish for spawning or rearing habitat (CDFG and NMFS 2001).
The potential outcome of these interactions could be reduced survival and productivity of natural
stocks. The current practice of releasing most fall‐run Chinook salmon hatchery production as
smolts in the estuary avoids potential competition or predation between hatchery and naturally
produced juveniles in upstream rearing areas. The tradeoff with this strategy is the potential for
greater adverse interactions in the estuary and possibly coastal marine areas. Field observations
in the Sacramento River indicate that hatchery Chinook salmon released as smolts do not compete
with naturally produced juveniles for freshwater rearing habitat because of their strong migratory
behavior (Weber and Fausch 2003). Although these hatchery releases substantially increase the
densities of smolts (hatchery and non‐hatchery) migrating through the estuary, the potential for
competition (for estuarine food resources) may be low because of relatively rapid migration rates
and limited dependence on the estuary for rearing (MacFarlane and Norton 2002). However,
concerns remain regarding the potential density‐dependent effects of hatchery releases on the
Page 12
survival and growth of naturally produced juveniles during their first year at sea, especially in
years of low marine productivity (Williams 2006).
2.1
Current Conditions of Affected Natural Populations
Four seasonal runs of Chinook salmon occur in the Sacramento-San Joaquin River system, and
each can potentially be affected by the Nimbus Hatchery program. Each run is defined by a
combination of adult migration timing, spawning period, and juvenile residency and smolt
migration periods. The runs are named after the season of adult upstream migration, winter,
spring, fall and late-fall. The fall and late-fall runs spawn soon after entering the natal streams,
while the spring and winter runs typically remain in their streams for up to several months before
spawning. Formerly the runs also could be differentiated to various degrees on the basis of their
typical spawning habitats; spring-fed headwaters for the winter run, the higher elevation streams
for the spring run, mainstem rivers for the late-fall run, and lower elevation rivers and tributaries
for the fall run (Yoshiyama et al. 2001).
The Central Valley fall/late fall-run Chinook salmon evolutionarily significant unit (ESU) was
classified as a federal Species of Concern on April 15, 2004 due to specific risk factors. The ESU
includes all naturally spawned populations of fall-run Chinook salmon in the Sacramento and San
Joaquin river basins and their tributaries east of Carquinez Strait, California.
The Central Valley spring-run Chinook salmon ESU was listed as a threatened species on
September 16, 1999; threatened status was reaffirmed on June 28, 2005. The ESU includes all
naturally spawned populations of spring-run Chinook salmon in the Sacramento River and its
tributaries in California, including the Feather River, as well as the Feather River Hatchery
spring-run Chinook program.
The Sacramento River winter-run Chinook salmon ESU was listed as endangered on January 4,
1994; endangered status was reaffirmed on June 28, 2005. The ESU includes all naturally
spawned populations of winter-run Chinook salmon in the Sacramento River and its tributaries in
California, as well as two artificial propagation programs: winter run Chinook from the
Livingston Stone National Fish Hatchery (NFH), and winter run Chinook in a captive broodstock
program maintained at Livingston Stone NFH and the University of California Bodega Marine
Laboratory.
The fall run is currently the most abundant Chinook run in the Central Valley, and historically,
probably was as well (Moyle 2002, Williams 2006). Moyle (2002) observed that the fall run life
history strategy makes it ideal for hatchery production, almost to the exclusion of other runs.
Historically, the other seasonal runs were also large (Yoshiyama et al. 2001), testifying to the
tremendous diversity of habitats and life histories that supported the pre-disturbance Central
Valley Chinook populations (Lindley e al. 2009). The spring run is considered to have been the
dominant run in the San Joaquin system, where the natural flow regime would have favored these
fish (Moyle 2002; Fisher 1994 cited in Lindley 2009). Over the decades, the spring runs in the
Sacramento system dwindled so that they now consist of few remnant populations; the San
Joaquin spring runs are extinct (Lindley et al. 2004). The extensive system of dams in the Central
Valley affected these runs much more than the fall run because the dams blocked much access to
the cold water habitats (Lindley et al. 2009).
Under existing conditions, fall-run Chinook are raised at five major Central Valley hatcheries
(Colman NFH, Feather River, Nimbus, Mokelumne River, and Merced River) which together
release more than 32 million smolts each year. As a result, they are currently the most abundant
Page 13
of the Central Valley races, contributing to large commercial and recreational fisheries in the
ocean and popular sport fisheries in the freshwater streams.
While the fall run is the most abundant run in the Central Valley, the aggregate population has
declined during the last several years from an average of 450,000 (1992-2005), to less than
200,000 fish in 2006 and to about 90,000 spawners in 2007. The population includes both
natural- and hatchery‐origin fish, but the proportion of hatchery fish can be as high as 90 percent
depending on location, year, and surveyor bias (Barnett‐Johnson et al. 2007, as cited in Moyle et
al. 2008).
Central Valley fall-run Chinook migrate upstream as adults from July through December and
spawn from early October through late December. Run timing varies from stream to stream.
Late fall run Chinook migrate into the rivers from mid-October through December and spawn
from January through mid-April. 2 In general, San Joaquin River populations tend to mature
earlier and spawn later in the year than Sacramento River populations. These differences could
have been phenotypic responses to the generally warmer temperature and lower flow conditions
found in the San Joaquin River Basin relative to the Sacramento River Basin. The majority of
young salmon of these races migrate to the ocean during the first few months following
emergence, although some may remain in freshwater and migrate as yearlings.
Adult Central Valley spring‐run Chinook salmon leave the ocean to begin their upstream
migration in late January and early February (CDFG 1998, as cited in NMFS 2009 Recovery
Plan), and enter the Sacramento River between March and September, primarily in May and June
(Yoshiyama et al. 1998). Spring‐run Chinook salmon generally enter rivers as sexually immature
fish and must hold in freshwater for up to several months before spawning (Moyle 2002). While
maturing, adults hold in deep pools with cold water. Spawning normally occurs between
mid‐August and early October, peaking in September (Moyle 2002, as cited in NMFS 2009
Recovery Plan). Spring‐run fry emerge from the gravel from November to March (Moyle 2002).
Juveniles may reside in freshwater for 12 to 16 months, but some migrate to the ocean as
young‐of‐the year in the winter or spring months within eight months of hatching (CALFED
2000, as cited in NMFS 2009 Recovery Plan).
Winter run Chinook salmon are unique because they spawn during summer months when air
temperatures approach their yearly maximum. As a result, they require reaches with cold water
sources to protect embryos and juveniles. Winter‐run Chinook are primarily restricted to the
mainstem Sacramento River. Adult immigration and holding (upstream spawning migration)
through the Delta and into the lower Sacramento River occurs from December through July, with
a peak from January through April (USFWS 1995, as cited in NMFS 2009 Recovery Plan).
Winter‐run Chinook salmon are sexually immature when upstream migration begins, and they
must hold for several months in suitable habitat prior to spawning. Primary spawning areas are in
the mainstem Sacramento River between Keswick Dam (RM 302) and Red Bluff Diversion Dam
(RBDD) (RM 243). Spawning occurs between late‐April and mid‐August, with a peak generally
in June. Fry rear in the upper Sacramento River, exhibiting peak abundance in September, with
fry and juvenile emigration past RBDD from July through March (although NMFS [1993; NMFS
1997] reports juvenile rearing and outmigration extending from June through April).
Except for Central Valley winter Chinook described above, the existing Central Valley fall‐run
Chinook population is unique among North American Chinook ESUs in having little or no
detectable geographically structured genetic variation (Williamson and May 2005; Banks et al.
2
Hhttp://www.dfg.ca.gov/fish/Resources/Chinook/CValleyFall.asp
Page 14
2000). The degree of this diversity in the historical population is unknown, although it was almost
certainly much greater than at present (Lindley et al. 2009). Central Valley late fall–run Chinook
are genetically distinguishable from fall‐run Chinook, yet they are closely related and have been
included in the same ESU (Myers et al. 1998).
For this review, existing Central Valley fall-run and late fall-run Chinook populations were
defined based on populations described in the CDFG Grand Tab worksheet. 3 Populations
included in the analysis were those reported in the last five years to have fall‐ or late-fall-run
Chinook and are consistent with those described in ICF Jones & Stokes (2010) (Table 3).
Table 3.
Populations in the Central Valley fall-run and late fall–run
Chinook ESU, ordered from north to south (unlisted ESU).
Population
Location
Sacramento River Fall Chinook (natural)
Sacramento River
Clear Creek Fall Chinook (natural)
Sacramento River
Cow Creek Fall Chinook (natural)
Sacramento River
Cottonwood Creek Fall Chinook (natural)
Sacramento River
Battle Creek Fall Chinook
Sacramento River
Battle Creek Late-Fall Chinook
Sacramento River
Mill Creek Fall Chinook (natural)
Sacramento River
Deer Creek Fall Chinook (natural)
Sacramento River
Butte Creek Fall Chinook (natural)
Sacramento River
Feather River Fall Chinook
Sacramento River
Yuba River Fall Chinook (natural)
Sacramento River
American River Fall Chinook
Sacramento River
Mokelumne River Fall Chinook
San Joaquin River
Stanislaus River Fall Chinook (natural)
San Joaquin River
Tuolumne River Fall Chinook (natural)
San Joaquin River
Merced River Fall Chinook
San Joaquin River
Historically, there were 19 independent populations and eight dependent populations of
spring‐run Chinook salmon in the Central Valley (Lindley et al. 2004). Currently, there are three
independent (Butte, Mill, and Deer) and six dependent (Antelope, Big Chico, Clear, Thomes,
Cottonwood/Beegum, and Stony) populations remaining, along with one “other” hatchery‐natural
integrated population in the Feather River and one “other” population in the Sacramento River
below Keswick Dam (Table 4). Currently, the Sacramento River winter run Chinook salmon
ESU consists of a single (independent) population in the mainstem Sacramento between Keswick
Dam and Red Bluff Dam.
The current conditions of each of these populations, which could be affected by the Nimbus
Hatchery program, are described in Appendix B. The American River fall Chinook population is
described below.
3
http://www.calfish.org/LinkClick.aspx?fileticket=Kttf%2boZ2ras%3d&tabid=104&mid=524
Page 15
Table 4.
Populations in the Central Valley spring-run Chinook ESU, ordered from north to south
(ESA listed threatened).
Population
Classification
Clear Creek Spring Chinook (natural)
Dependent
Beegum-Cottonwood Spring Chinook (natural)
Dependent
Battle Creek Spring Chinook (natural)
Dependent
Other Sacramento River Spring Chinook
(natural production above Red Bluff Diversion
Dam)
Other
Antelope Spring Chinook (natural)
Dependent
Mill Creek Spring Chinook (natural)
Independent
Thomes Spring Chinook (natural)**
Dependent
Deer Creek Spring Chinook (natural)
Independent
Stony Creek Spring Chinook (natural)*
Dependent
Big Chico Spring Chinook (natural)
Dependent
Butte Creek Spring Chinook (natural)
Independent
Feather River Spring Chinook (integrated)
Other
* Because there are no data available for Stony Creek spring-run Chinook in CDFG’s Grand Tab
database, this population is not included in our description of affected natural populations.
** Thomes Creek was excluded from our description of affected natural population s because
only two spring-run Chinook have been documented here in the past 10 years.
2.1.1 American River Fall Chinook
The lower American River watershed begins at Folsom Dam and flows 30 miles to its confluence
with the Sacramento River near downtown Sacramento. Flows from Folsom Lake are reregulated by Nimbus Dam below which the American River enters the floodplain and the
urbanized Sacramento area. The river is buffered by the 30-mile-long American River Parkway,
extending from Folsom to the Sacramento River confluence near Old Sacramento. Water quality
in the lower American River is considered to be very good and it has been designated a
“Recreational River” under both the California Wild and Scenic Rivers Act and the National Wild
and Scenic Rivers Act. 4
Historically, Chinook salmon and steelhead had access to approximately 125 miles of spawning
and rearing habitat in the upper reaches of the American River. According to Yoshiyama et al.
(2001), spring, fall and possibly late-fall runs of salmon, as well as steelhead, ascended the
American River and its major tributaries, impeded to varying degrees by a number of natural
barriers. Clark (1929) as cited in Yoshiyama et al. (2001) described the 1927-1928 salmon run as
“very good” and noted spawning occurred from the river mouth to Old Folsom Dam, about one
mile above the City of Folsom.
In the 1940s, both the spring and fall runs began to reestablish themselves in the American River
above Old Folsom Dam. Counts at the fishway at Old Folsom Dam showed that the spring run
reached a maximum of 1,138 fish in 1944 and the fall run reached 2,246 fish in 1945. The
4
Hhttp://www.sacriver.org/documents/2010/Roadmap/American_LowerAmerican.pdf
Page 16
spring-run count dropped to 42 fish in 1945, 16 in 1946, and three fish in 1947; both the spring
and fall runs reportedly were decimated after the fish ladder on Old Folsom Dam was destroyed
by flood waters in 1950. The spring run was finally extirpated during construction of present-day
Folsom Dam and Nimbus Dam (Gerstung 1971 unpublished report as cited in Yoshiyama et al.
2001).
From 1944–1959, combined Chinook run sizes were 6,000 to 39,000 spawners annually; these
fish were mainly fall Chinook (Fry 1961 as cited in Yoshiyama et al. 2001). From 1944–1955, an
estimated average of 26,500 salmon (range 12,000 to 38,652) spawned annually in the mainstem
American River below the City of Folsom (Gerstung 1971 unpublished report as cited Yoshiyama
et al. 2001).
When the Folsom-Nimbus project was completed in 1958, access to about 70% of the spawning
habitat historically used by Chinook salmon and 100% of the spawning habitat used by steelhead
was blocked. As a result, the Nimbus Salmon and Steelhead Hatchery was constructed to replace
the affected runs. The fish weir and ladder now direct these fish to the Nimbus Fish Hatchery.
In recent decades, fall Chinook spawning escapements have ranged from about 5,700 (in 2008) to
178,000 (in 2003) fish annually. From 2001 through 2010, Chinook salmon escapement to the
Nimbus Hatchery has averaged approximately 11,500 fish (Table 5). During this same period,
natural spawners averaged 64,240 fish, or approximately 73% of the total run. According to ICF
Jones & Stokes (2010), approximately 84% of the natural fall Chinook spawners in the American
River are considered to be hatchery-origin fish.
Table 5.
Year
Fall-run Chinook salmon escapement in the American River basin (2001-2010).
Nimbus
Hatchery
In-River
(American)
Total
Percent In-River
(American)
2001
11,750
135,384
147,134
92.0%
2002
9,817
124,252
134,069
92.7%
2003
14,887
163,742
178,629
91.7%
2004
26,400
99,230
125,630
79.0%
2005
22,349
62,679
85,028
73.7%
2006
8,728
24,540
33,268
73.8%
2007
4,597
10,073
14,670
68.7%
2008
3,184
2,514
5,698
44.1%
2009
4,789
5,297
10,086
52.5%
2010
9,095
14,688
23,783
61.8%
Average
11,560
64,240
75,800
73.0%
Source: http://www.calfish.org/LinkClick.aspx?fileticket=Kttf%2boZ2ras%3d&tabid=104&mid=524
2.2
Long–term Goals for Natural Populations
The USFWS Anadromous Fish Restoration Plan (AFRP) states that the natural production of
anadromous fish in Central Valley rivers and streams will be sustainable on a long-term basis at
levels not less than twice the average attained during the period of 1967-1991 (USFWS 2001).
The AFRP defines natural production and other key terms used to interpret and measure whether
the goal has been achieved as follows:
Page 17
Natural Production: Fish produced to adulthood without direct human intervention in the
spawning, rearing, or migration processes. Natural production should be self-sustaining. The
program should not depend on hatchery-produced fish to sustain populations of naturally
spawning fish.
