Nimbus Salmon and Steelhead Hatchery
The First 50 Years of Chinook Culture with a note on steelhead
By
Randall L. Brown
For the
Water Forum
660 J Street, Suite 260
Sacramento, CA 95814
March 2006
1
Acknowledgements
Special thanks to the following for helping make this report possible
- Leo Winternitz, Water Forum, for funding and for his patience.
- Terry West, DFG, the current Nimbus Hatchery manager, for providing
information and clarification and reviewing the draft report.
- Armando Quinones, DFG, the Region II Senior Hatchery Supervisor, for
reviewing the manuscript and providing helpful comments.
- Kris Jones, PSMFC (now at Oxford) and Joe Duran, DFG, for helping
organize the tag recovery data.
- Mike Healey, DFG, for organizing and conducting the escapement and tag
recovery surveys on the lower American River.
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Executive Summary
The year 2005 marked the golden anniversary of the Nimbus Hatchery.
Construction of the hatchery was funded by the United States Bureau of Reclamation
(Reclamation) with concurrence from the United States Fish and Wildlife Service
(USFWS). The purpose of the hatchery construction and operation is to mitigate for fall
run Chinook salmon and steelhead rainbow trout spawning and rearing habitat lost due to
construction of Nimbus and Folsom dams on the lower American River. The California
Department of Fish and Game (DFG) operates the hatchery under contract to
Reclamation.
This report mainly discusses the Chinook culture operations but a note on
steelhead culture is included. The objective of this report is to describe hatchery
operations, the fate of the fish produced at the hatchery and to offer some suggestions
how hatchery and fishery managers should evaluate and adjust hatchery operations to
meet environmental and fishery goals. An ancillary objective is to provide some of the
information that may lead to productive discussions of the hatchery, the American River
and Central Valley salmonids.
Over the past 50 years hatchery staff has collected over 750,000,000 Chinook
salmon eggs and released more than 250,000,000 fry or fingerlings, 120,000,000 smolts
and 4,,000,000 yearlings. The fish have been released in the American River (and to a
much lesser extent other Central Valley streams) in the Sacramento-San Joaquin Delta
and in San Pablo Bay. In the past several years the Chinook salmon run to the American
River has averaged more than 100,000 fish. This is much higher than had been seen in the
previous four decades. The average annual runs during that period were closer to 40,000
to 50,000 spawners) and much higher than during the 10 year period immediately before
Nimbus and Folsom dams were constructed (average of about 26,000 adults). Thus the
Hatchery appears to have more than met its mitigation obligation in terms of numbers of
adult salmon returning to spawn.
During the first 50 years of Nimbus Hatchery operations constant improvements
in Hatchery practices have resulted in increased ocean and freshwater harvest while
ensuring that enough fish returned to the Hatchery to meet its egg take goals. These
3
changes include changes in fish ladder operations to bring fish into the Hatchery later in
the fall to minimize temperature problems, changes in egg incubation and size at release
(now all smolts), a change in release location (release is now exclusively in the San Pablo
Bay) and change in the method of release. (This is now done via net pens as compared to
direct releases from the transport trucks to the bay.) Early disease problems were largely
eliminated (or controlled) with the help of DFG pathologists. (Although experiences
during the winter and spring of 2006 demonstrated that disease can still disrupt Hatchery
operations.) Bird depredation has been largely eliminated by constructing exclusion nets
over the raceways.
Nimbus Hatchery production contributes to the ocean fisheries and helps support
a growing recreational fishery on the lower American River. The exact extent of this
contribution is unknown due to lack of tagging and tag return data as fish are not tagged
prior to release for data collection upon return.
Nimbus Hatchery has also become an important local attraction and a
“classroom” for many school children. More than 15 million people have visited the
Hatchery, with more than 1 million visitors per year in the past decade. The annual fall
salmon festival attracts several thousand visitors alone. In 2005 about 20,000 visitors
attended the event. Local universities, including the University of California, Davis use
the Hatchery to obtain test fish and samples for various salmonid-related studies.
The useable spawned out salmon carcasses are distributed for food and about 2.5
million pounds have been given to local charities.
Hatchery managers, staff and supervisors have worked in a production mode
(similar to farm crop production) and have arguably made Nimbus Hatchery one of the
most successful (along with most of the Central Valley salmon hatcheries) of the West
Coast salmon production facilities.
However, analyses of the potential adverse biological effects of Nimbus Hatchery
production (and that from other Central Valley hatcheries) have not kept pace with
advances in hatchery operations. To say that DFG’s mitigation hatcheries have suffered
from benign neglect on the part of biologists (not only in DFG but other resource
agencies) for most of the past 50 years is an understatement. The hatcheries appear to
have been viewed as a source of fish for the fisheries and to meet escapement goals. As
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shown in this report, hatchery fish from Nimbus were previously planted somewhat
randomly in several Central Valley streams. Genetic material (mostly green or eyed
egged and fry) were routinely transferred among the state and federal hatcheries. Nimbus
Hatchery moved to planting all of its production in San Pablo Bay instead of the lower
American River. This was all done without providing for concurrent data collection and
interpretation that is needed to evaluate the potential benefits and adverse impacts of
hatchery operations on Chinook salmon in the American River and other Central Valley
streams. Local biological input was especially critical, and lacking, during the past two
or so decades when the attitude towards mitigation and production hatcheries has shifted
from acceptance to, at best, skepticism.