Sustainable: This is defined as capable of being maintained at target levels without direct human
intervention in the spawning, rearing or migration processes.
Direct Human Intervention: Hatchery and artificial propagation, including supplementation and
out-planting of eggs or any other life-stage, requires handling of fish by humans during the
spawning and rearing processes and therefore are forms of direct intervention. Title 34 of the
Central Valley Project Improvement Act clearly states that fish produced with direct human
intervention should not be included in counts of natural production.
Counting: All naturally produced adult fish shall be counted, including those that are harvested
prior to spawning.
The AFRP production target for all Central Valley fall Chinook populations was set at 750,000
adults. The production target for the American River is 160,000 fish (harvest plus spawning
escapement).
3
Fisheries Affected by the Hatchery Program
The Nimbus fall Chinook hatchery program affects both marine and freshwater fisheries. These
fisheries provide significant economic benefit to many communities, as well as being highly
valued for recreational purposes. The ocean feeding grounds of Central Valley Chinook runs are
primarily off the coasts of California and Oregon, though relatively small numbers of fish from
these runs migrate further north (Moyle 2002).
Ocean fisheries off the coasts of California, Oregon, and Washington within the United States
Exclusive Economic Zone (three to 200 miles offshore) are managed by the Pacific Fisheries
Management Council which is responsible for the developing annual recommendations for ocean
salmon harvest within this zone. The Council’s Salmon Fishery Management Plan describes the
goals and methods for salmon management. Management tools such as season length, quotas,
and bag limits are used to regulate the fishery based on the estimated number of salmon available
for harvest. Each year the Council follows a preseason process to develop recommendations for
management of the ocean fisheries. Recommendations are implemented by the NMFS on May 1
of each year. The California Fish and Game Commission has authority for setting seasons and
bag limits for California ocean commercial and sport harvest within three miles of the coast, and
inland sport and tribal fisheries.
3.1
Current Status of Fisheries
Total smolt-to-adult survival rates for fall Chinook released from NFH between 1982 and 2001
ranged from 0.06% in 1982 to 9.3% in 1985 (Table 6). No coded-wire tagged groups were
released from NFH in brood years 1990 to 1999. Based on CWT data summarized from the
Regional Mark Processing Center (www.rmpc.org), the average total exploitation rate on fish
produced in brood years 2000 and 2001 was estimated to be 68%, though the rate does not
account for all strays (thereby biasing the harvest rate estimates high).
Page 18
Table 6.
Total percent smolt-to-adult survival (catch plus escapement), for Nimbus Hatchery fall
Chinook, 1982-2001 brood years.
Brood Year
SAR1
1982
0.06
1983
2.87
1984
4.98
1985
9.30
1986
2.02
1987
1.57
1988
1.43
1989
0.18
2000
4.32
2001
1.30
Average Total Exploitation Rate
(2000, 2001 Brood Year only)
68%
1Annual data are averages of multiple tag codes and includes all age classes of recoveries.
Source: www.rmpc.org
Total smolt to adult survival rates for fingerling fall Chinook brood years released from Nimbus
Hatchery at Wickland in 2000 and 2001 are shown in Table 7. Survival rates vary significantly
by brood year. The range of SARs for fingerlings was 4.32% in 2000 and 1.3% in 2001.
Table 7.
Total percent survival of fingerling fall Chinook reared at Nimbus Fish Hatchery by
release location (catch plus escapement)1.
Release Location
Brood Year
2000
2001
Wickland
4.32%
1.3%
1
Data are averages of multiple tag codes.
Figure 4 depicts the percent total survival of Nimbus fall Chinook to selected fisheries (20002001 brood year average). The California ocean troll fisheries had the largest contribution (32%)
followed by California spawning ground recoveries (26%), Oregon ocean troll (21%) and
California ocean sport (9%). California hatchery escapement (return to all hatcheries) accounted
for 5% of the total recoveries. Small numbers of recoveries were also reported in Washington
treaty Indian troll, non-treaty ocean troll and ocean sport fisheries (less than 1% in each fishery).
The percentage of two year-old recoveries (all fisheries plus escapement) average 4% of the total
(www.rmpc.org).
Page 19
All JACKS
4%
OR 40‐ Ocean Sport
3%
OR 10‐
Ocean Troll
21%
CA 10‐Ocean Troll
32%
CA 54‐ Spawning Ground
26%
CA 40‐ Ocean CA 50‐ Hatchery Sport
9%
Escapement
5%
Figure 4.
3.2
Percent of total survival of Nimbus fall Chinook to selected fisheries and escapement
(average of 2000-2001 brood years).
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
Nimbus Hatchery to address issues that potentially affect achieving the goals for the fish
populations. Issues to be considered in evaluating hatchery strategies are first identified,
followed by brief descriptions of how possible strategies relate to those issues.
4.1
Issues Affecting Achievement of Goals
A host of issues exist that might affect fishery, fish production, and conservation goals for the
Sacramento 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, followed by important questions associated with the issues.
4.1.1 Natural Production Issues
Status of viable salmonid population (VSP) parameters for American River fall Chinook
populations: What are the expected effects of the Nimbus fall Chinook hatchery program on
VSP parameters of natural Chinook populations? Can hatchery strategies be updated to enhance
the VSP parameters for the natural populations?
Page 20
Hatchery stock genetic management: What are the effects of current management on genetic
diversity of the hatchery stock and possible effects of strays on natural-origin fish? Can hatchery
strategies be updated to improve hatchery stock genetic diversity and adaptation to the natural
environment (when fish leave the hatchery), both for fish that return to the hatchery and for those
that spawn in nature?
Natural population genetics: Is the hatchery program affecting the genetic integrity and
productivity of the natural populations and, if so, can the program be modified to reduce, or even
reverse, effects?
Performance of the hatchery stock unrelated to genetic composition: Do hatchery fish
released into nature exhibit behavioral traits that adversely affect their performance, unrelated to
domestication effects on genetics, prior to returning to the hatchery or if they spawn in nature,
and if so, can hatchery strategies be modified to ameliorate effects?
4.1.2 Ecological Interaction Issues
Predation effects: What are the predation effects of the hatchery fish released as part of this
program on sensitive natural populations? What are the predation effects of other hatchery
programs on fish released as part of this program? Can the hatchery strategies for this program be
updated to ameliorate these effects?
Competition: What are the competition effects of the hatchery fish released as part of this
program on sensitive natural populations? What are the competition effects of other hatchery
programs on fish released as part of this program? Can the hatchery strategies for this program be
updated to ameliorate these effects?
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 process of Northwest
salmon hatcheries. The California Hatchery Scientific Review Group 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 (BMP) and “no”
answer implies a potential risk. The CA HSRG requested five-year disease histories from
resource managers as part of this questionnaire, but summaries were not provided for all years.
This limited the Group’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.
Page 21
4.3
Programmatic Strategies
The California HSRG identified a suite of issues that are applicable to hatchery programs
statewide. These issues were organized under five topics (1) broodstock management; (2)
program size and release strategies; (3) incubation, rearing and fish health management; (4)
monitoring and evaluation; and (5) direct effects of hatchery operation on local habitat and
aquatic or terrestrial organisms. For each topic, hatchery standards to be achieved were defined
and in many cases, suggested implementation guidelines to meet the standard were developed.
All standards and guidelines are listed in Chapter 4 of the California Hatchery Review Report.
Standards that the California HSRG determined apply to this program are presented below.
Where their evaluation determined that this program complies with a standard, this is noted.
Where their evaluation determined that this program does not comply with a standard, “standard
not met” is noted, and recommended guidelines to resolve the issue are identified. In many cases,
the California HSRG provided program-specific comments as well.
4.3.1
Broodstock
Table 8.
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: Large number of out-or-basin fall Chinook
broodstock have previously been transferred to this facility,
and large numbers of out-of-basin strays return to this facility
and are incorporated into the broodstock.
Table 9.
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.
Standard met.
Standard 1.3: Collection methods are appropriate for the
program goals.
Standard NOT met.
Comment: pNOB is unknown. The estimated value for
2010 exceeded the minimum threshold.
Standard 1.4: Trapping is designed to collect sufficient fish
as potential broodstock to be representative of the entire run
timing and life history distribution of the population or
population component with which it is integrated.
Standard NOT met.
Page 22
Guideline
Guideline 1.1.1. Broodstock should be chosen from
locally adapted stocks native to the basin and with life
history characteristics appropriate for the program
goals.
Guideline
Guideline 1.3.1. Trapping locations should include
mechanisms for collecting sufficient numbers and
diversity of both hatchery- and natural-origin fish to
meet program goals. If inadequate numbers of
natural-origin fish are available with current collection
methods, then additional collection methods are
required.
Guideline 1.4.1. Fish traps should be operated for at
least the entire temporal period of the run and should
not exclude fish with any particular life history
characteristics. An exception to this guideline is
allowable when non-representative broodstock
collection is necessary to achieve program goals, such
as separating broodstock of differing eco-types.
Standard
Comment: Spawning doesn’t begin at Nimbus until late
October.
Standard 1.5: Hatcheries have effective facilities for the
extended holding of unripe fish and males that will be used
for multiple spawning.
Guideline
Comment: Water temperatures may preclude earlier
spawning.
Standard met.
Comment: 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).
Table 10. Broodstock Composition.
Standard
Standard 1.6: Broodstock is primarily comprised of fish
native to the hatchery location, with incorporation of fish
from other locations not exceeding the rate of straying of
natural-origin fish.
Standard NOT met.
Comment: Coded-wire tag analysis indicates that large
numbers of out-of-basin fish return to Nimbus and are
included in the broodstock.
Guideline
Guideline 1.6.1. Broodstock should originate in the
subbasin in which the hatchery is located, except
when estimates of natural straying from proximate
locations are known, in which case, incorporation of
returning adults from those locations should not
exceed this natural straying.
Comment: Until off site releases are eliminated in the
entire Central Valley, tag analysis should be used to
identify stray hatchery-origin fish among those fish
selected for broodstock. Strays from other hatchery
programs should not be used as broodstock, or if eggs
are collected from or fertilized by such fish, they
should be culled soon after spawning.
Standard 1.7: The levels of natural-origin broodstock are
appropriate for program goals.
Standard met.
Comment: pNOB is unknown.
Comment: Recent coded-wire tag data from CDFG
indicated NORs may be available.
Natural-origin fish should be incorporated into
broodstock at a minimum rate of 10% to prevent
divergence of the hatchery and natural components of
the integrated population. This may require auxiliary
adult collection facilities or alternative collection
methods (e.g., seining or trapping).
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
Page 23
Standard
Guideline
capture.
Standard 1.8: Fish from different runs are not crossed.
Standard met.
Comment: The timing of weir installation may provide
unintentional separation of spring run (Feather River) from
fall run.
Standard 1.10: For Chinook and coho salmon, fish from all
age classes and sizes are incorporated into broodstock at
rates that are commensurate with their relative reproductive
success in natural areas, when known.
Guideline 1.10.1. For Chinook salmon, the number of
jacks to be incorporated into broodstock should not
exceed the lesser of: 1) 50% of the total number of
jacks encountered at the hatchery, and 2) 5% of the
total males used for spawning.
Standard NOT met.
Comment: Jacks are incorporated into brood at a rate of
1% of the males, but should be higher.
Table 11. Mating Protocols.
Standard
Standard 1.11: The program uses genetically conscious
mating protocols to control or reduce inbreeding and genetic
drift (random loss of alleles), to retain existing genetic
variability and avoid domestication, while promoting local
adaptation for integrated stocks.
Guideline
Standard NOT met.
Standard 1.12: Inbreeding is avoided.
Standard met.
Standard 1.13: The proportion of natural-origin fish used as
broodstock does not negatively affect the long-term viability
of the donor population. For conservation-oriented
programs, extinction risk of the ESU may take precedence.
Standard met.
Page 24
4.3.2 Program Size and Release Strategies
Table 12. 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).
Comment: Juvenile production numbers are based
on historical adult production (average number of fish
spawning between Nimbus and Folsom).
Standard 2.3: Annual assessments are made to determine if
adult production goals are being met.
Standard NOT met.
Comment: Program size is based on juvenile production,
not adult production.
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.
Consistency with Standard Unknown.
Comment: Consideration of deleterious ecological effects is
unclear. Few data available for assessing ecological effects.
Standard 2.5: Natural spawning populations not integrated
with a hatchery program should have less than five percent
total hatchery-origin spawners (i.e., pHOS less than five
percent). Spawners from segregated hatchery programs
should be absent from all natural spawning populations (i.e.,
pHOS from segregated programs should be zero).
Comment: 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).
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.
Comment: Populations have not been identified and
population boundaries have not been delineated. This
has been identified as an area of needed research
(Chapter 6.2 of the California Hatchery Review
Report).
Consistency with standard unknown
Page 25
Table 13. 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).
Comment: Fish are released at a larger size and later
release than wild fish (the effect on adult characteristics is
unknown).
Standard 2.7: Juveniles are released at or in the near vicinity
of the hatchery.
Standard NOT met.
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.
Comment: 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 14. 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: The current “working” CDFG fish health policy is
inadequate.
Page 26
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
Standard
Guideline
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.
Table 15. 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.
Comment: Unknown if BKD management strategy is
effective due to lack of documentation.
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
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
Page 27
Standard
and laboratory findings are reported on a standard fish
health monitoring form.
Guideline
the discretion of the fish health specialist.
Standard NOT met.
Comment: Diagnostic exams alone do not met the standard
of routine, preventative fish health monitoring.
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
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.
Page 28
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
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.
Table 16. Facility Requirements.
Standard
Guideline
Standard 3.8: Physical facilities and equipment are
adequate, and operated in a manner that promotes quality
fish production and optimum survival throughout the rearing
period. If facilities are determined to be inadequate to meet
all program needs, and improvements are not feasible, then
the hatchery program(s) must be re-evaluated within the
context of what the facility can support without compromising
fish culture and/or fish health, or causing adverse
interactions between hatchery and natural fish populations.
Standard met.
Standard 3.9: Distinct separation of spawning operations,
egg incubation, and rearing facilities is maintained through
appropriate sanitation procedures and biosecurity measures
at critical control points to prevent potential pathogen
introduction and disease transmission to hatchery or natural
fish populations, as follows:
a)
Disinfect/water harden eggs in iodophor prior to
entering “clean” incubation areas. In high risk situations,
disinfect eggs again after shocking and picking, or
movement to another area of the hatchery.
b)
Foot baths containing appropriate disinfectant will
be maintained at the incubation facility’s entrance and exit.
Foot baths will be properly maintained (disinfectant
concentration and volume) to ensure continual
effectiveness.
c)
Sanitize equipment and rain gear utilized in
broodstock handling or spawning after leaving adult area.
d)
Sanitize all rearing vessels after eggs or fish are
removed and prior to introducing a new group.
e)
Disinfect equipment, including vehicles used to
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 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: Program should install physical barriers
between areas and follow biosecurity measures.
Current Plexiglas barrier is inadequate.
Guideline 3.10.1. Follow existing statutes, including
NEPA, CEQA, ESA, CESA, and current court
decisions.
Standard NOT met.
Page 29
Standard
Comment: CDFG statewide fish screening policy provides
that under the provisions of the U.S. Fish & Wildlife
Coordination Act the CDFG shall require the installation of
fish screens on all unscreened diversions where fish are
present (i.e., hatchery intake).
Table 17. 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 18. 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.
Guideline
Standard met.
Page 30
Table 19. Best Management Practices.
Standard
Standard 3.14: The rationale, benefits, risks, and expected
outcomes of any deviations from established best
management practices 5 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.
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 written 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 3.16.2. 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.
Standard met.
Comment: The lack of an egg inventory prevents
assessment of survival by life stage.
Comment: Guideline 3.16.2 is not always followed.
Managers need to record culling separately from
actual mortality by life stage to generate accurate
mortality rates.
The cause of the low egg-to-juvenile release survival
rate (43.6 percent) should be determined.
5
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 31
Standard
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.
Guideline
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.
Comment: Guideline 3.17.4 is not always followed.
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.
Standard met.
4.3.4 Monitoring and Evaluation
Table 20. 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.
Page 32
Table 21. 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 22. 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.
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 23. 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).
Page 33
Standard
c) Record sex-specific age composition of the fish spawned,
as determined by reading scales and/or tags, from a
systematic sample of the fish spawned (n>550, or all
spawned fish for programs with less than 550 spawned fish).
d) Describe in detail the spawning protocols used for each
program (by family group for conservation-oriented
programs), including the number of times individual males
were used.
e) Describe in detail the culling protocols used for each
program, including purpose.
f) Calculate and record effective population size (in
conservation-oriented programs).
g) Measure and record mean egg size, fecundity, and fish
length for each individual in a systematic sample of spawned
females (n>50), to establish and monitor the relation
between fecundity, egg size, and length in the broodstock.
(Include a table of all measurements in annual report.)
h) Record survival through the following life stages: green
egg to eyed egg, eyed egg to hatch, hatch to ponding,
ponding to marking/tagging, and marking/tagging to release.
i) Record mean, standard deviation, and frequency
distribution based on n>100 measurements of fish length, by
raceway, at periodic intervals (no less than monthly) prior to
release and at time of release for all release types, to
assess trends and variability in size throughout the rearing
process. (Report means and standard deviations in annual
reports; individual measurements and frequency
distributions in electronic files.)
j) Maintain records of disease incidence and treatment,
including monitoring of treatment efficacy.
k) Report CWT releases and recoveries to relevant
databases (i.e., RMIS) on a timely annual basis.
Standard NOT met.
Comment: In-hatchery data are generally lacking for a
number of important biological criteria.
Page 34
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.
Table 24. Marking and Tagging Programs.
Standard
Standard 4.5: Chinook salmon marking and tagging
programs allow for:
a)Estimation of ocean and freshwater fishery impacts, and
natural area and hatchery escapement at the age-, stockand release group-specific levels,
b)Estimation of the proportion of hatchery-origin fish in
natural spawning areas,
c) Estimation of the proportion of natural-origin fish in
hatchery broodstock,
d) Real-time identification of hatchery-origin juveniles and
adults (i.e., hatchery vs. non-hatchery origin),
e) Identification of stock of origin for hatchery-origin fish,
f) Real-time identification of yearling vs. fingerling releasetype fish at the adult stage.
Standard NOT met.
Comment: Currently 25% of fish receive a coded wire tag
and an adipose fin-clip.
Guideline
Guideline 4.5.1. For mitigation/harvest programs (fall-,
late fall-, and spring run), all releases should be 100
percent CWT and 25 percent adipose fin-clipped.
Yearling releases should receive an additional
distinguishing external mark or tag (e.g., a ventral finclip) allowing real-time discrimination from fingerling
releases at the adult stage. Deviation from this
guideline must be rigorously justified, and in no
circumstance can marking and tagging programs fail
to meet Standard ((a) through (f) above).
Comment: Program fish should be 100 percent
coded wire-tagged and 25 percent adipose fin-clipped.
Table 25. Post-Release Emigration Monitoring.
Standard
Guideline
Standard 4.8: The quantities listed below are monitored in
the freshwater environment following release of juvenile
Chinook and coho. Summaries of collected data and
associated estimates, along with comparisons to established
targets, are included in annual or periodic (every 5 to 10
years) reports produced by the monitoring agencies/entities.
a) Annual: Document length (mean, standard deviation, and
frequency distribution) of hatchery fish at release as
compared to naturally produced smolts.
b) Periodic: Document the number of days (mean, standard
deviation, and frequency distribution) from release of
hatchery fish to passage at a location near entry to salt
water (e.g., using PIT tags/detectors or acoustic tags/arrays)
and the degree of overlap with natural-origin fish.
c) Periodic: Estimate the percent hatchery-origin fish among
outmigrating juveniles and, where feasible, estimate total
juvenile production.
Standard NOT met.
Comment: Post-release information on juvenile NORs and
HORs is unavailable.
Page 35
Table 26. Adult Monitoring Programs.
Standard
Standard 4.10: Monitoring programs for Chinook salmon
allow for estimation of the following on an annual basis.
a) Total recreational and commercial ocean harvest,
Guideline
and harvest of hatchery-origin fish at the age-, stock-,
and release group-specific (CWT) level,
b) Total freshwater harvest, and harvest of hatchery-origin
fish at the age-, stock-, and release group-specific (CWT)
level,
c) Total returns (hatchery -and natural-origin) to hatchery,
and returns at the age-, stock-, and release group-specific
(CWT) level,
d) Age composition of hatchery returns,
e) Total escapement by tributary and by species/run,
f) Proportion of hatchery-origin fish among natural area
spawners (pHOS) by tributary and at age-, stock-, and
release group-specific (CWT) level,
g) Age composition of individual tributaries important for
natural production.
Standard NOT met.
Comment: An estimated percent of first generation
hatchery and natural fish on the spawning grounds is not
known. Hatchery has no genetic monitoring plan for this
program.
Table 27. Evaluation Programs.
Standard
Standard 4.13: Evaluation programs for Chinook salmon
assess the following fundamental issues on a brood-specific
basis:
a) Survival from release to pre-fishery recruitment,
b) Age-specific maturation schedules,
c) Straying (here defined as failure of hatchery-origin fish to
return to the hatchery from which they originated or to the
watershed in the immediate vicinity of the hatchery),
d) Age-specific fishery contribution rates,
e) Pre-fishery age-3 ocean recruitment.
Evaluation programs for Chinook salmon assess the
following fundamental issues on a periodic basis (e.g., every
5 to 10 years):
f) The relationship of hatchery fish survival rates and
maturation schedules to size and/or date of release;
g) Long-term trends in phenotypic traits (age, maturity,
fecundity at size, run/spawn timing, size distribution) and
genetic traits (divergence among year classes, effective
population size, divergence from natural populations) of
hatchery populations;
Page 36
Guideline
Guideline 4.13.1. Use tag recovery data and cohort
reconstruction (cohort analysis) methods to estimate
the following quantities. In the future, alternative
technologies or analytical methods may generate
other data suitable for estimating these quantities.
• Brood survival from release to ocean age-2 at
the release group-specific (CWT) level,
• Brood maturation schedule (age-specific
conditional maturation probabilities) at the
• Straying and geographic distribution of stray
hatchery-origin fish at the release groupspecific (CWT) level,
• Age-specific ocean and freshwater fishery
contributions and exploitation rates at the
Pre-fishery ocean recruitment of hatchery-origin fish at
age-3 at the release group-specific (CWT) and
program level.
Standard
h) Spatial and temporal overlap and relative sizes of
emigrating juvenile hatchery- and natural-origin fish and total
(hatchery plus natural-origin) spawner distribution and
densities to assess the likelihood or magnitude of
deleterious effects of hatchery-origin fish on naturally
spawning fish due to competition, predation, or behavioral
effects.
Guideline
Standard NOT met.
4.3.5 Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial
Organisms.
Table 28. 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
watershed 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.
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.
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.
Guideline 5.2.3. Barrier weirs should effectively block
adult passage either for broodstock
congregation/collection or as required for in-river
fishery management.
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.
Page 37
Standard
Standard NOT met.
Comment: Working conditions during weir installation,
operations, and removal are dangerous.
5
Guideline
Literature Cited
Banks, M.A., V.K. Rashbrook, M.J. Calavetta, C.A. Dean, and D. Hedgecock. 2000. Analysis of
microsatellite DNA resolves genetic structure and diversity of Chinook salmon (Oncorhynchus
tshawytscha) in California's Central Valley. Canadian Journal of Fisheries and Aquatic Sciences
57:915-927.
CDFG (California Department of Fish and Game) and NMFS (National Marine Fisheries Service). 2001.
Joint Hatchery Review Committee. Final Report on Anadromous Fish Hatcheries in California.
California Department of Fish & Game, Sacramento, CA. 40p.
Hedgecock, D., M.A. Banks, V.K. Rashbrook, C.A. Dean, and S.M. Blankenship. 2001. Applications of
population genetics to conservation of Chinook salmon diversity in the Central Valley. California
Department of Fish and Game Fish Bulletin No. 179(1). 26 p.
Garza, J.C, S.M. Blankenship, C. Lemaire, and G. Charrier. 2008. Genetic population structure of
Chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley. Final report for
Calfed project “Comprehensive evaluation of population structure and diversity for Central
Valley Chinook Salmon.”
Hatchery Scientific Review Group (HSRG). 2010. Columbia River Hatchery Reform System-Wide
Report. Prepared by the Hatchery Scientific Review Group.
ICF Jones & Stokes. 2010. Hatchery and Stocking Program Environmental Impact
Report/Environmental Impact Statement. Final. Sacramento, California. Prepared for the
California Department of Fish and Game and U.S. Fish and Wildlife Service, Sacramento,
California. January 2010.
Leitritz, E. and E. Lewis. 1976. Trout and Salmon Culture (Hatchery Methods). California Department
of Fish and Game Fish Bulletin 164. 197 p.
Lindley, S.T., C. B. Grimes, M. S. Mohr, W. Peterson, J. Stein, J. T. Anderson, L.W. Botsford, D. L.
Bottom, C. A. Busack, T. K. Collier, J. Ferguson, J. C. Garza, A. M. Grover, D. G. Hankin, R. G.
Kope, P. W. Lawson, A. Low, R. B. MacFarlane, K. Moore, M. Palmer-Zwahlen, F. B. Schwing,
J. Smith, C. Tracy, R. Webb, B. K. Wells, T. H. Williams. 2009. What caused the Sacramento
River fall Chinook stock collapse? Pre-publication report to the Pacific Fishery management
Council. March 18, 2009.
Lindley, S.T., R. Schick, B.P. May, J.J. Anderson, S. Greene, C. Hanson, A. Low, D. McEwan, R.B.
MacFarlane, C. Swanson, and J.G. Williams. 2004. Population structure of threatened and
endangered Chinook salmon ESUs in California's Central Valley basin. NOAA Technical
Memorandum NMFS-SWFSC-360.
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Lindley, S.T., C.B. Grimes, M.S. Mohr, W. Peterson, J. Stein, J.T. Anderson, L.W. Botsford, McFarlene,
R.B, and E.C. Norton. 2002. Physiological ecology of juvenile Chinook salmon (Oncorhynchus
tshawytscha) at the southern end of their distribution, the San Francisco Estuary and Gulf of the
Farallones, California. Fisheries Bulletin 100:244-257.
LCFRB (Lower Columbia Fish Recovery Board). 2004. Lower Columbia salmon recovery and fish and
wildlife subbasin plan, volume 1. LCFRB, Longview, WA.
MacFarlane, R.B., and E.C. Norton. 2002. Physiological Ecology of juvenile Chinook salmon
(Oncorhynchus tshawytscha) at the southern end of their distribution, the San Francisco Estuary
and Gulf of the Farallones, California. Fishery Bulletin 100:244-257. 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.
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.
Moyle, P.B., W.A. Bennett, W.E. Fleenor, and J.R. Lund. 2010. Habitat Variability and Complexity in
the Upper San Francisco Estuary. Working Paper, Delta Solutions Program, Center for
Watershed Sciences, University of California – Davis.
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Waknitz, K. Neely, S.T. Lindley, and R. S. Waples. 1998. Status review of Chinook salmon from
Washington, Idaho, Oregon, and California. NOAA Technical Memorandum NMFS-WFSC-35.
National Marine Fisheries Service (NMFS). 1993. Biological Opinion: Sacramento River Winter‐Run
Chinook Salmon.
NMFS. 1997. Proposed Recovery Plan for the Sacramento River Winter‐Run Chinook Salmon. Long
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Central Valley of California, USA. North American Journal of Fisheries Management 25 9931009.
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Page 40
Appendix VIII
Program Report
Appendix A-1
June 2012
APPENDIX A-1
HATCHERY PROGRAM REVIEW QUESTIONS
NIMBUS FISH HATCHERY FALL CHINOOK
BACKGROUND INFORMATION
1
Name of Hatchery and Program
Hatchery:
Nimbus Hatchery
Program:
Fall Chinook
2
Species and Population (or stock) under Propagation and ESA Status
Species:
Fall-run Chinook salmon
ESA Status:
Species of Concern
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
[email protected]
Kent Smith, Regional Manager
1701 Nimbus Road
Rancho Cordova, CA 95670
(916) 358-2900
FAX: (916) 358-2912
[email protected]
Nimbus Fish Hatchery Fall Chinook 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
[email protected]
Bob Burks, Hatchery Manager I
2001 Nimbus Road
(916) 358-2820
FAX: (916) 358-1466
[email protected]
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 employws 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
The NFH fall-run Chinook salmon program is an integrated harvest program that propagates fish
for commercial and recreational fishing opportunities and harvest. They are not produced to
spawn in the wild or to be genetically integrated with any specific natural population.
7
Purpose (Goal) of Program
Replace lost adult production above Nimbus Dam (and below Folsom Dam). To do that, the
Nimbus Hatchery produces 4 million fall Chinook juveniles.
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:
Yes. Original broodstock was taken from the river. Over the years, some eggs have been
imported from Feather River, etc.
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:
N/A.
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:
The assumption is yes. Data has not been collected to compare hatchery with wild for fish size,
age structure, etc.
4
Does the broodstock have a pathogen history that indicates no threat
to other populations in the watershed?
Clarification:
Request a 5-year pathogen history.
The broodstock chosen poses no threat to other populations in the watershed from pathogen
transmission.
Answer:
Yes. A history of pathogen incidence is available in Appendix A-3.
Page A-1 4
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:
No. In the last two years, scales have been taken for age analysis as part of the Ocean Salmon
Project. Since constant fractional marking, estimates of natural origin broodstock are starting to
be made from marks and CWTs.
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:
Unknown. (See question 10)
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:
Unknown (See question 10).
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:
No. Once trapped, even green fish are not returned.
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, for the last two years.
Wild Fish: No, samples are not collected.
Jacks are considered 26.5 inches or less.
See Table 4 for collected and spawned. See egg culling discussion. Jacks are less than 5% of
the broodstock. See goals and constraints document.
13
Does the proportion of the spawners brought into the hatchery follow
a “spread-the-risk” strategy that attempts to improve the probability
of survival for the entire population (hatchery and natural
components)?
Clarification:
The Review Panel will also consider timing of run and collection over all components of the run.
The proportion of spawners brought into the hatchery improves the likelihood that the population
will survive a catastrophic loss from natural events or hatchery failure.
Answer:
Yes.
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. Previous to that, there were imports from Feather River (approximately 1983).
16
Is the broodstock collected and held in a manner that results in less
than 10% pre-spawning mortality?
Clarification:
If NO, ask questions to help the Review Panel evaluate the cause and consequences of prespawning mortality. What is the pre-spawning mortality in the program? Why does it exceed
10%? Are there any issues with bias in pre-spawning mortality? Are there facility needs that
would reduce mortality?
Maintaining pre-spawning survival higher than 90% maintains an effective population size and
reduces domestication selection.
Answer:
Yes. In hatchery records are kept of losses.
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 and provide ambient
river water. Most common pathogens are ectobacteria. See pathogen reports and annual health
certifications.
Page A-1 9
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?
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.