The DFG approach to hatchery operations began to change in 1999 when the
National Oceanic and Atmospheric Administration National Marine Fisheries Service
(NOAA Fisheries) urged DFG to adopt a standard operating procedure, or SOP, for
Nimbus Hatchery and its other anadromous salmonid mitigation hatcheries. The SOP
clearly laid out egg take and production goals, as well as hatchery procedures. This SOP
is now being revised. The change in attitude as to how hatcheries are viewed took
another significant step in 2001 with release of a joint DFG/NOAA Fisheries review of
DFG’s hatcheries (DFG and NOAA Fisheries 2001). This review called for some
hatchery changes and a recommendation that all hatcheries prepare Hatchery and
Genetics Management Plans (HGMPs) under which the hatcheries would be operated in a
more biologically responsive manner. The Feather River and Mokelumne hatcheries are
embarking on the HGMP process and Nimbus and other DFG hatcheries are expected to
follow soon.
So what was the impetus for this look at the American River and Nimbus
Hatchery? The Sacramento Region Water Forum and others are close to achieving a new
flow standard for the lower American River which is designed, at least in part, to benefit
Chinook salmon. To determine if these new flow regimes actually benefit naturally
spawning and rearing Chinook salmon an increased understanding of how the hatchery,
stream and ocean conditions and fisheries interact to produce Chinook salmon is needed.
To accomplish this goal, there will have to be increased data collection (mark hatchery
fish and recover the tags), more interaction among biologists in Nimbus and other Central
5
Valley hatcheries, and increased use of conceptual and mechanistic models to help tie all
the pieces together. We must have at least a semi-quantitative determination regarding
the reasons for the recent large runs to the American River (and other Central Valley
streams. Are they due to?

Good ocean conditions

Reduced ocean fisheries

Better hatchery practices

Better in stream conditions

Some combination of the above
I recommend the Water Forum take the lead in efforts to develop a monitoring
and analyses organizational structure for the lower American River and offer some
suggestions on how it could work. It is important to recognize that the Central Valley
systems of fisheries and hatchery management (including the ocean) must include all the
hatcheries. We collectively need to look at the entire Central Valley hatchery and salmon
management system and develop a biologically sound management plan. A promising
first step in this process may be the creation of a hatchery project work team under the
Interagency Ecological Program’s Central Valley Salmon Team. Although this team had
not met as of June 2006, one of its objectives was to coordinate development of HGMPs,
the purpose of which are to address hatchery impacts on naturally spawning fish
populations.
Table of Contents
List of Tables
List of Figures
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Introduction
The Nimbus Salmon and Steelhead Hatchery (Nimbus Hatchery) began operation
on the American River below Nimbus Dam in the fall of 1955. Over the past one-half
century, Reclamation has funded DFG to operate the Nimbus Hatchery as mitigation for
American River anadromous salmonid spawning and rearing habitat lost due to
construction of Nimbus and Folsom dams. During this period, Hatchery staff has done an
admirable job of trapping, spawning, rearing and releasing millions of juvenile fall
Chinook salmon and steelhead rainbow trout. Fish reared and released from the Hatchery
have undoubtedly made major contributions to commercial and recreational fisheries in
the ocean and an ever-increasing recreational fishery in the lower American River (LAR)
and other Central Valley streams. The Hatchery itself has also become a recreational and
educational destination in the Sacramento region by providing opportunities for children
and adults to observe fall Chinook spawning and salmon rearing first hand.
From the beginning DFG staff has released a series of annual reports to document
such important hatchery operational information as number of females spawned, eggs
taken and numbers of juveniles. These valuable accounts provide the basis for much of
this report. A few publications (for example Warner et al. 1961 and Hallock and
Reisenbichler 1979) have presented limited information on the fate of tagged Nimbus fall
Chinook and steelhead released from the Hatchery at different sizes and locations.
Dettman and Kelley (1987) and Cramer (1990) took a broader look at Central Valley
salmon hatcheries and attempted to estimate the hatchery contributions (including
Nimbus Hatchery) to fisheries, escapement, and to straying. However, there has been no
overall description of Nimbus Hatchery operations, assessment of its success at
mitigating for Nimbus Dam construction and operation, contribution to the fisheries and
escapement, or the effects of the Hatchery on naturally spawning salmonid in the LAR
and other Central Valley streams.
The original impetus for this report was one outcome of a proposal by the Water
Forum and others to establish a new flow regime on the LAR, a flow regime that would
be more protective of naturally spawning anadromous salmonids. In considering the
request for more protective flows, one of the basic questions was, “What is the relative
7
contribution of the Nimbus Hatchery, and other Central Valley hatcheries to the Chinook
salmon and steelhead populations in the LAR?” Without this information it will not be
possible to assess the relative benefits of the new flow regime on natural salmon
production in the LAR as compared to the Hatchery contribution. The Water Forum
sponsored this report, which attempts to gather what is known about the Nimbus
Hatchery, its contribution and impacts.