Some coagulated yolk has occurred when water temp drops below 50s from fish that were held
and spawned in warmer water. There is lower survival on these early eggs (approximately 810% loss). Early 77%, late is more like 90% for fertilization rate.
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 alarms specifically for
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.
Page A-1 10
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.
Answer:
Yes, 1:1 mating. There is no selection process. Jacks are included as 1 male out of every 100
pairs (99 males, 1 jack, 100 females).
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).
Page A-1 11
Use of precocious males for spawning as a set percentage or in proportion to their contribution to
the adult run promotes within population diversity.
Answer:
Yes. Jacks are included as 1 male out of every 100 pairs (99 males, 1 jack, 100 females). Jills
may be included when there are very few females, but are not typically included.
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. The American River historically had a spring run of Chinook salmon. Some spring
Chinook may be trapped above the weir when it is installed in mid-September. These fish
cannot enter the hatchery.
Marked fish were not historically collected for brood after December 1 (special plantings in
Discovery Park (mouth of the American River) Coleman late fall Chinook. Discontinued after
2007.).
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.
Page A-1 12
29
Does the water used for incubation provide natural water temperature
profiles that result in hatching/emergence timing similar to that of the
naturally produced stock?
Clarification:
Use of water resulting in natural water temperature profiles for incubation ensures hatching and
emergence timing similar to naturally produced stocks with attendant survival benefits.
Answer:
Yes.
30
Can incubation water temperature be modified?
Clarification:
If YES, why is the temperature manipulated? This question will be asked for all programs to
provide information about the facility use (e.g., otolith marking).
The ability to heat or chill incubation water to approximate natural water temperature profiles
ensures hatching and emergence timing similar to naturally produced stocks with attendant
survival benefits.
Answer:
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 intake pipe for the hatchery, but no alarm specific to incubation
flow.
Page A-1 13
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.
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 culling would occur if BKD became a problem.
Page A-1 14
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.
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. Approximately 800 oz for
green eggs, 65,000-75,000 eggs per jar for hatching. Jars are 12 inch diameter, 36 inch height.
Page A-1 15
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.
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 (5.5 million). All
fish that enter the hatchery are spawned, regardless of egg take target. The total number of eggs
is calculated and the reduction to 5.5 million 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:
Yes, to provide a more steady water temperature. Heaters may be useful for late egg take to get
up to size for release.
Page A-1 16
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.
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.
Page A-1 17
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 for the hatchery intake valve, but no alarm specific to rearing flow.
45
Is the water supply [for rearing] protected by back-up power
Clarification:
Security during rearing is maintained by back-up power generation for the pumped water supply.
Answer:
Yes, 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. See Appendix A-3.
Page A-1 18
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, not 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?
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 60-80 fpp by May 1 for in river releases. Net pen releases target 60 fpp. No
length frequencies are taken. There is an interim goal of 120 fpp by first week of April for
vaccination for red mouth and tagging trailer. Length frequency may be acquired from the
marking trailer.
Fish are fed to satiation in order to maximize growth.
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.
Page A-1 19
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:
Yes. (In general, maximize growth in the spring) The state has a contract to buy a certain type
of food and the hatchery cannot stray from that type.
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.
Page A-1 20
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.
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.
Page A-1 21
Answer:
This facility only releases subyearlings. The first 3M fish go to river. Later egg takes
(approximately 1M) tend to go to net pens. There is a paired release with net pens and in river
fish, but neither of those released represent the spectrum of the egg take. An experimental paired
release of 270,000 each to the river and the net pens are 100% marked (Ad and CWT) – 2009
release and continuing.
Net pens survival is much higher than on station release during 2000-2003 study period.
However, now net pens are operated differently. Predators are responding differently now than
when the study was conducted. Historically, the net pens were used as an acclimation site and
fish were held for several hours before being released. Now fish are hauled out and immediately
released.
Programmatic net pen discussion is in progress.
HATCHERY OPERATION PHASE: RELEASE
59
Is there a protocol to produce fish to a set size at release (fpp and
length)?
Clarification:
If so, what is the protocol? What is the basis for the set size at release?
Producing fish that are qualitatively similar to natural fish in size may improve performance and
reduce adverse ecological interactions.
Answer:
Yes, 60-80 fpp for in river releases, 60 fpp for net pens. Yes, based on site-specific successes
and best professional judgment. Historical research was used to set release size.
Net pen mesh size 3/8, so fish cannot be smaller than 70 fpp.
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)?
Page A-1 22
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 of release 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. Net pen releases rely on water temperature and other logistical constraints.
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:
Answer:
Yes, maximize growth to reach size at release.
63
Are there protocols for physiological status of fish at release?
Clarification:
If so, what is the protocol? Are gill ATPase and blood chemistry tested prior to smolt releases?
Page A-1 23
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, 60-80 fpp for in river release, 60 fpp for net pens. The goal is to release smolts that can
survive sea water.
65
Are volitional releases during natural out-migration practiced?
Clarification:
The Review Panel noted that in some cases, a non-volitional release may be the best practice.
Follow up with implementation questions (how long is the volitional release period, what occurs
if fish remain, etc.).
Volitionally releasing smolts during the natural outmigration timing may improve homing,
survival, and reduce adverse ecological interactions.
Answer:
No. Fish are trucked to release location. 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.
Page A-1 24
Answer:
Yes. Fish size, water temperature, and water diversions.
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. There are no releases adjacent to the hatchery. In river plants are released approximately 22
miles downstream (Jiboom Street) and downstream 5 miles (Sunrise Boat Ramp).
Small inland Chinook program using tested and certified IHN negative progeny. Approximately
100,000 released. This program is ongoing and is dependent on availability of IHN negative
fish.
Net pens are used to release 3 or 4 hatchery’s production. Logistical constraints for fish
transportation prevent release at optimal time for all 3 hatcheries at the same time. Currently, net
pens suffer from lack of acclimation, too few net pens for all hatchery fish, fish being stocked in
pens and immediately being released. There is a question of age at maturity changing due to use
of net pens. Plan is to continue to use net pens under current operation in Carquinez Straits.
68
Are data routinely collected for released fish?
Clarification:
If YES, provide a table describing all releases for the last 10 years (including date, size, type,
release method, location, number, purpose, and mark groups). The Review Panel has asked that
the table include fish released for experimental purposes.
Are pre-release exams done? If so, are results provided to the hatchery manager or appropriate
staff prior to release?
Answer:
Yes, 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.
Page A-1 25
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. See previous questions for release locations.
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:
Yes, in river releases are in the first week of May, net pen releases are in the first week of June.
Net pen releases are composed of the later egg takes. Egg allocation is approximately 1.2M to
net pens, 270,000 to Sunrise for paired releases with net pens (also in river release), 2.7M to
Jibboom.
Page A-1 26
69C Additional Question: Does the hatchery have a method to estimate
the number of fish released?
Clarification:
If YES, what are these inventory procedures?
If NO, does the hatchery estimate the numbers of fish released and how?
Answer:
Yes, 100% of fall Chinook are machine counted in trailers less than one month prior to release.
Mortalities are tracked after counts are made.
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 27
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 28
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 29
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?
Answer:
No.
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?
Page A-1 30
Answer:
Yes, the HGMP is draft completed, currently being updated. There is an administrative draft.
By June 2014 HGMP should be complete.
M&E4
Additional Question: Is there an ongoing genetic monitoring
program? If so, please describe.
Clarification:
Answer:
No.
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. The Ocean Salmon Program collects CWT data for other
purposes, but collects data on Nimbus fish. A summary is provided to Nimbus Hatchery.
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, constant fractional marking (25%), started in 2006 brood, released in 2007. There is 100%
marking (Ad clip and CWT) on study groups. Funding for marking is questionable.
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 run through marking trailer.
Page A-1 31
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:
All fish collected in weir are recorded in log book for run timing. Recently, age structure will be
available from constant fractional marking. Since all fish trapped are eventually spawned, then
the presumption is there is no difference between fish collected and broodstock.
M&&E9
Additional Question: Is there coordination in tagging and
recovery of marks/tags among watersheds, hatcheries and/or other
programs?
Answer:
Yes, the Ocean Salmon Program collects CWT data. Data on sport fisheries is not collected
everywhere. Spawning ground surveys are done on the American River (carcass surveys mark
recapture to estimate abundance, but no scale samples, CWT are collected, but accuracy is
unknown). American River is closed for fishing when fall Chinook are in the river.
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.
This question is used to evaluate the level of hatchery influence on the population.
Answer:
Assumed to be high (> 50 percent). Alice Low was to provide information on HOR abundance
based on fractional marking program.
Page A-1 32
85
Is the percent hatchery-origin fish (first generation) in natural
spawning areas estimated?
Clarification:
If YES, provide information about how the contribution to spawning is estimated (via weir
counts, live counts, carcass recovery, etc.). Provide information on the relative reproductive
success of hatchery fish on the spawning grounds.
Estimating the proportion of hatchery fish spawning in the wild allows evaluation of composition
targets and prevents hatchery returns from masking the status of the natural population.
Answer:
Yes. Carcass surveys are used to count Ad-clips and collect CWT’s. Hatchery fish are assumed
to make up a large percentage of the natural escapement. Alice Low was to provide 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.
87
Are in-culture performance standards met? How often?
Meeting these standards is assumed to be the best management practice.
Page A-1 33
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 60 fpp was more successful than
smaller. The only post release performance standard specified is adult return to hatchery to
achieve egg take.
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.
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.
Page A-1 34
Answer:
No.
Page A-1 35
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 36
Appendix VIII
Program Report
Appendix A-2
June 2012
Appendix A‐2 Nimbus Hatchery Fall Chinook Program Data Tables Table 1.
Date
Results of fish pathologist reports for Nimbus Hatchery Fall Chinook, 2007-2010.
Purpose
Weight Length
(g)
(mm)
Condition
Factor
(average)
Hematocrit Mesenteric
(%)
Fat Score
5/30/2007 pre-release
1.07
40
1.3
0.88
38
1.0
3/23/2008
8.0
93.5
1.00
47.7
1.5
Internal
Assessment
External
Assessment
Pathogens
healthy
appearance
Treatment
approved for
release
approved for
release
perfect
condition
Flavobacterium
columnare
Flavobacterium
psychrophilum
tetramycin feed
tetramycin feed
Page A-2 1
Table 2.
Brood
Year
Egg to release survival of fall Chinook salmon reared at Nimbus Hatchery, 1999-2009.
Release
Year
1999
2000
2000
2001
2001
2002
2002
2003
2003
2004
2004
2005
2005
2006
2006
2007
2007
2008
2008
2009
2009
2010
Average
Page A-2 2
Egg Take
Eyed Eggs
Fish Ponded
7,874,238
12,561,539
8,502,971
11,244,062
15,537,842
13,952,850
12,565,105
13,289,655
10,660,698
6,752,566
5,764,184
9,822,273
4,998,484
5,354,632
5,933,749
5,785,471
6,955,977
6,466,196
6,435,249
6,203,441
6,266,952
5,134,526
5,169,672
5,882,214
4,148,741
4,444,345
4,925,012
4,386,174
6,018,465
5,336,147
5,072,860
5,219,950
5,033,276
4,239,419
4,811,618
5,148,728
Smolts
Released
3,851,700
4,518,006
2,485,232
5,321,300
9,271,866
4,570,000
3,002,600
5,045,900
4,076,000
4,191,880
4,612,057
4,631,504
Egg to
Release
Survival
48.9%
36.0%
29.2%
47.3%
59.7%
32.8%
23.8%
38.0%
38.2%
62.1%
80.0%
43.6%
Nimbus Fish Hatchery Fall Chinook Program / Appendix A-2 / June 2012 Table 3.
Actual number, release location and average size of fall Chinook releases from the Nimbus Hatchery, 1985-2010.
Release
Year
Brood
Year
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
American
River
4,600
1,685,480
410,710
5,530,901
Release Location1
San
Other
Sacramento
Francisco Anadromous
River
Bay
Waters
5,272,100
5,290,290
4,681,725
216,000
5,331,360
5,240,390
366,700
4,900,100
1,170,300
6,995,625
438,140
9,963,840
939,652
9,540,285
602,705
8,795,300
638,000
8,578,437
3,314,750
601,120
5,733,951
2,363,400
646,440
9,209,896
310,800
1,253,570
3,970,450
377,760
4,538,008
732,670
3,851,700
4,273,950
142,200
2,485,232
5,321,300
9,156,800
4,570,000
3,002,600
5,045,900
4,076,000
NonAnadromous
Waters
101,856
115,066
Pounds
Average
Weight
(fpp)
89,760
120,075
89,648
91,555
117,861
58.7
44.1
73.4
62.7
47.6
61,050
38,600
88,541
131,516
75,400
49,500
67,618
70,276
74.0
64.4
60.1
70.5
60.6
60.7
74.6
58.0
Total
Marks Applied
5,272,100
5,294,890
6,583,205
5,742,070
5,607,090
11,601,301
7,433,765
10,903,492
10,142,990
9,433,300
12,494,307
8,743,791
9,520,696
5,601,780
5,270,678
3,851,700
4,518,006
2,485,232
5,321,300
9,271,866
4,570,000
3,002,600
5,045,900
4,076,000
25% Ad clip/ CWT
25% Ad clip/ CWT
25% Ad clip/ CWT
25% Ad clip/ CWT
25% Ad clip/ CWT
25% Ad clip/ CWT
Page A-2 3
Release
Year
Brood
Year
2009
2010
Totals
2008
2009
American
River
269,9802
3,220,3623
10,852,053
Release Location1
San
Other
Sacramento
Francisco Anadromous
River
Bay
Waters
3,921,900
1,391,695
81,576,973 70,763,561
7,182,487
NonAnadromous
Waters
Pounds
Average
Weight
(fpp)
71,049
80,349
216,922
Total
Marks Applied
59.0
4,191,880 25% Ad clip/ CWT
57.4
4,612,057 25% Ad clip/ CWT
61.7 170,591,996
All fish are trucked to release sites. There are no releases (volitional or forced) at the hatchery.
2 100% tagged unique code.
3 274,540 100% tagged with unique code
1
Table 4.
Number of fall Chinook salmon returns to Nimbus Hatchery by sex, age, females spawned and eggs harvested for BY 1998
through BY 2009.
Brood
Year
Season
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
1998-1999
1999-2000
2000-2001
2001-2002
2002-2003
2003-2004
2004-2005
2005-2006
2006-2007
2007-2008
2008-2009
2009-2010
Page A-2 4
Male
4,980
3,923
6,211
6,569
3,752
6,868
7,327
8,290
3,814
2,065
1,612
1,671
Female
4,961
2,280
4,108
3,222
2,479
5,007
5,414
12,279
4,508
2,525
1,272
1,176
Total
Adults
9,941
6,203
10,319
9,791
6,231
11,875
12,741
20,569
8,322
4,590
2,884
2,847
Grilse
1,853
3,557
841
1,836
3,586
3,012
13,659
1,780
406
7
348
653
Adult
Females
Spawned
2,701
1,787
3,043
2,287
2,103
3,215
2,947
3,890
2,526
1,817
1,099
1,015
Grilse
Spawned
849
260
47
7
8
23
26
20
11
0
8
34
Eggs Take
12,055,059
7,874,238
12,561,539
8,502,971
11,244,062
15,537,842
13,952,850
12,565,105
13,289,655
10,659,758
6,752,566
5,764,184
Fecundity
3,396
4,406
4,128
3,718
5,347
4,833
4,735
3,214
5,238
5,867
6,144
5,679
Nimbus Fish Hatchery Fall Chinook Program / Appendix A-2 / June 2012 Table 5.
Annual return of fall Chinook salmon to the American River, 1955-2009.
Year
Estimated
Total InRiver Run
Below
Nimbus
Dam
1955
1956
1957
1958
1959
1960
1961
1962
1963
1964
1965
1966
1967
1968
1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
118,114
43,660
37,810
70,096
158,516
130,785
6,832
49,372
65,951
98,705
48,225
46,888
24,145
88,747
82,242
56,120
53,596
26,200
41,605
4,000
37,315
23,159
41,680
32,132
43,042
26,400
33,000
18,000
31,332
26,786
28,680
17,459
27,447
56,843
22,900
18,145
38,529
Estimated
In-river
Run Above
Nimbus
Dam
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
Total
Estimated
Chinook
Salmon Inriver
Spawning
Population
Number
of Ddult
Chinook
Salmon
Trapped
at NFH
Number
of Grilse
Chinook
Salmon
Trapped
at NFH
Total
Number
of
Chinook
Salmon
Trapped
at NFH
Estimated
Total Inriver Run
Chinook
Salmon
118,114
43,660
37,810
70,096
158,516
130,785
6,832
49,372
65,951
98,705
48,225
46,888
24,145
88,747
82,242
56,120
53,596
26,200
41,605
4,000
37,315
23,159
41,680
32,132
43,042
26,400
33,000
18,000
31,332
26,786
28,680
17,459
27,447
56,843
22,900
18,145
38,529
6,231
2,549
2,428
5,128
11,875
9,791
638
4,785
6,888
10,319
6,203
5,819
3,345
12,741
10,859
7,788
7,529
4,058
6,370
769
7,173
4,342
7,877
6,567
9,941
6,567
8,348
4,414
7,675
7,343
7,854
5,447
10,296
20,569
8,322
6,769
16,008
3,586
521
813
1,370
3,012
1,836
252
910
505
841
3,557
1,674
2,913
13,659
1,676
1,305
671
1,175
498
774
3,067
894
1,267
846
1,853
2,514
2,576
733
893
3,313
770
1,659
1,953
1,780
406
359
4,436
9,817
3,070
3,241
6,498
14,887
11,627
890
5,695
7,393
11,160
9,760
7,493
6,258
26,400
12,535
9,093
8,200
5,233
6,868
1,543
10,240
5,236
9,144
7,413
11,794
9,081
10,924
5,147
8,568
10,656
8,624
7,106
12,249
22,349
8,728
7,128
20,444
127,931
46,730
41,051
76,594
173,403
142,412
7,722
55,067
73,344
109,865
57,985
54,381
30,403
115,147
94,777
65,213
61,796
31,433
48,473
5,543
47,555
28,395
50,824
39,545
54,836
35,481
43,924
23,147
39,900
37,442
37,304
24,565
39,696
79,192
31,628
25,273
58,973
Page A-2 5
Year
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Subtotal
Mean
Page A-2 6
Estimated
Total InRiver Run
Below
Nimbus
Dam
34,259
43,462
18,604
12,929
17,300
15,879
17,900
25,031
14,347
17,078
6,708
25,200
9,000
4,472
11,200
9,986
2,742
2,060,555
38,158
Estimated
In-river
Run Above
Nimbus
Dam
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
blocked
Total
Estimated
Chinook
Salmon Inriver
Spawning
Population
34,259
43,462
18,604
12,929
17,300
15,879
17,900
25,031
14,347
17,078
6,708
25,200
9,000
4,472
11,200
9,986
2,742
2,060,555
38,158
Number
of Ddult
Chinook
Salmon
Trapped
at NFH
Number
of Grilse
Chinook
Salmon
Trapped
at NFH
Total
Number
of
Chinook
Salmon
Trapped
at NFH
13,675
17,783
7,532
6,115
8,160
7,964
10,369
12,890
9,226
9,230
4,024
19,942
7,439
5,107
12,703
4,590
2,884
2,847
7,165
441,270
7,880
2,068
2,805
550
2,047
2,050
661
2,866
744
3,442
511
826
9,331
1,771
1,349
1,638
7
348
653
1,939
106,473
1,901
15,743
20,588
8,082
8,162
10,210
8,625
13,235
13,634
12,668
9,741
4,850
29,273
9,210
6,456
14,341
4,597
3,232
3,500
9,104
547,743
9,781
Estimated
Total Inriver Run
Chinook
Salmon
50,002
64,050
26,686
21,091
27,510
24,504
31,135
38,665
27,015
26,819
11,558
54,473
18,210
10,928
25,541
14,583
5,974
2,595,694
48,068
Nimbus Fish Hatchery Fall Chinook Program / Appendix A-2 / June 2012 California Hatchery Review Project
Appendix VIII
Program Report
Appendix A-3
June 2012
Appendix A‐3 Hatchery Program Review Analysis Nimbus Hatchery Fall Chinook 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
Y
This program uses a broodstock
representing populations native or
adapted to the watershed, which
increases the likelihood of long term
survival of the stock, helps avoid loss
of among population diversity, and
reduces the likelihood of unexpected
ecological interactions.
Selection of a broodstock not
representing populations native or
adapted to the watershed poses a
risk of loss of among population
diversity and may pose additional
risks of adverse ecological
interactions with non-target stocks.
NA
Choice of a broodstock with a similar
life history and evolutionary history to
the extirpated stock improves the
likelihood of successful reintroduction.
Y
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
NA
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
N
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.
N
Not recycling adults to the lower river
to provide additional harvest reduces
the likelihood of straying and
unintended contribution to natural
spawning
N
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 Fall Chinook 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
Y
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
Y
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
Y
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
Y
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
Y
Y
Y
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.
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
Y
NA
Y
NA
Y
NA
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
NA
Facilities
Does hatchery intake screening
comply with California State,
National Marine Fisheries Service,
and/or other agency facility
standards?
Y
Y
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.
Y
Estimating the proportion of hatchery
fish spawning in the wild allows
evaluation of composition targets and
prevents hatchery returns from
masking the status of the natural
population.
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 Fall Chinook
Appendix B
Natural Populations Potentially Affected by the Hatchery Program
In addition to the natural population of fall Chinook in the American River, numerous other
salmonid populations may be affected by operation of this program. These are summarized
below.
1
Sacramento River (Spring, Fall, Late-fall, and Winter Chinook)
The Sacramento River is approximately 384 miles long from its headwaters near Mount Shasta to
its mouth at the Delta with a watershed that covers approximately 27,000 square miles in the
north central part of California. The Sacramento River has an annual runoff of 22,000,000 acrefeet; approximately one third of the total runoff in the state. The upper watershed includes the
drainages above Lake Shasta and Lake Oroville. 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.
Land use in the mountainous regions of the basin is principally forest, while 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 Sacramento River has the sole distinction among the salmon-producing rivers of western
North America of supporting four runs of Chinook salmon: spring, fall/late-fall and winter runs.
Historically, the Central Valley drainage as a whole is estimated to have supported spring‐run
Chinook salmon runs as large as 700,000 fish between the late 1880s and 1940s (Yoshiyama et al.
1998). The general indication is that the winter run formerly numbered in the high tens of
thousands and occasionally may have exceeded 100,000 fish. Similar estimates can be inferred
from historical catch data for the fall, and late-fall runs; pre-twentieth century run sizes, including
harvest, for the entire Central Valley may have approached 900,000 fish for the fall-run and
100,000 for the late-fall run (Fisher 1994, as cited in Yoshiyama et al. 1998).
Presently, the upstream distribution of salmon in the Sacramento River is delimited by Keswick
Dam, a flow-regulating dam located nine miles below Shasta Dam. The only known streams that
currently support viable populations of spring‐run Chinook salmon in the Central Valley are Mill,
Deer and Butte creeks (see below). Each of these populations is small and isolated (NMFS
2009); however, between 2001 and 2010, an average of 152 spring-run Chinook also spawned
sporadically in the mainstem Sacramento River (Table B-1).
1
http://ca.water.usgs.gov/sac_nawqa/study_description.html
Nimbus Fish Hatchery Fall Chinook Program / Appendix B / June 2012
Page B 1
Table B-1.
Spring-run Chinook salmon escapement in the mainstem Sacramento River (20012010).
Mainstem Sacramento River
Upstream
Downstream
Year
of RBDD
of RBDD
Total
2001
600
21
621
2002
195
0
195
2003
0
0
0
2004
370
0
370
2005
0
30
30
2006
0
0
0
2007
248
0
248
2008
0
52
52
2009
0
0
0
2010
0
0
0
Average
141
10
152
Fall-run and late-fall run Chinook salmon spawn in the mainstem Sacramento River where
spawning gravels occur for about 67 miles downstream of Keswick Dam. Between 2001 and
2010, an average of nearly 25,000 fall Chinook and approximately 11,000 late-fall Chinook
spawned in the mainstem Sacramento River, largely above the Red Bluff Diversion Dam (RBDD)
(Tables B-2 and B-3). Those numbers were heavily influenced by fish produced in hatcheries on
Battle Creek and the Feather and American rivers.
Table B-2.
Fall-run Chinook salmon escapement in the mainstem Sacramento River (2001-2010).
Upstream
Downstream
Year
of RBDD
of RBDD
Total
2001
57,920
17,376
75,296
2002
45,552
20,138
65,690
2003
66,485
22,744
89,229
2004
34,050
9,554
43,604
2005
44,950
12,062
57,012
2006
46,568
8,900
55,468
2007
14,097
2,964
17,061
2008
23,134
1,609
24,743
2009
5,311
516
5,827
2010
13,824
2,548
16,372
Average
35,189
9,841
45,030
Page B 2
Table B-3.
Late-fall run Chinook salmon escapement in the mainstem Sacramento River (20012010).
Downstream of
Upstream of RBDD
RBDD
Year
In-River
Coleman NFH*
Total
In-River (Total)
Nov 2000 – Apr 2001
18,351
18,351
925
Nov 2001 – Apr 2002
36,004
36,004
0
Nov 2002 – Apr 2003
5,346
38
5,384
148
Nov 2003 – Apr 2004
8,824
60
8,884
0
Nov 2004 – Apr 2005
9,493
79
9,572
1,031
Nov 2005 – Apr 2006
7,678
12
7,690
2,485
Nov 2006 – Apr 2007
7,678
66
7,744
1,470
Nov 2007 – Apr 2008
3,673
0
3,673
291
Nov 2008 - Apr 2009
3,424
32
3,456
65
Nov 9009 – Apr 2010
3,843
81
3,924
439
Average
10,431
46
10,468
685
* Transferred from Coleman NFH from Keswick Dam and/or RBDD.
Currently, winter Chinook spawning habitat is likely limited to the reach extending from Keswick
Dam downstream to the RBDD. The Livingston Stone NFH on the upper Sacramento River has
been producing and releasing winter Chinook since 1998. This conservation program has
apparently resulted in a net increase in returning adult winter‐run Chinook salmon, although
hatchery fish make up a significant portion of the population (Brown and Nichols 2003, as cited
in NMFS 2009). Between 2001 and 2010, an average of approximately 7,500 winter-run
Chinook spawned in the Sacramento River (Table B-4). According to IFC Jones & Stokes
(2010), approximately 38% of the natural fall-run Chinook spawners and 52% of the natural
spring-run Chinook spawners in the Sacramento River above RBDD are hatchery-origin fish.
Table B-4.
Winter-run Chinook salmon escapement in the mainstem Sacramento River (20012010).
Upstream of
Downstream
Year
RBDD
of RBDD
Total In-River
Dec 2001-Aug 2002
7,325
12
7,337
Dec 2002-Aug 2003
8,105
28
8,133
Dec 2003-Aug 2004
7,784
0
7,784
Dec 2004-Aug 2005
15,730
0
15,730
Dec 2005-Aug 2006
17,149
48
17,197
Dec 2006-Aug2007
2,487
0
2,487
Dec 2007-Aug 2008
2,725
0
2,725
Dec 2008-Aug 2009
4,416
0
4,416
Dec 2009-Aug 2010
1,533
0
1,533
Average
7,473
10
7,482
Page B 3
2
Clear Creek (Spring and Fall Chinook)
The Clear Creek watershed begins in the Trinity Mountains east of Trinity Lake and flows
approximately 50 miles to its confluence with the Sacramento River just south of Redding. The
watershed is divided into upper and lower Clear Creek, with Whiskeytown Reservoir forming the
boundary between them. Below Whiskeytown Reservoir, Clear Creek flows approximately 18.1
river miles to the Sacramento River with a watershed area of about 48.9 square miles. Inflow is
contributed from a cross-basin transfer between Lewiston Lake in the Trinity River watershed
and Whiskeytown Reservoir. Most of the land in the lower Clear Creek watershed is
undeveloped, with scattered private residences, gravel mining operations, light industrial and
commercial uses. Land ownership is a combination of private, commercial, state, and federal
entities (including the Bureau of Land Management and National Park Service) (Greenwald et al.
2003).
For the 50-year period from 1954 to 1994, fall-run Chinook salmon populations in lower Clear
Creek averaged around 2,000 fish annually, ranging from around 500 to as many as 10,000
depending on the year. In recent years, CALFED and its member agencies, and the Western
Shasta Resource Conservation District (RCD) have invested heavily in restoration work to
enhance anadromous fish populations, while at the same time, the BLM has aggressively pursued
acquisition of private lands in lower Clear Creek to expand public access and recreation
opportunities. 2 Beginning in 1995, Clear Creek flows were increased to benefit fall and late-fall
Chinook spawning and rearing. The flows improved fish passage into Clear Creek, improved
water temperatures during spawning and rearing periods, increased the amount of spawning and
rearing habitat, and contributed to record numbers of fall Chinook salmon spawning in Clear
Creek (Brown 1996 as cited in Greenwald et al. 2003). Beginning in 1999, stream flows were
also increased in the summer to benefit spring-run Chinook and steelhead. Other significant
actions taken specifically for spring-run Chinook and steelhead have included the removal of
McCormick-Saeltzer Dam in 2000, and placement of spawning-sized gravel for steelhead below
Whiskeytown Dam and the Placer Road Bridge (Greenwald et al. 2003).
As a direct result of these enhancements, Clear Creek currently supports a substantial population
of fall-run Chinook salmon, though large numbers of spawners are believed to be of hatchery
origin (IFC Jones & Stokes 2010). Between 2001 and 2010, an average of over 8,900 fall
Chinook returned to Clear Creek annually (Table B-5). In order to re-establish spring Chinook in
Clear Creek, 200,000 juveniles from the Feather River Hatchery were planted in 1991, 1992 and
1993. As a result, Clear Creek also currently supports a relatively small spring Chinook
population. Between 2001 and 2010, an average of 87 spring Chinook returned to Clear Creek
each year (Table B-5). According to IFC Jones & Stokes (2010), approximately 40% of the
natural fall-run Chinook spawners and none of the natural spring-run Chinook spawners in Clear
Creek are hatchery-origin fish.
2
http://www.sacriver.org/documents/2010/Roadmap/Westside_ClearCreek.pdf
Page B 4
Table B-5.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall-run and spring-run Chinook salmon escapement in Clear Creek (2001-2010).
Fall-Run
Spring-Run
Chinook
Chinook
Total
10,865
0
10,865
16,071
66
16,137
9,475
25
9,500
6,365
98
6,463
14,824
69
14,893
8,422
77
8,499
4,129
194
4,323
7,677
200
7,877
3,228
120
3,348
7,192
21
7,213
8,825
87
8,912
3
Cow Creek (Fall Chinook)
The 275,000-acre Cow Creek watershed is a generally uncontrolled tributary to the Sacramento
River located in eastern Shasta County. The watershed is unique in that land ownership is
divided almost evenly among commercial forestland, commercial agriculture (predominantly
cattle ranching), and small private residential properties, with minimal public ownership. The
watershed includes five principal tributaries: North Fork Cow, Oak Run, Clover, Old Cow, and
South Fork Cow creeks. It provides important habitat for both fall-run and late fall-run Chinook
salmon and steelhead. There are no major reservoirs in the watershed, but numerous small dams
divert water for irrigation and hydropower production.