After an initial examination of the available information, I concluded that there
were not enough data to study the steelhead component thoroughly. At the request of the
Water Forum, a short note on steelhead production is included and the discussion section
includes some suggestions for upgrading our knowledge of this somewhat enigmatic
species. Even for Chinook salmon it would have been impossible to get beyond basic
descriptions of hatchery operations had it not been for the rather fortuitous experimental
coded wire tagging (CWT) program that took place at Coleman, Feather River and
Nimbus hatcheries in 2000 and 2001. This program was funded by the CALFED BayDelta Program. The purpose of this experimental program was to examine the feasibility
of using an automated tagging machine, not to look at the effects of the hatcheries.
Unfortunately neither DFG nor CALFED documented the results of this study. In both
years more than 500,000 juvenile Chinook salmon from Nimbus Hatchery were tagged
and released. Although such a limited tagging program could not answer the
fundamental question regarding the percent of Nimbus Hatchery fish harvested in the
ocean and inland fisheries that strayed to other Central Valley streams or returned to the
LAR, the tag recoveries from this tag machine evaluation do provide tantalizing hints
regarding some of the answers. The annual Hatchery operations reports are very useful
for describing what went on at the Hatchery but have much less value in evaluating the
impacts and contribution of the Hatchery.
Given the data limitations, this report focuses on summarizing operations of the
Nimbus Hatchery over the past 50 years as they relate to Chinook salmon and the
information that can be obtained from the 2000 and 2001 tagging program. The report is
a qualitative description of what happened. There are not enough data to evaluate why it
happened; that was beyond the scope of this limited effort. The operations data
demonstrate that successive Hatchery managers successfully used an ad hoc adaptive
8
management process to improve and optimize Hatchery operations to produce adult
salmon for the fisheries and escapement. Over the years spawning, incubation, rearing
and release (both size of fish at release and release location), and disease and depredation
control practices were modified to help ensure reliability and maximize returns to the
fisheries and the stream. However, as will be pointed out in the discussion, Hatchery
managers and DFG biological staff did not always consider the impacts of their actions
on salmonid resources and in some cases optimizing production to put more fish in the
boat, creel or back in the stream may not have been the best for the overall Central Valley
Chinook salmon resources.
Although not organized around the framework for a NOAA Fisheries HGMP
(NOAA Fisheries 1999), much of the information contained in this report can be used to
meet many of the HGMP information needs. It is likely that all Central Valley
anadromous salmonid hatcheries will eventually prepare HGMPs. As the title implies,
the HGMPs are to help hatchery managers and biologists evaluate, and modify hatchery
operations to reduce any detrimental hatchery effects on naturally spawning salmonid
stocks.
Before describing Nimbus Hatchery itself, I will set the stage somewhat by briefly
describing the genetic structure in which American River fall Chinook are found and the
newly emerging context into which production and mitigation salmonid hatcheries are
being considered. These sections are followed by a summary of what we know about the
Nimbus Hatchery and its operations, drawing on the limited literature containing data
from the Nimbus Hatchery. I wind up the report with discussion of the implications
information presented about Central Valley Chinook and suggestions for additional
monitoring and an organizational structure in which the monitoring data can be collected
and evaluated. In reading this report it is important to recognize that there are five
Chinook salmon hatcheries in the Central Valley that collectively produce and release
more than 25 million juvenile fall Chinook into Sacramento and San Joaquin Valley
streams and the San Francisco estuary. To successfully manage Central Valley salmonid
resources, all hatcheries, and the naturally spawning stocks, must be considered using an
ecosystem approach. As you will see they all work, or don’t work, together.
9
I should also stress that by and large hatchery managers have done a great job
growing and releasing juvenile Chinook. Reports such as this should not be taken as
criticism of the hatcheries or those that manage them. The managers did what they were
asked to do and did it well. Times and situations have changed and it is now time for
Central Valley biologists and managers to work together to assess the hatchery role in
salmon management. Such an assessment will likely result in changes in hatchery
practices.
The environmental setting is important to understanding the Nimbus Hatchery and
its relation to the LAR and this setting has been described well elsewhere. Interested
readers are referred to Williams (2001) for a description of the river and a summary of
what was known about Chinook salmon in the LAR through about 1998. A recent and
more popular view of the LAR, including its health, can be found in Water Forum State
of the Lower American River Report (2005). The Water Education Foundation (1995)
published a very readable “Layperson’s Guide to the American River.” Also Winternitz
and Holtz (2005) provide a good description of the LAR and the conflicts competing
demands have placed on this recreationally, ecologically and economically important
system. For this report it is now sufficient to say that the Nimbus Hatchery is located just
downstream of Nimbus Dam, at about river mile 23. As will be described later, this
relatively low elevation combined with the limited cold water pool in Folsom Reservoir
have affected Hatchery operations, particularly early in the fall for Chinook salmon.
Figure 1 provides a general layout of the LAR between Nimbus Dam and its confluence
with the Sacramento River.