The distribution of fall-run Chinook is generally restricted to the valley floor and lower foothill
elevations of Cow Creek and its major tributaries; however, smaller portions of the population
can be expected to ascend to the upper-most waterfall barriers in the system (typically to an upper
limit of 1,000 feet of elevation). More detailed study and analysis is required to precisely
describe the distribution of spawning activity in the creek system (SHN 2001).
While historical information describing fall Chinook abundance in Cow Creek is limited, during
1953–1969, the Cow Creek drainage supported a fall-run that averaged 2,800 fish (Yoshiyama et
al. 2001). Fall-run salmon presently occur in the mainstem Cow Creek up to where the South
Fork joins, and they ascend the South Fork up to Wagoner Canyon. In the North Fork Cow
Creek, fall Chinook are stopped by falls near the Ditty Wells fire station. Occasionally, late-fall
run salmon occur in Cow Creek (Yoshiyama et al. 2001). From 2006-2010 (the period of
available data), the annual number of fall Chinook retuning to Cow Creek ranged from 261 to
4,130 fish, and averaged 1,490 (Table B-6). According to IFC Jones & Stokes (2010),
approximately 32% of these spawners were hatchery fish.
Page B 5
Table B-6.
Fall-run Chinook salmon escapement in Cow Creek (2001-2010).
Year
Fall-Run Chinook
2006
4,130
2007
2,044
2008
478
2009
261
2010
536
Average
1,490
According to SHN (2001), data describing the late-fall-run Chinook salmon are very limited.
There are no estimates of the late fall-run population in Cow Creek, although their presence has
been documented. According to CDFG file data, the most recent survey for late-fall-run
spawning was an aerial survey of Cow Creek on February 26, 1965. Fifty-four carcasses and 14
live fish were observed in the entire Cow Creek watershed. Most of the live salmon were
observed below the Highway 44 Bridge, while the carcasses were evenly distributed between
Millville and the confluence with the Sacramento River.
According to IFC Jones & Stokes (2010), approximately 32% of the natural fall-run Chinook
spawners in Cow Creek are considered to be hatchery-origin fish.
4
Beegum-Cottonwood Creek (Spring and Fall Chinook)
The Cottonwood Creek drainage area lies within Shasta and Tehama counties on the northwest
side of the Central Valley. The lower two-thirds of the drainage is part of the Central Valley
uplands, extending to slopes of the North Coast Mountain Range, Klamath Mountains and the
Trinity Mountains. The creek flows eastward through the valley to the Sacramento River, the
confluence lying approximately 16 miles north of Red Bluff and about 150 miles northwest of
Sacramento. The watershed has three main tributaries: North Fork, Middle Fork (flowing along
the Shasta-Tehama County line), and the South Fork. The watershed drains approximately 938
square miles. With an annual runoff of 586,000 acre-feet, Cottonwood Creek is the third largest
watershed tributary west of the Sacramento River. Cottonwood Creek has a natural pattern of
high flows and peak runoff events in winter and low flows in the summer and fall (CH2M Hill
2002).
Cottonwood Creek historically supported both spring and fall runs and, presumably, also a latefall run. The spring-run fish formerly migrated to the headwaters of the South and Middle forks
of Cottonwood Creek above Maple Gulch on the South Fork and about eight miles into Beegum
Creek on the Middle Fork (Yoshiyama et al. 2001). The CDFG has not monitored fall-run
escapement into Cottonwood Creek on a consistent basis. From 1953 to 1969, seventeen annual
estimates were made based on carcass counts and occasional aerial redd counts. During this
period, an average of approximately 2,500 fall Chinook spawned in Cottonwood Creek annually
(range 350 to 6,000). From 2007 through 2010, an average of just less than 1,000 fall Chinook
returned to Cottonwood Creek annually (Table B-7). From 2001 through 2010, an average of
only 61 spring Chinook returned to Cottonwood Creek. According to IFC Jones & Stokes
(2010), approximately 59% of the natural fall Chinook spawners and none of the natural springrun Chinook spawners in Beegum-Cottonwood Creek were hatchery-origin fish.
Page B 6
Table B-7.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall and spring Chinook salmon escapement in Beegum-Cottonwood Creek
(2007-2010).
Fall-Run Chinook Spring-Run Chinook
245
125
73
17
47
55
1,250
34
510
0
1,055
0
1,137
15
988
61
5
Battle Creek (Spring, Fall, and Late-Fall Chinook)
Battle Creek drains the southern Cascade Range in the northern Central Valley and flows into the
Sacramento River at RM 272, approximately two miles east of the town of Cottonwood. Battle
Creek is comprised of two main branches, the North Fork (approximately. 29.5 miles long) and
the South Fork (approximately 28 miles long), the mainstem valley reach (approximately 15.2
miles long), and numerous tributaries. The upper 16 miles of the North Fork and the upper 10
miles of the South Fork are inaccessible to anadromous salmonids due to natural barriers (Ward
and Kier 1999). Battle Creek has the largest base flow or dry-season flow (approximately 225
cfs) of any of the tributaries to the Sacramento River between the Feather River and Keswick
Dam.
Historically, both spring and fall runs of salmon occurred in Battle Creek, and there is evidence
that a winter-run was also present. The Coleman National Fish Hatchery (CNFH) began
operations in 1943 and took small numbers (<1,200) of spring-run fish from Battle Creek in
1943-1946. In 1946, CNFH also began taking fall-run fish from Battle Creek (Fry 1961 as cited
in Yoshiyama et al. 2001). From 1946 to 1956, the spring run numbered about 2,000 fish in most
years, but by the late 1980s, it was close to being extirpated (Yoshiyama et al. 2001).
Currently, natural Chinook salmon spawning in Battle Creek is heavily concentrated in the reach
between the creek mouth and the CNFH weir (six miles upstream from the mouth). The
predominant fall-run Chinook are blocked at the hatchery weir (Yoshiyama et al. 2001). During
recent years when stream flows were adequate, small numbers of spring and winter Chinook have
been able to ascend past the weir and spawn in upstream reaches (Yoshiyama et al. 2001). At
present, the only other population of winter-run Chinook outside of Battle Creek occurs in the
Sacramento River downstream of Shasta Dam. The majority of this population spawns in the
reach between Keswick Dam and Cottonwood Creek where high water temperatures periodically
threaten these fish (Ward and Kier 1999). Between 2000 and 2010, an average of 114,457 fallrun Chinook and 4,762 late fall-run Chinook returned to Battle Creek annually (Table B-8 and B9). During this same time period, an average of only 170 spring Chinook returned to Battle Creek
(Table B-10).
spawners, 73% of the natural late fall-run Chinook spawners, and 12% of the natural spring
Chinook spawners in Battle Creek are considered to be hatchery-origin fish.
Page B 7
Table B-8.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall-run Chinook salmon escapement in Battle Creek (2001-2010).
Downstream of
Upstream of
Coleman NFH Coleman NFH
Coleman NFH
Total
24,698
100,604
0
125,302
65,924
397,149
0
463,073
88,234
64,764
0
152,998
69,172
23,861
0
93,033
142,673
20,520
0
163,193
57,832
19,493
0
77,325
11,744
9,904
0
21,648
10,639
4,286
0
14,925
6,152
3,047
0
9,199
17,238
6,631
1
23,870
49,431
65,026
0
114,457
Table B-9.
Late fall-run Chinook salmon escapement in Battle Creek (2001-2010).
Upstream of
Year
Coleman NFH
Coleman NFH
Total
Nov 2000 – Apr 2001
2,439
98
2,537
Nov 2001 – Apr 2002
4,186
216
4,402
Nov 2002 – Apr 2003
3,183
57
3,240
Nov 2003 – Apr 2004
5,166
40
5,206
Nov 2004 – Apr 2005
5,562
23
5,585
Nov 2005 – Apr 2006
4,822
50
4,872
Nov 2006 – Apr 2007
3,360
72
3,432
Nov 2007 – Apr 2008
6,334
19
6,353
Nov 2008 – Apr 2009
6,429
32
6,461
Nov 2009 – Apr 2010
5,505
27
5,532
Average
4,699
63
4,762
Table B-10. Spring-run Chinook salmon escapement in Upper Battle Creek (2007-2010).
Year
Fall-Run Chinook
2001
111
2002
222
2003
221
2004
90
2005
73
2006
221
2007
291
2008
105
2009
194
2010
172
Average
170
Page B 8
6
Antelope Creek (Spring Chinook)
Antelope Creek originates in the Lassen National Forest in Tehama County and flows southwest
to RM 235 of the Sacramento River, nine miles southeast of Red Bluff. The 123-square-mile
Antelope Creek watershed is in various ownerships, dominated by agriculture and ranchettes
along the valley floor. Most of the canyon reach is managed by the CDFG (Tehama Wildlife
Area) and the Lassen National Forest. The Antelope Creek headwaters is in an area of corporate
timber lands.
The Antelope Creek watershed produces on average 110,800 acre feet of water per year. Average
winter flows range from 200 to 1,200 cfs in the wettest years and 50 cfs in the driest years
(NMFS 2009). Summer and early fall flows typically average from 20 to 50 cfs (NMFS 2009).
There are two diversions on Antelope Creek, both located at the canyon mouth. One is operated
by the Edwards Ranch, which has a water right of 50 cfs, and the other is operated by the Los
Molinos Mutual Water Company, which has a water right of 70 cfs (NMFS 2009). Unimpaired
natural flows are often less than the combined water rights of the two diverters, resulting in a total
dewatering of Antelope Creek during critical migration periods (NMFS 2009).
Both spring and fall runs, and probably a late-fall run, originally occurred in Antelope Creek
(Yoshiyama et al. 2001). Spring-run salmon ascended the creek at least to where the North and
South forks join, and they probably held there over the summer. The few spring-run fish that
now enter the creek ascend the North and South forks about five to six miles, their probable
historical upper limit, beyond which there is little suitable habitat (Yoshiyama et al. 2001). Under
existing conditions, relatively few spring Chinook enter Antelope Creek each year. From 2001
through 2010, an average of only 33 spring-run Chinook were observed in Antelope Creek
annually (Table B-11). The fall run in Antelope Creek generally has been small. From 1953–
1984, the fall run numbered 50 to 4,000 fish annually (an average of about 470 fish). Population
estimates have not been made in more recent years due to the scarcity of the salmon, and the fall
run may be extirpated (Yoshiyama et al. 2001). According to IFC Jones & Stokes (2010), none
of the natural spring-run Chinook spawners in Antelope Creek are considered to be hatcheryorigin fish.
Table B-11.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Spring-run Chinook salmon escapement in Antelope Creek (2001-2010).
Spring-Run Chinook
(Antelope Creek)
8
46
46
3
82
102
26
2
0
17
33
Page B 9
7
Mill Creek (Spring and Fall Chinook)
Mill Creek originates on the southern slopes of Lassen Peak and flows generally to the southwest
for approximately 60 miles to its confluence with the Sacramento River. The stream is confined
within a steep-sided, narrow canyon except for a few alluvial meadows at the 5,000 foot level.
Below this canyon, Mill Creek flows for eight miles through irrigated agricultural land (mainly
pasture and orchard crops) before entering the Sacramento River near the town of Los Molinos. 3
Historically, Clough Dam, Ward Dam, and Upper Diversion Dam impeded the upstream passage
of salmonids under low‐flow conditions. Clough Dam was removed in 2003 and Ward Dam was
modified in 1997 to improve upstream passage. In recent years, stream flows have been
augmented through a water exchange program to improve upstream passage for spring‐run
Chinook. Because the upper watershed is relatively inaccessible, it is undisturbed, pristine,
salmonid spawning habitat (CH2M Hill 1998; CDWR 2009). No significant water storage
impoundments in the watershed allow for a natural hydrograph that is supported by both seasonal
rainfall and snowmelt.
Both spring and fall-run Chinook salmon are present in Mill Creek. Fry (1961) (as cited in
Yoshiyama et al. 2001) reported spring-run numbers of less than 500 to about 3,000 fish during
1947-1959, while the fall run ranged between 1,000 to 16,000 spawners. Most of the fall run
spawned below Clough Dam, while most of the spring run passed upstream beyond the dam. In
recent decades, the spring-run spawning escapement has varied from no fish during the severe
drought in 1977, to 3,500 fish in 1975, but the trend has been downward from an annual average
of 2,000 fish in the 1940s to about 300 in the 1980s (Yoshiyama et al, 2001). Fall-run
escapements have been zero to 16,000 spawners since 1952; generally hovering near 1,500 fish
(Yoshiyama et al. 2001; CDFG unpublished data). From 2001 through 2010, an average of 926
spring-run Chinook were observed in Mill Creek annually (Table B-12).
Table B-12.
Spring-run Chinook salmon escapement in Mill Creek (2001-2010).
Spring-Run Chinook Fall-Run Chinook
Year
(Mill Creek)
(Mill Creek)
2001
1,104
2002
1,594
2,611
2003
1,426
2,426
2004
998
1,192
2005
1,150
2,426
2006
1,002
1,403
2007
920
796
2008
362
166
2009
220
102
2010
482
144
Average
926
1,252
Spring‐run holding pools are present in the upper canyon areas, and spawning occurs between the
Little Mill Creek confluence and the Highway 36 Bridge (CH2M Hill 1998; CDWR 2009).
Armentrout et al. (1998)(as cited in CDWR 2009) noted that the amount of holding habitat is
limited in the upper 7.6 miles of Mill Creek and that holding habitat was more abundant in the
3
http://www.sacriver.org/documents/2010/Roadmap/Eastside_MillCreek.pdf
Page B 10
section below the Mill Creek Campground. Low flows in the lower portion of the watershed can
impede upstream passage of adult salmonids in some years (CH2M Hill 1998). No physical
passage barrier limits upstream migration on Mill Creek; however, the combined effect of high
stream gradients, low flows and habitat availability sets the upper limit for migration in the
headwater reaches.
According to Yoshiyama et al. (2001), the CDFG (1993) reported an average annual fall-run
escapement in Mill Creek of 2,200 fish for the 38 years of record up to that time. In the 1990s,
the fall run numbered from about 600 to 2,100 fish but was absent in some years due to low
seasonal stream flows. Since 2001, fall-run Chinook salmon escapement to Mill Creek has
averaged approximately 1,252 fish.
As in Deer Creek (see below), the spring and fall runs in Mill Creek are separated temporally, the
fall run ascending the creek during fall flows after the spring-run fish have finished spawning.
There is also spatial separation of the spring and fall runs in both Mill and Deer creeks, with
spring-run fish spawning well upstream from the fall-run fish 4 and thus further minimizing the
possibility of hybridization (Yoshiyama et al. 2001).
According to IFC Jones & Stokes (2010), approximately 18% of the natural fall Chinook
spawners and none of the natural spring Chinook spawners in Mill Creek are considered to be
hatchery-origin fish.
8
Deer Creek (Spring and Fall Chinook)
Deer Creek flows from its mountainous headwaters in eastern Tehama County to its confluence
with the Sacramento River near the town of Vina. As is common with neighboring watersheds,
the upper watershed is flatter with significant alluvial valleys, connected to lowland agricultural
lands via a steep and deeply incised middle reach. Timber production, cattle ranching, and
orchards are the dominant agricultural land uses. Except for three small diversions, the watershed
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). 5
Historically, both spring and fall Chinook salmon occurred in Deer Creek, which is a cold,
spring-fed stream. Before the 1940s, spring Chinook ascended Deer Creek for about 40 miles
from its mouth up to 16-foot-high Lower Deer Creek Falls, located about one mile below the
mouth of Panther Creek (Yoshiyama et al. 2001). Salmon were never known to pass Lower Deer
Creek Falls. Fall Chinook were known to spawn from the creek mouth to about ten miles into the
foothills (Yoshiyama et al. 2001).