Nimbus Hatchery staff currently releases the Hatchery’s entire production in the
San Pablo Bay, thus the young salmon bypass the Sacramento-San Joaquin Delta and
Suisun Bay (Figure 2). Hatchery managers selected the downstream release site to
reduce losses of juvenile fish between the American River and San Pablo Bay. (Note that
fish from the Feather River Hatchery and enhancement fish from the Mokelumne River
Hatchery are also released at this downstream site.) Towards the end of this report I
suggest that Hatchery managers consider releasing part of the production in the American
River – mainly to evaluate the hypothesis that considerable losses still occur in the Delta
and to assess the differential straying that may occur between the two release sites. The
10
NOAA Fisheries/DFG hatchery review (DFG and NOAA Fisheries 2001) also
recommended that DFG consider releasing Nimbus Hatchery production in the LAR.
It may help the reader to have some understanding of the issues in the Delta that
could affect the decision to release some or all of the Nimbus Hatchery production
Chinook in the American River, a decision I recommend be considered. For a more
complete description, see Brandes and McLain (2001). The following summary is based
loosely on how an emigrating juvenile salmon might perceive the Delta and the perils it
encounters on the way to the ocean.
The progeny of naturally spawning Chinook generally leave the LAR by the end
of March as fry (Williams 2001). This emigration pattern is similar to that observed in
the Feather River (Sees Holtz et al. 2004). It is not clear where the young salmon rear to
smolt size before heading for the ocean.
After entering the Sacramento River, the juveniles have a pretty clear and direct
path until they reach the Delta Cross Channel (DCC) near Walnut Grove. (And they may
rear in the Delta for extended periods, Brandes 2006, in review: Williams 2006, in press.)
Reclamation constructed the gated Delta Cross Channel (DCC) in the early 1950s to
allow Sacramento River water to enter the interior Delta and thence flow to federal and
state water export facilities in the South Delta. The DCC gates are typically open when
Sacramento River flows were less than 25,000 cfs. Fish studies demonstrated that the
survival of young fall Chinook leaving the main river channel through the DCC was less
than if the fish had remained in the river (Brandes and McLain, 2001). The difference in
survival was most likely due to the longer path the fish had to traverse before leaving the
Delta – which made them more subject to predation and effects of water project pumping
in the South Delta.
To protect juvenile Chinook salmon, the gates are now closed from February 1
through about the end of May each year. Since this is the time Nimbus Hatchery
production would be released, DCC operation should not enter into the decision whether
to release the fish on site. Just downstream of the DCC, Georgiana Slough, a natural
channel, carries water and fish towards the interior Delta, lower San Joaquin River and
the pumps. Flow into the slough is a function of river flows, DCC gate operation (open
or closed) and tidal stage (Jon Burau, United States Geological Survey, personal
11
communication). It is not clear if fish go into the slough in proportion to the flow leaving
the river but some fish do take that route. In any event, survival of those fish entering
Georgiana Slough is much less than for fish that remained in the main stem and there is a
weak relationship between that survival and water project pumping from the South Delta
(Pat Brandes, USFWS, personal communication and see Brown and Kimmerer, 2005, for
a link to the original data and descriptive text.) Fish that remain in the main Sacramento
River are considered to have a good chance to survive to Chipps Island, the western edge
of the Delta.
To make the picture complete, I need to briefly describe the water project
pumping and fish salvage facilities in the south Delta and the concern about the effects of
their operations on salmon survival. More information can be found in Brown et al.
(1996).

State Water Project (SWP) – The SWP is operated by the California Department
of Water Resources (DWR) and the pumping plant is located near the town of
Byron. The pumps have a capacity of over 10,000 cfs, although daily average
pumping is almost always less than 7,000 cfs. The SWP pumps from a regulating
reservoir (Clifton Court Forebay), with the reservoir gates opened on high tides to
restore the water levels. The SWP intake has fish salvage facilities to screen,
collect and transport the salvaged fish to a release site away from the draft of the
pumps. Fish tests have led to the conclusion that 3 of 4 juvenile Chinook salmon
entering the Forebay are lost to predators on their way to the fish screens (Gingras
1997, Kimmerer and Brown 2006).

Central Valley Project (CVP) – The CVP is operated by Reclamation with its
intake located about one mile from the SWP intake. CVP pumps have a capacity
of around 4,600 cfs and to the extent possible, are operated around the clock, 365
days a year. (The SWP often pumps at night – off peak power – to reduce power
costs.) Unlike the SWP, the CVP takes water directly from the channel. The
CVP intake also has a fish screening system which uses the same louver concept
as the SWP and was, in fact, the basis for the state design. Since there is no
forebay, calculated predation losses indicate that about 1 in 7 juvenile salmon is
lost to predators in front of the fish screens.
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When contemplating releasing Nimbus Hatchery production into the LAR (and I
think we must), the Vernalis Adaptive Management Plan (VAMP) should enter into the
equation. The VAMP consists of an annual series of studies that often result in water
project pumping at a minimum between April 15 and May 15 (see San Joaquin River
Group Authority, 2005 for a program description). In keeping with the recommendation
in DFG and NOAA Fisheries (2001) any releases of Nimbus Hatchery fish in the LAR
should be timed to coincide with the lower pumping. It must be noted that a 2006 Third
Appellate Court District decision regarding State Water Resources Control Board
Decision 1641 (which included VAMP) cast doubts on the continuation of VAMP. With
regard to VAMP, the court said the Board had to go back to the San Joaquin River pulse
flows that were included in the Board’s 1995 Water Quality Control Plan. In any event
there will likely be times in the timing of spring in-river releases from the Nimbus Fish
Hatchery could coincide with Delta conditions most conducive to through-Delta survival.
LAR fall Chinook as part of CV Chinook salmon genome
The LAR currently only supports a run of fall Chinook and this is the only race
reared in the Nimbus Hatchery. Banks et al. 2000 and Williamson and May (2005) used
micro satellite genetic markers to show that Central Valley fall Chinook form a
homogenous subpopulation of the overall Chinook salmon population genome, with late fall
Chinook being their closest kin. This grouping, illustrated in Figure 3, includes American River
fall Chinook. The genetic diversity of Central Valley fall Chinook populations is lower than that
Winter ‘91 - ‘97
(256)
Spring ‘96 - ‘97
Butte Creek
(193)
1001
1002
783
664
711
Spring ‘94 - ‘97
Deer and Mill Creeks
(232)
642
613
434
991
972
973
Fall ‘94 - ‘96
(729)
994
0.01
Late fall ‘93 & ‘95
(235)
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Figure 3. UPGMA phenogram derived from the Cavalli-Sforza (1967) chord measure
using adjusted data from ten microsatellite loci. From Banks et al. 2000.
found in populations in other areas that occupy a similar breadth of geographic scales
(Williamson and May 2005).
The lack of genetic diversity in Central Valley fall Chinook populations can not
be explained with the available data. Extensive genetic examination of Central Valley
Chinook salmon populations did not begin until the mid 1990s and as yet investigators
have not been able to examine the DNA from tissues collected before the major dams
were built and mitigation hatcheries constructed. Williamson and May (2005) concluded
that the lack of genetic diversity and the lack of temporal differences in allele frequencies
between hatchery and naturally spawning salmon indicate extensive gene flow between
fall Chinook salmon populations throughout the Central Valley. The gene flow could be
due in part to such hatchery management practices as off-site production releases,
transfers of genetic material among hatcheries and straying from experimental releases of
juvenile salmon in the Delta and elsewhere. I return to the subject of gene flow between
hatchery and naturally spawning salmon, through straying and interbasin transfers of
genetic material, later in this report.
The evolving role of hatcheries in salmon management
When DFG and USFWS recommended that the Nimbus Hatchery be constructed
in the early 1950s to mitigate for habitat lost due to construction of Nimbus Dam, there
was likely little adverse public or scientific reaction to the proposal. Once the decision
was made to build the dam and block fish passage, a hatchery was a logical mitigation
measure. A mitigation goal was established and Nimbus Hatchery was sized to meet that
goal. Over the half century since the USBR constructed the Nimbus Hatchery, the
attitude towards hatcheries, at least among the scientific community, has shifted. Now
14
hatchery operators and resource biologists must carefully weigh the benefits and adverse
impacts of proposed hatchery operations.
The literature on the impacts and benefits of hatcheries is extensive and it is
beyond the scope of this report to conduct a major review of that literature. Below I cite
a few examples of papers that should be read to obtain a better sense of the controversy.
These papers also contain extensive references for those interested in the topic, that is,
about anyone involved in evaluating future operations of the Nimbus and other Central
Valley hatcheries.
Adverse Hatchery Effects
The National Research Council (1996) reviewed the literature regarding salmon
and society in the Pacific Northwest and hypothesized a variety of possible explanations
for observed declines of wild salmonid populations, including the potential adverse
effects of production hatcheries. The authors, members of a 10-person Committee on
Protection and Management of Pacific Northwest Anadromous Salmonids, listed the
following as potential adverse hatchery effects.
Demographic Risk, mostly due to the indirect effect that large numbers of
hatchery fish in fisheries can exert on weaker natural stocks. The hypothesis is
that the fisheries are based on the abundant hatchery fish and harvest rates that are
acceptable for hatchery stocks may result in over-harvest of naturally spawning
stocks and could drive these stocks to extinction.
Genetic and Evolutionary Risks can show up in four main areas (as identified by
Busack and Currens 1995 and cited in NRC 1996):

Inbreeding depression

Loss of between-population genetic variation.

Loss of within-population genetic variation.

Domestication in which the fish become genetically adapted to the hatchery
environment, with an accompanying loss of overall fitness. (Fitness can be
described as the ability to survive to a reproductive age and leave viable
offspring, Hallerman 2003.)
Behavior Risks are associated with the differences between the behavior of wild
and hatchery stocks. The behavior traits of hatchery fish may result in loss of
fitness (for example, reduced predator avoidance by hatchery fish (Berejikian
15
1995) or adverse affects on the natural populations into which the hatchery fish
are released (for example, increased aggressive behavior by hatchery as compared
to their wild cousins (Peery and Bjorn 1996).
Fish Health and Disease, both in the released hatchery fish and in the interactions
between hatchery and naturally spawning populations.
The Physiological State of Hatchery Fish is often sub-optimal, due perhaps to
hatchery conditions, handling, and transportation.