To compensate for the loss of spawning habitat in the upper Sacramento drainage caused by
construction of Shasta and Keswick dams, Sacramento River spring-run salmon were caught at
Keswick and transported to Deer Creek during the 1940s to mid-1950s, but those transfers had no
noticeable effect on the spring run in Deer Creek (Fry 1961 as cited in Yoshiyama et al. 2001).
Deer Creek is currently believed to have sufficient habitat to support “sustainable populations” of
4,000 spring-run and 6,500 fall-run salmon (Reynolds and others 1993, as cited in Yoshiyama et
al. 2001).
4
5
Fall-run salmon use mainly the lower six miles of Mill Creek.
http://www.sacriver.org/documents/2010/Roadmap/Eastside_DeerlCreek.pdf
Page B 11
Yoshiyama et al. (2001), citing Fry (1961), reported Deer Creek spring-run spawner estimates of
less than 500 to 4,000 fish for 1940–1956. Using DFG unpublished data, those authors reported
that the spring-run ranged between 400 and 3,500 fish annually from 1950–1979 (average of
2,200) and 80 to 2,000 fish during 1980–1998 (average of 660). More recent data show that the
run has been between 220 to 1,594 fish during 2001-2010, averaging 926 in this period (Table B13).
Fall Chinook were estimated by Fry (1961 as cited in Yoshiyama et al. 2001) to range from less
than 500 fish to 12,000 fish from 1947–1959. From the 1960s through 1980s, the number of fallrun spawners in Deer Creek ranged from 60 to 2,000 fish (average 500). From 2004 through
2010, fall Chinook have numbered 58 to 1,905 fish (average 585) (Table B-13).
spawners and none of the natural spring-run Chinook spawners in Deer Creek are considered to
be hatchery-origin fish. It should be noted that the spring-run population in Deer Creek is one of
only three or four remaining naturally spawning spring Chinook populations in California that
can be considered genetically intact and demographically viable. Two of the other populations in
the Central Valley drainage occur in nearby Mill and Butte creeks.
Table B-13.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Spring and fall Chinook salmon escapement in Deer Creek (2001-2010).
Spring-Run Chinook Fall-Run Chinook
(Deer Creek)
(Deer Creek)
1,104
1,594
1,426
998
300
1,150
963
1,002
1,905
920
508
362
194
220
58
482
166
926
585
9
Big Chico Creek (Spring Chinook)
Big Chico Creek is located within Butte and Tehama counties and has watershed area of
approximately 72 square miles. The headwaters of Big Chico Creek are on the southwest slope
of Colby Mountain, from where it flows approximately 45 miles to the Sacramento River west of
Chico.
Big Chico Creek contains marginally suitable habitat for salmon and probably was
opportunistically used in the past. Spring, fall and late-fall runs have occurred in this creek
(Yoshiyama et al. 2001). Fry (1961) (as cited in Yoshiyama et al. 2001) gave estimates of 50
fall-run (including late-fall-run) fish in 1957, 1,000 spring-run fish in 1958, and 200 spring-run in
1959. The average annual spring Chinook run size is believed to have been less than 500 fish
during the 1950s to 1960s and more recently has been considered to be only a remnant. Big
Chico Creek has been heavily stocked with Feather River spring-run fish, which evidently had
been genetically mixed with fall-run fish. In the last decade, an average of only 46 spring-run
Chinook returned to Big Chico Creek (Table B-14). According to IFC Jones & Stokes (2010),
Page B 12
none of the natural spring-run Chinook spawners in Big Chico Creek are considered to be
hatchery-origin fish.
Table B-14.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Spring-run Chinook salmon escapement in Big Chico Creek (2001-2010).
Spring-Run Chinook
(Big Chico Creek)
39
0
81
0
37
299
0
0
6
2
46
10
Butte Creek (Spring and Fall Chinook)
Butte Creek is a major tributary to the Sacramento River originating in the Lassen National Forest
at an elevation of 7,087 feet. Encompassing approximately 510,000 acres, the watershed drains
the northeast portion of Butte County and enters the Sacramento Valley southeast of Chico. Butte
Creek then meanders in a southwesterly direction to its confluence with the Sacramento River at
Butte Slough. 6 A second point of entry into the Sacramento River is through the Sutter Bypass
and Sacramento Slough. 7
The hydrology of the upper watershed has been modified significantly by multiple diversions for
hydroelectric power generation, while the lower watershed is managed primarily for irrigation
and flood control. Land use is dominated by agriculture in the lower portions (largely rice,
orchards, and row crops), with timber and grazing predominant in the upper watershed. 8
Historically, Butte Creek supported a relatively large run of spring Chinook salmon that that
likely ascended the creek at least as far as Centerville Head Dam near DeSabla (Yoshiyama et al
2001). However, Butte Creek reportedly had almost no fall run, setting it apart from most small
streams in the northern Sacramento Valley which had mainly, or only, a fall run. According to
Fry (1961) (as cited in Yoshiyama et al. 2001), the many removable dams on the creek blocked or
reduced flows late into the fall, and the fall Chinook could not surmount them.
Fry (1961 as cited in Yoshiyama et al. 2001) reported that the spring Chinook ranged from less
than 500 fish to 3,000 fish from 1953 to 1959. During the 1960s, at times the spring run
numbered over 4,000 fish in Butte Creek (CDFG 1998), with smaller numbers of fall-run and
late-fall-run fish (Reynolds and others 1993). More recently, estimated spring-run numbers were
100 to 700 fish during the 1990s, rising to 7,500 fish in 1995 and 20,000 fish in 1998. The source
of the surprisingly numerous spring-run spawners that entered Butte Creek in 1998 is not known,
6
Butte Creek flows are regulated into the Sacramento River by the Butte Slough outfall gates to accommodate both
flood flows and agricultural needs in the Sutter bypass area.
7
http://buttecreekwatershed.org/Watershed/ECR.pdf
8
http://www.sacriver.org/documents/2010/Roadmap/Eastside_ButteCreek.pdf
Page B 13
but presumably they could be attributed to the strong escapement in 1995. Since 2001, spring
Chinook escapement to Butte Creek has averaged approximately 4,900 fish (Table B-15).
The Butte Creek fall-run remains relatively small, numbering approximately 2,000 fish (Table B15). There are also late-fall-run salmon here, but their numbers are unknown (Reynolds and
others 1993 as cited in Yoshiyama et al. 2001). According to IFC Jones & Stokes (2010),
approximately 21% of the natural fall-run Chinook spawners and none of the natural spring-run
Chinook spawners in Butte Creek are considered to be hatchery-origin fish.
Table B-15.
Spring and fall-run Chinook salmon escapement in Butte Creek (2001-2010).
Fall-Run
Spring-Run
Year
Butte Creek (In-River)
Butte Creek (Snorkel)
2001
4,433
9,605
2002
3,665
0
2003
3,492
4,398
2004
2,516
7,390
2005
4,255
10,625
2006
1,920
4,579
2007
1,225
4,943
2008
275
3,935
2009
306
2,059
2010
370
1,160
Average
2,246
4,869
11
Feather River (Spring and Fall Chinook)
The Upper Feather River watershed includes all tributaries to the Feather River from the
headwaters in the Sierra Nevada crest downstream to Lake Oroville. The Upper Feather is a
major source of the state’s water supply and provides virtually all the water delivered by the
California State Water Project. Most of the watershed lies in Plumas County and is roughly 65
percent publicly owned, primarily by the US Forest Service. The lower Feather River watershed,
downstream of Lake Oroville (a fish migration barrier), encompasses approximately 803 square
miles. The river flows approximately 60 miles north to south before entering the Sacramento
River at Verona. Flows are regulated for water supply and flood control through releases at
Oroville Dam. The river is almost entirely contained within a series of levees as it flows through
the agricultural lands of the Sacramento Valley. 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 urban uses), demands on water supply, preservation of water
quality and aquatic habitat, and potential risks from fire and floods. 9
Historically, the Feather River supported both spring and fall-run Chinook salmon and was
renowned as one of the major salmon-producing streams of the Sacramento Valley (Yoshiyama et
al. 2001). The major spawning areas extended from the river’s mouth to Oroville (Yoshiyama et
al 2001), a distance of over 60 miles, with important spawning areas continuing upstream. Fry
(1961 as cited in Yoshiyama et al. 2001) reported annual fall Chinook runs of 10,000 to 86,000
fish from 1940 to 1959, and about 1,000 to 4,000 spring Chinook. The fall-run spawned largely
9
http://www.sacriver.org/
Page B 14
in the mainstem, while most of the spring-run spawned in the Middle Fork, with a few spring run
entering the North Fork, South Fork and West Branch.
Just before the completion of Oroville Dam (in 1967), a small naturally-spawning spring Chinook
population still existed in the Feather River, but the Oroville project blocked access to the
majority of its habitat. Currently, the fall run extends to Oroville Dam and spawns from there
downstream to a point about two miles above the Gridley Road crossing. There is also a
hatchery-sustained population of “spring-run” fish that has been genetically mixed with the fall
run and that spawns in the 0.5-mile reach below the Oroville fish barrier. The hybrid spring-run
fish hold over the summer in deep pools in the “low-flow” section of the river between
Thermalito Diversion Dam (five miles below Oroville Dam) and the downstream Thermalito
Afterbay Outlet. They are spawned artificially in the Feather River Hatchery and also spawn
naturally in the river during late September to late October. The “spring run” thus overlaps
temporally as well as spatially with the fall run, which is the cause of the hybridization between
the runs (Yoshiyama et al 2001).
The Feather River Hatchery, located at the town of Oroville, was completed in 1967 by the
California Department of Water Resources (DWR) to mitigate for the loss of upstream spawning
habitat of salmon and steelhead due to the building of Oroville Dam. The Feather River Hatchery
is the only source of eggs from “spring-run” Chinook salmon in the Central Valley and is viewed
as a key component in plans to restore spring Chinook populations (Yoshiyama et al 2001).
In recent decades, the majority of Chinook salmon production in the Feather River has been
heavily supported by hatchery production. Since 2001, both spring-run and fall-run Chinook
salmon escapement to the Feather River Hatchery has averaged approximately 15,000 fish (Table
B-16). During this same period, river returns (natural spawners) averaged approximately 79,000
fish. According to DWR (2005), approximately two-thirds of natural fall Chinook spawning
occurs between the Fish Barrier Dam and the Thermalito Afterbay Outlet (RM 67 - RM 59), and
one-third of the spawning occurs between the Thermalito Afterbay Outlet and Honcut Creek (RM
59 - RM 44). IFC Jones & Stokes (2010) concluded that approximately 82% of the natural fallrun Chinook spawners and 91% of the natural spring-run Chinook spawners in the Feather River
basin are considered to be hatchery origin-fish.
Table B-16.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Chinook salmon escapement in the Feather River basin (2001-2010).
Feather River1
Feather River
Percent In-River
Hatchery
In-River
Total
(Feather)
24,870
178,645
203,515
87.8%
20,507
105,163
125,670
83.7%
14,976
89,946
104,922
85.7%
21,297
54,171
75,468
71.8%
22,405
49,160
71,565
68.7%
14,034
76,414
90,448
84.5%
5,341
21,886
27,227
80.4%
5,082
5,939
11,021
53.9%
9,963
4,847
14,810
32.7%
19,972
44,914
64,886
69.2%
15,845
63,109
78,953
71.8%
1 Note: Feather River survey data does not provide separate estimates for fall and spring escapement. Spring-run
estimates are included with fall-run estimates.
Page B 15
12
Yuba River (Fall Chinook)
The Yuba River watershed drains approximately 1,340 square miles and extends from the crest of
the Sierra Nevada to the confluence of the Feather River near Marysville and Yuba City. The
principal tributaries include the North Yuba River, with a drainage area of approximately 490
square miles; the Middle Yuba River, with a drainage area of about 210 square miles; and the
South Yuba River, with a drainage area of about 350 square miles. The North Yuba and the
Middle Yuba rivers join below New Bullards Bar Reservoir to form the Yuba River. Farther
downstream, the South Yuba River flows into Englebright Lake (CDWR 2007).
Englebright Dam was completed in 1941 to capture gold-rush era hydraulic mining debris
(sediment) that posed a flood threat to downstream residents. Located at RM 25, the 260-foothigh dam marks the division between the upper and lower Yuba River and defines the upper
extent of the anadromous fishery. Consequently, anadromous fish do not have access to the
North, South and Middle Yuba rivers (CDWR 2007). An additional influence on both the
hydraulics of the lower Yuba River and fish passage is Daguerre Point Dam. Located
approximately 11.4 miles upstream from the confluence with the Feather River, Daguerre Point
Dam stores sediment and creates head for irrigation diversions, but is also an impediment to the
movement of anadromous fish. The Daguerre Point Dam Fish Passage Improvement Project was
recently initiated with a goal of improving fish passage at the dam. 10
The lower Yuba River is used by spring and fall Chinook salmon. Although late fall-run Chinook
populations occur primarily in the Sacramento River (CDFG Website 2007), incidental
observations of late fall-run Chinook have been reported in the lower Yuba River.
Historically, the Yuba River contained about 80 miles of potentially accessible Chinook salmon
habitat. The California Fish Commission reported that in 1850 “the salmon resorted in vast
numbers to the Feather, Yuba, American, Mokelumne, and Tuolumne Rivers,” and on the Yuba
River as late as 1853 “the miners obtained a large supply of food from this source”; however, by
1876 the salmon no longer entered those streams (CFC 1877 as cited in Yoshiyama et al. 2001).
By the late 1950s, Fry (1961 as cited in Yoshiyama et al. 2001) noted that the spring salmon run
had “virtually disappeared.” Fall Chinook escapements from 1953 to 1989 ranged from 1,000 to
39,000 fish, averaging 13,050 annually (Yoshiyama et al. 2001). More recently (2001-2010), the
annual number of fall Chinook returning to the Yuba River has ranged from 2,604 to 28,316
spawners (Table B-17). Under existing conditions, most of the salmon spawning habitat is in the
7.8-mile reach of river on the open valley floodplain downstream of Daguerre Point Dam;
however, the greater part of the run generally spawns above Daguerre Point (Yoshiyama et al.
2001). According to IFC Jones & Stokes (2010), approximately 36% of the natural fall-run
Chinook spawners in the Yuba River are considered to be hatchery-origin fish.
10
http://www.water.ca.gov/pubs/environment/fish/daguerre_point_dam_fish_passage_improvement_project__2002_water_resources_studies/daguerre_fish_passage.pdf
Page B 16
Table B-17.
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall-run Chinook salmon escapement in the Yuba River basin (2001-2010).
Fall-run Chinook
Escapement (Yuba River)
23,392
24,051
28,316
15,269
17,630
8,121
2,604
3,508
4,635
14,375
14,190
13
Mokelumne River Fall Chinook
The Mokelumne River originates in the Sierra Nevada Mountains and flows through the Central
Valley before entering the Delta forks of the Mokelumne just downstream of the Delta Cross
Channel. The watershed drains some 627 square miles and contains a number of dams and
reservoirs. Pardee Dam and Reservoir (at RM 73) serves multiple purposes that include water
supply and maintenance of the Camanche Reservoir hypolimnion. Camanche Dam and
Reservoir, completed by EBMUD in 1964 at RM 29.6, is the upstream limit of anadromous
salmonid migration.