Ecological Problems that may be associated with effects of planted hatchery fish
on the competition for available carrying capacity in streams, estuaries and the
ocean between hatchery and naturally spawning stocks.
To this list of hatchery effects, I think one should add the false sense of
environmental security engendered by large numbers of returning hatchery fish. If tens of
thousands of Chinook salmon spawn in the LAR and other Central Valley streams, and
the commercial and recreational fisheries are harvesting large numbers of salmon,
managers and the general population may believe that salmon are doing fine. In reality,
many natural stocks are in trouble and in need of drastic action to prevent their extinction.
To obtain a different view of the role of hatcheries in salmon management, see
Brannon and 10 co-authors (2004). The authors, all associated with hatcheries in one
way or another, make the case that hatcheries have an important role in the
supplementation and recovery of wild salmonid stocks. The authors intended to give
balance to the discussion about the use of hatcheries and provide a critical review of
some of the relevant literature.
Waples (1999) wrote a thoughtful essay on hatcheries entitled “Dispelling some
myths about hatcheries”. I think his conclusions should be kept in mind when
considering hatcheries – namely:
-
Hachteries are intrinsically neither good nor bad – their value can only be
determined in the context of clearly defined goals.
16
-
-
Genetic changes in cultured populations can be reduced but not entirely
eliminated.
Empirical evidence of many adverse effects of hatcheries exists, but some risks
have been overstated.
Monitoring and evaluation programs are important but should not be used as a
substitute for developing risk-averse strategies in the first place.
Waples also stated that major efforts are needed in four areas:
Identifying goals,
Conducting cost-benefit analyses to guide policy decisions,
Improving the information base, and
Dealing with uncertainty.
Finally, Lichatowich et al. (2006) reviewed the history and problems with salmon
production hatcheries in the Pacific Northwest with emphasis on the Columbia River
Basin. Much of their discussion applies equally to Sacramento Valley hatcheries, with
their recommendations grouped under the following categories that must be considered
with regard to hatcheries.






Risk assessment and adpative management
Comprehensive evaluation of artificial propagation
Link harvest management with hatchery operations
The experimental nature of artificial propagation
The need for regional decision documents
Hatcheries as genetic reserves and refugia
Three recent documents directly related to Central Valley salmonids and hatchery
operations are also important in the sense that they are among the first local documents to
look at hatchery operations and production from a biological standpoint. The first is the
biological assessment (BA) of artificial propagation at the federal Coleman National and
Livingston Stone national fish hatcheries as related to the take of the listed Chinook
salmon races and steelhead trout (USFWS 2001). The assessment includes a complete
description of the programs at the two hatcheries and an evaluation of the impacts of
hatchery operation on salmon populations. This assessment represents the first serious
examination of the effects of a major Central Valley hatchery program – albeit after about
60 years of operation. (The BA also served as a Hatchery Genetic Management Plan for
Coleman.) Overall the BA concluded that operation of the two hatcheries has had no or
minimal effects on all four Central Valley Chinook salmon races and steelhead (Their
Table 2-4).
17
The second report summarizes the results of a joint DFG/NOAA Fisheries review
of California’s anadromous salmonid hatcheries (DFG and NOAA Fisheries 2001). To
my knowledge this is the first comprehensive review of California’s salmon and
steelhead hatchery system. Although DFG and NOAA Fisheries biologists participating
in this review were hampered by a lack of data, their overall recommendations, listed
below, helped shape DWR’s efforts to evaluate the Feather River Hatchery (FRH).
1. Feather River spring Chinook should be released “in-river” and not be trucked
to distant downstream sites.
2. The production of fall run Chinook salmon at Feather River and Nimbus
hatcheries should be considered for “in-river” releases instead of being
trucked downstream.
3. Hatchery “in-river” releases and water management practices (including water
exports from the Sacramento-San Joaquin Delta) should be coordinated so that
emigration survival is maximized.
4. A formal process should be identified for the periodic review and assessment
of hatchery production levels , for example every six to nine years or two to
three brood years.
5. All agencies should pursue efforts to establish a constant fractional marking
program at all hatcheries.
6. All agencies should pursue efforts to develop adequate sampling programs to
recovered marked and tagged fish in the Central Valley.
7. A Hatchery and Genetics Management Plans (HGMP) should be prepared for
each hatchery.
The hatchery implementation committee formed as a result of these efforts is
working to implement many of the recommendations contained in the original report.
For example, on the Feather River, DWR and DFG agreed to tag all Feather River
Hatchery (FRH) spring Chinook and release one-half the production in the Feather River
and the remainder in the estuary. Analysis of the return data will be used to determine
the benefits and risks of releasing all spring Chinook in the Feather River. The FRH is
also embarking on the process of developing an HGMP and has established a Feather
River Technical Team to help assemble the information needed for the document.