Historically, the Mokelumne River supported both spring and fall Chinook salmon. Some
evidence suggests that a late-fall run also entered the river at one time (Yoshiyama et al. 2001).
Salmon ascended the river at least as far as the vicinity of present-day Pardee Dam. A large
waterfall one mile downstream of the Pardee Dam site posed a significant barrier to the fall run;
however, spring Chinook likely ascended the falls to reach elevations where water temperatures
were suitable for over-summering (FERC 1993). While historical abundance data are limited,
Fry (1961 as cited in Yoshiyama et al. 2001) reported that counts of fall-run spawners passing
Woodbridge Dam (RM 39) ranged from less than 500 (in two separate years) to 7,000 fish from
1945 to1958, with partial counts of 12,000 fish each in 1941 and 1942. Fry also stated that the
spring run appeared to be “practically extinct”. During the period 1940–1990, total annual run
sizes ranged between 100 and 15,900 fish (Yoshiyama et al. 2001).
Under current conditions, fall Chinook are stopped at the lower end of Camanche Reservoir,
about nine miles below Pardee Dam. They spawn in the reach from Camanche Dam (RM 64)
downstream to Elliott Road (RM 54), and 95% of the suitable spawning habitat is within 3.5
miles of Camanche Dam.
The Mokelumne River Fish Hatchery was constructed in 1964 to produce both fall-run Chinook
salmon and steelhead trout. Average production from the facility since the early 1990s has been
approximately 3.0 to 5.0 million fall-run Chinook smolts, 500,000 yearling Chinook, and 100,000
yearling steelhead. Approximately 2.0 million salmon are raised to post-smolt stage each year for
an ocean enhancement program. These fish are trucked downstream to San Pablo Bay or reared
in net pens on the coast. Remaining salmon smolts that were Mokelumne-origin fish were
planted below Woodbridge Dam (IFC Jones & Stokes 2010, Miyamoto and Hartwell no date).
Page B 17
Since 2001, fall-run Chinook salmon escapement to the Mokelumne River Hatchery has averaged
fewer than 5,000 fish (Table B-18). During this same period, fish spawning naturally averaged
approximately 2,400 fish (about 31% of the total return).
Table B-18
Year
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
Average
Fall-run Chinook salmon escapement in the Mokelumne River Basin (2001-2010).
Mokelumne River
Cosumnes Mokelumne River
Percent In-River
River
Hatchery
In-River
Total
(Mokelumne)
5,728
2,307
8,035
28.7%
1,350
7,913
2,840
10,753
26.4%
122
8,117
2,122
10,239
20.7%
1,208
10,356
1,588
11,944
13.3%
370
5,563
10,406
15,969
65.2%
530
4,139
1,732
5,871
29.5%
77
1,051
470
1,521
30.9%
15
239
173
412
42.0%
0
1,553
680
2,233
30.5%
740
5,275
1,912
7,187
26.6%
490
4,993
2,423
7,416
31.4%
Source:http://www.calfish.org/LinkClick.aspx?fileticket=Kttf%2boZ2ras%3d&tabid=104&mid=524
14
Stanislaus River (Fall Chinook)
The Stanislaus River watershed is bordered by the Mokelumne watershed to the north and the
Tuolumne watershed to the south. The river is 95.9 miles long and has north, middle and south
forks. The headwaters of the Stanislaus River are in the Emigrant Wilderness area at elevations
above 9,000 feet, and it flows in a general southwesterly direction to its confluence with the San
Joaquin River 23 miles above Stockton. The watershed has been heavily dammed and diverted
and currently contains 13 large reservoirs. Goodwin Dam, located at RM 52 on the Stanislaus
River is a barrier to anadromous fish migration.
Both spring and fall-run Chinook salmon historically occurred throughout the Stanislaus River
basin (Yoshiyama et al. 2001). Spring-run and likely some fall-run salmon migrated considerable
distances up the forks because there were few natural obstacles. The spring run was said to have
been the primary salmon run in the Stanislaus River, but after the construction of dams which
regulated the stream flows (namely, Goodwin Dam and, later, New Melones and Tulloch dams),
the fall run became predominant. Fry (1961 as cited in Yoshiyama et al. 2001) described the
Stanislaus River as “a good fall run stream for its size” but it had “almost no remaining spring
run.”
The Stanislaus River fall run has contributed up to 7% of the total salmon spawning escapement
in the Central Valley (Yoshiyama et al. 2001). From 1946 through 1959 (before construction of
Tulloch Dam), annual escapements of fall-run Chinook were estimated at 4,000 to 35,000
spawners (averaging about 11,100 spawners) (Fry 1961 as cited in Yoshiyama et al. 2001). In the
following 12-year period (1960–1971), the average run size was about 6,000 fish. Fall-run
abundances during the 1970s and 1980s ranged up to 13,600 (averaging about 4,300) spawners
annually; however, the numbers of spawners returning to the Stanislaus River were very low
during most of the 1990s (less than 500 fish annually in 1990–1992, 600 to 1,000 fish in 1994–
1995, and less than 200 fish in 1996). Since 2001, fall Chinook escapement to the Stanislaus
Page B 18
River has averaged approximately 3,100 fish (Table B-19). Only the fall run has sustained itself
in the Stanislaus River, although small numbers of late-fall Chinook have been reported to enter
the river. As in the Tuolumne River, the recent occurrence of late-fall Chinook in the Stanislaus
River could be due to strays from the Sacramento River system (Yoshiyama et al. 2001).
spawners in the Stanislaus River are considered to be hatchery-origin fish.
Table B-19. Fall-run Chinook salmon escapement in the Stanislaus River basin (2001-2010).
Year
In-River (Stanislaus)
2001
7,033
2002
7,787
2003
5,902
2004
4,015
2005
1,427
2006
1,923
2007
443
2008
1,392
2009
595
2010
1,086
Average
3,160
15
Tuolumne River Fall Chinook
The 150-mile-longTuolumne River is the largest of three major tributaries to the San Joaquin
River. Originating in Yosemite National Park, it flows west between the Merced River and
Stanislaus River to its confluence with the San Joaquin River at the tailrace of the Don Pedro
powerhouse. The 1,960-square-mile watershed can be subdivided into three river reaches: the
upper Tuolumne River above roughly RM 80, the foothills reach between RM 54 and 80, and the
valley reach from the mouth to RM 54. Upstream fish passage is blocked at RM 54 by La Grange
Dam.
The lower Tuolumne River watershed (RM 0 to 54), covers approximately 430 square miles and
contains one major tributary, Dry Creek. Other tributaries include Peaslee Creek and McDonald
Creek (via Turlock Lake). The lower Tuolumne River watershed is long and narrow and is
dominated by irrigated farmland and the urban/suburban areas associated with the cities of
Modesto, Waterford, and Ceres. Flows in the lower Tuolumne River are significantly controlled
by La Grange Dam, a diversion dam constructed in 1893 that diverts water from the Tuolumne
River for irrigation, municipal and industrial supply purposes.
While both spring and fall-run Chinook salmon were once abundant in the Tuolumne River, only
the fall run presently occurs in appreciable numbers. In the past, the number of fall-run Chinook
returning to the Tuolumne River was sometimes larger than in any other Central Valley streams
except for the mainstem Sacramento River, reaching as high as 122,000 spawners in 1940 and
130,000 in 1944 (Fry 1961 as cited in Yoshiyama et al. 2001). At times, Tuolumne River fall run
Chinook comprised up to 12% of the total fall-run spawning escapement in the Central Valley,
but run sizes during the early 1990s fell to extremely low levels (i.e., less than 500 spawners).
The fall run rebounded in the late-1990s, approaching 9,000 spawners in 1998; however, from
Page B 19
2001 through 2010, the fall run has averaged only 2,259 fish (Table B-20). Since 2005, the
number of Chinook retuning to the Tuolumne River has averaged less than 500 fish.
The fall run historically has been a naturally sustained population because there is no hatchery on
the Tuolumne River. Increasing numbers of hatchery-derived spawners have ascended the
Tuolumne River in recent years, mainly due to large releases of hatchery juveniles (from Merced
River Hatchery) for study purposes into this stream and elsewhere in the San Joaquin River Basin
and Sacramento-San Joaquin Delta (Yoshiyama et al. 2001). According to IFC Jones & Stokes
(2010), approximately 31% of the natural fall Chinook spawners in the Tuolumne River are
considered to be hatchery-origin fish.
Table B-20.
Fall-run Chinook salmon escapement in the Tuolumne River basin (2001-2010).
In-River Escapement
Year
(Tuolumne)
2001
8,782
2002
7,173
2003
2,163
2004
1,984
2005
668
2006
562
2007
224
2008
372
2009
124
2010
540
Average
2,259
16
Merced River (Fall Chinook)
The Merced River is a tributary to the San Joaquin River in the southern portion of the Central
Valley. The river, which drains a 1,276-square-mile watershed, originates in Yosemite National
Park and flows southwest through the Sierra Nevada range before joining the San Joaquin River
87 miles south of Sacramento. Elevations in the watershed range from 13,000 feet at its crest to
49 feet at the confluence with the San Joaquin River (Stillwater Sciences 2006).
Similar to other rivers in the Central Valley, the Merced River has been affected by numerous
human activities, including water storage and diversion, land use conservation, introduction of
exotic plant and animal species, gold and aggregate mining, and bank protection. 11 Alteration to
the flow and sediment supply within the lower Merced River began with construction of the
original Exchequer Dam in 1926. Currently, flow is controlled by four dams on the mainstem
Merced River, New Exchequer Dam, McSwain Dam, Merced Falls Dam, and the
Crocker‐Huffman Dam (Stillwater Sciences 2006).
Historically, both spring and fall-run Chinook salmon occurred in the Merced River, but only the
fall run has survived and is now the southernmost native Chinook salmon run in existence
(Yoshiyama et al. 2001). Fry (1961 as cited in Yoshiyama et al. 2001) considered the Merced
11
http://sanjoaquinbasin.com/merced-river.html
Page B 20
River to be “a marginal salmon stream” due to the removal of water by irrigation diversions, and
he stated that there was “a poor fall run and poor spring run.”
The CDFG has been conducting escapement surveys in the Merced River since 1953. Data
collected from the surveys allow CDFG to estimate fall-run Chinook escapement; evaluate the
distribution of redds in the study area; collect length and sex data; collect scale and otoliths for
age determination and cohort analyses; and collect and analyze coded-wire tag data. The
escapement surveys cover a 24.7-mile reach extending from Crocker-Huffman Dam at the
Merced River Hatchery (RM 51.9) to Santa Fe Road (RM 27.1).
During the 1950s and 1960s, Merced River fall-run Chinook escapement averaged less than 500
fish in most years. Escapement began to increase substantially in 1970 following flow increases
from the New Exchequer Dam and releases of hatchery-reared fish into the river. However,
spawning escapements in the Merced River, including returns to the Merced River Hatchery,
dropped significantly in the early 1990s to less than 100 fish in 1990 and less than 200 in 1991
(Yoshiyama et al. 2001). From 2001 through 2010, the fall Chinook run in the Merced River,
including fish returning to the Merced River Hatchery, has averaged just over 3,500 fish, with
total escapement experiencing another dramatic decline beginning in 2007 (Table B-21).
According to IFC Jones & Stokes (2010), approximately 67% of the natural fall Chinook
spawners in the Merced River are considered to be hatchery-origin fish.
Table B-21.
Fall-run Chinook salmon escapement in the Merced River basin (2001-2010).
Merced River Fish
In-River
Percent In-River
Year
Facility
(Merced)
Total
(Merced)
2001
1,663
9,181
10,844
84.7%
2002
1,840
8,866
10,706
82.8%
2003
549
2,530
3,079
82.2%
2004
1,050
3,270
4,320
75.7%
2005
421
1,942
2,363
82.2%
2006
150
1,429
1,579
90.5%
2007
79
495
574
86.2%
2008
76
389
465
83.7%
2009
246
358
604
59.3%
2010
146
651
797
81.7%
Average
622
2,911
3,533
80.9%
17
References
Armentrout, S., H. Brown, S. Chappell, M. Everett-Brown, J. Fites, J. Forbes, M. McFarland, J. Riley, K.
Roby, A. Villalovos, R. Walden, D. Watts, and M.R. Williams. 1998. Watershed Analysis for
Mill, Deer, and Antelope Creeks. U.S. Department of Agriculture. Lassen National Forest.
Almanor Ranger District. Chester, CA. 299 pp.
Brown, M. R. 1996. Benefits of increased minimum instream flows on Chinook salmon and steelhead in
Clear Creek, Shasta County, California 1995-6. USFWS Report. U.S. Fish and Wildlife Service,
Northern Central Valley Fishery Resource Office, Red Bluff, California.
Brown, R. and F. Nichols. 2003. The 2003 CALFED Science Conference: A Summary of Key Points
and Findings. Submitted to CALFED Science Program, Sam Luoma, Lead Scientist, May 2003.
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CFC (California State Board of Fish Commissioners). 1877. (4th) Rep. Comm. Fish. Of the State of
California for 1876 and 1877. Sacramento, Calif.
CH2M Hill. 1998. Central Valley Project Improvement Act Tributary Production Enhancement Report.
Draft report to Congress. Prepared for U.S. Fish and Wildlife Service. Sacramento, CA.
CH2M Hill. 2002. Cottonwood Creek Watershed Assessment. Red Bluff, CA. 712 pp.
Clark G.H. 1929. Sacramento-San Joaquin salmon (Oncorhynchus tshawytscha) fishery of California
Division of Fish and Game Fish Bulletin 17.p 1–73.
DWR. 2007. Upper Yuba River Watershed Chinook Salmon and Steelhead Habitat Assessment.
Prepared by the Upper Yuba River Studies Program Study Team. California Department of
Water Resources. November 2007.
Fisher F.W. 1994. Past and present status of Central Valley Chinook salmon. ConservBiol 8(3):870–3.
Fry D.H., Jr. 1961. King salmon spawning stocks of the California Central Valley, 1940–1959.
California Fish and Game 47(1):55–71.
Gerstung E.R. 1971. A report to the California State Water Resources Control Board on the fish and
wildlife resources of the American River to be affected by the Auburn Dam and Reservoir and the
Folsom South Canal and measures proposed to maintain these resources. California Department
of Fish and Game. June 1971. Sacramento, Calif.
Greenwald, G. M., J. T. Earley, and M. R. Brown. 2003. Juvenile salmonid monitoring in Clear Creek,
California, from July 2001 to July 2002. USFWS Report. U.S. Fish and Wildlife Service, Red
Bluff Fish and Wildlife Office, Red Bluff, California.
ICF Jones & Stokes. 2010. Hatchery and Stocking Program Environmental Impact
Report/Environmental Impact Statement. Final. January. Sacramento, California. Prepared for
the California Department of Fish and Game and U.S. Fish and Wildlife Service, Sacramento,
California.
NMFS (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.
Sacramento Protected Resources Division. October 2009.
Reynolds F.L., T.J. Mills, R. Benthin, and A. Lowe. 1993. Restoring Central Valley streams; a plan for
action. Sacramento (CA): California Department of Fish and Game. 129 p.
SHN (SHN Consulting Engineering & Geologists, Inc.). 2001. Cow Creek Watershed Assessment.
www.sacriver.org/documents/watershed/cowcreek/assessment/Cow_Creek_FinalWatershedAsses
sment.pdf
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Plan. Stillwater Sciences, Berkeley, California. Available at:
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Page B 22
Yoshiyama, R. M., E. R. Gerstung, F. W. Fisher, and P. B. Moyle. 2001. Historical and present
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salmon in the Central Valley region in California. North American Journal of Fisheries
Management 18: 487–521.
Page B 23

Nimbus Fall Chinook Program - California Hatchery Review Project

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