The third report is a 2004 analysis of the effects of the FRH on naturally
spawning Chinook salmon and steelhead in the Feather River and the Central Valley
(Brown et al. 2004). This analysis was part of a comprehensive examination of DWR’s
Oroville complex, including the FRH, being undertaken by DWR as part of the Federal
Energy Regualatory Commission (FERC) process to renew its hydropower license. The
analysis demonstrated that FRH production Chinook stray to most Central Valley
18
streams, make a significant contribution to ocean and inland fisheries and that the
hatchery has inadvertenly mixed fall and spring Chinook in hatchery spawning. Most
importantly perhaps, the analysis demonstrated that tagging, genetic and other data are
required to evaluate the benefits and impacts of hatchery operation and that these data
need to be compiled and analyzed periodically. These analyses can then be used in
adaptively managing hatchery operations to achieve its multiple goals and minimize any
adverse impacts.
A final recent paper that bears consideration as we ponder the role of hatcheries is
by Bottom et al. (2005). The authors of this study recommend we think more in terms of
population biology instead of the production thinking that has been the approach used by
many salmonid bioloigsts and managers in the past. The difference in the two types of
approaches is shown in Table 1.
Table 1. Comparison of production thinking and population thinking, reproduced
from Table 2 in Bottom et al. (2005).
Goals
Production Thinking
Efficiency, production
Population Thinking
Resilience, reproduction
Population Units
Arbitrarily defined
Biologically defined
Time Frame
Short
Evolutionary
Objectives
Control survival and abundance
Estuary Function
Corridor for a single, homogenous
group of salmon
Control predators, promote rapid
salmon out-migration
Conserve local populations and
life-history diversity
Nursery area for many selfsustaining populations
Protect habitats of diverse lifehistory types
Estuary Management
In summary, many conditions have changed since the Nimbus Hatchery commenced
operations in 1955. The environment itself has changed, mainly due to natural and anthropogenic
factors such as ocean conditions and climate and water development and flood control,
respectively. The regulatory environment has tightened to protect the three listed Central Valley
salmonid stocks – winter and spring Chinook and steelhead. For example, the winter run
biological opinion on operation of the state and federal water projects (NOAA Fisheries 2004 is
the latest version) has increased protection for emigraing smolts by requiring that the Delta Cross
Channel gates be closed from February 1 though the end of May. In recent years the ocean
19
fisheries have been restricted to protect Klamath River fall Chinook and the listed winter and
spring Chinook. Finally, the role of hatcheries is being reexamined in view of increasing
evidence that production salmon hatcheries may have had significant adverse effects on naturally
spawning salmonid populations. One of the objects of this review is to provide information that
can be used by managers when considering possible changes in operation of the Nimbus
Hatchery under new baseline conditions.
The Nimbus Fish Hatchery and its operations
Construction of the Nimbus Hatchery was accepted as complete on October 17,
1955, with a total construction cost slightly in excess of $1 million. Upon completion of
the Hatchery a contract was drawn up between the United States and the State of
California that identified the following main responsibilities:
-
The State will accept responsibility for the installation’s operation and
maintenance.
-
The United States will transfer to the State at the beginning of each fiscal year the
sum of money estimated to be necessary to operate, maintain and repair the
installation. The contract will be for a period of five fiscal years, or until such
time as the runs of salmon and steelhead spawning naturally in the American
River equal the average rate which prevailed in American River during the period
1944 to 1954.
The annual contract has remained in place ever since.
Following are brief descriptions of the major features of the Nimbus Hatchery
installation: An overall site map is found in Figure 4
Fish rack and weir: The fish rack is 306 feet long, with 10 concrete supporting
piers permanently embedded in the river bed. Nine rack support frames are placed on
these piers. Twenty pipe rack frames, holding the galvanized pipe pickets, are then
placed on the rack support frames. A steel wire fabric mat seven feet wide is then placed
6-12 inches below the surface of the river bed. This fabric may not be placed every year.
The pickets are then driven through the mat into the bed to restrict salmon and steelhead
from digging under the rack.
20
An electric hoist is provided to place and remove the racks and rack support frame
each year.
The rack and weir system can be adversely affected by high flows and during
many years extensive maintenance is required before annual fall installation. Even with
this maintenance, many adult salmon are able to get above the weir and are likely lost to
the system. (See section on salmon entering the Hatchery for estimates of the number of
fish that get past the weir.)
Fish ladder: The fish ladder is 502 feet long and contains 30 pools with each pool
being 9’Wx16’Lx5’D. Salmon blocked by the weir enter the Hatchery and use the fish
ladder to ascend the approximately ten feet elevation difference between the river bed
and the holding ponds.
Water supply: Water for the Hatchery is obtained directly from Nimbus
Reservoir. A 40-inch pipe conveys the water from the south abutment of Nimbus
Dam to a terminal control structure. The line is capable of carrying 60 cubic feet per
second (cfs); however the water requirement for existing operations is 30 cfs.
To minimize the effects of water level fluctuations on flow in the supply line,
DFG installed an electronically operated gate at the terminal control structure. A
series of manually operated valves controls flow from the terminal structure to pipes
leading to the ponds, Hatchery building, and the Hatchery’s domestic water supply.
Discharge of water from the Hatchery: The effluent from the Hatchery raceways
goes to two settling ponds before it enters the American River by seepage or direct
discharge, either through the fish ladder or downstream of the ladder. DFG has a
National Pollutant Discharge Elimination System (NPDES) permit from the Regional
Water Quality Control Board and permit conditions require compliance with water
quality standards in the effluent and in the river.
Hatchery building: The Hatchery building is 100 x 80 feet. Originally the
building was designed to accommodate hatching in trays suspended in channels. In
recent years Hatchery staff has gone to the use of Hatchery jars to improve survival
from fertilization to the eyed egg stage.
21
Office and shop building: This 40 x 40 building contains the office, employee
break room, and public restrooms.
Food processing and storage building: This 100 x 40 foot building houses the
machinery and cold storage system for processing and storing fish food. This area is
also used to store heads removed from spawned Chinook salmon that had clipped
adipose fins. The heads are periodically collected by DFG staff in Santa Rosa to
extract and decode the tags contained in the jaws of these fish. Finally, the
processing building contains the pumps, pressure tank and chlorine injector for the
facility’s domestic water supply system.
Mitigation responsibility
The initial estimate of the Nimbus Hatchery’s mitigation responsibility was
derived from escapement surveys that began in 1944. The pre-Nimbus Dam data (no
data in 1947 and 1950) indicated that the average run size was 25,948 adult fall Chinook.
(By this time the spring run had been virtually extirpated from the American River
system by non-CVP related causes and thus there was no mitigation responsibility for this
run.) The biologists estimated that 72.5 percent of the run spawned above the site of the
soon to be constructed Nimbus Dam (Table 2). Average sex composition was 38.8
percent females and 62.2 percent males, thus an estimated 7,019 females would have
spawned above the dam site. Using the average fecundity of fall Chinook of 6,500
eggs/female (derived from data collected from females from other streams in the Central
Valley and at the Coleman Hatchery – no fecundity data were available from the
American River), the biologists estimated that the approximately 7,000 females would
have deposited approximately 46 million eggs annually during the period 1944-1952
(range of about 20 million to 77 million).
Table 2. Estimated numbers and geographic distribution of Chinook salmon runs to the
lower American River for the period 1944-1952. (Data from USFWS and DFG 1953)
Year
Estimated
Estimated
Percent of
Estimated
total run
run above
run above
run below
Nimbus
Nimbus
Nimbus
Percent
22
1944
30,552
23,762
77.7
6,830
22.3
1945
38,656
24,815
64.2
13,841
35.8
1946
38,388
30,684
79.7
7,704
20.3
1948
15,000
12,060
80.4
2,940
19.6
1949
12,000
8,028
66.9
3,972
31.1
1951
22,000
13,684
62.2
8,326
37.2
1952
25,000
19,050
76.2
5,950
23.8
Average
25,948
18,689
72.6
7,079
27.5
1947*
1950*
*No survey
After considering the escapement, sex ratio and fecundity data, Reclamation, in
cooperation with the USFWS and DFG, designed Nimbus Hatchery to handle 30 million
Chinook salmon eggs with the provision that the egg capacity could be expanded to 50
million if needed.
Although never stated directly in the annual DFG Hatchery reports, it seems that
the Chinook salmon mitigation responsibility for the Nimbus Hatchery is to replace the
approximately 19,000 fall Chinook that would have spawned in the reach of the river
now covered by Lake Natoma.
The 1999 Production Goals and Constraints for the Nimbus Hatchery
(Operational Plan, DFG and Reclamation 1999 and Appendix 1) call for an annual take
of 8 million Chinook salmon eggs and a mitigation release of 4 million Chinook salmon
smolts (at least 60 per pound) in the Carquinez Strait, which is in the San Pablo Bay area.
The remainder of the production may be allocated to an inland Chinook recreational
fishing program or for transfer to the Mokelumne River Hatchery as needed to meet
Mokelumne production goals. Even using low survival rates from release to returning
adults, the production seems to be far in excess of the original mitigation goals.
Although not tied to mitigation goals, the Central Valley Project Improvement
Act’s Anadromous Fish Restoration Program (AFRP) has a goal to double the production
of naturally spawning Chinook salmon and steelhead as compared to the base period of
23
1967 through 1991. For the American River the goal is to have an average production of
160,000 naturally spawning Chinook salmon. This goal was based on historical data and
assumed that one-half the fish were naturally spawning during this period. Based on
historical abundance (pre-Folsom) and the unknown but likely major impacts of the
Hatchery, the goal seems unrealistically high. As I will discuss later, one of the first
things the Hatchery manager and fish biologists need to do is develop a realistic goal for
the numbers of Chinook salmon that spawn naturally in the LAR, including Hatchery fish
that do not enter into the Hatchery. This total is likely to be less than the 160,000 natural
production salmon called for in the AFRP doubling plan.
Hatchery administration, staffing and budget
The Nimbus Hatchery facilities and land is owned by Reclamation. Reclamation
contracts with DFG to operate the Hatchery, with the current operating costs (staff, feed,
supplies, etc.) running around $1 million annually (A. Quinones, DFG, personal
communication).
The Nimbus Hatchery is under the overall supervision of a Senior Hatchery
Supervisor, who reports directly to the Regional Manager, Central Valley Region,
Rancho Cordova (Figure 6). (The Senior Hatchery Supervisor also provides overall
supervision to the Feather River and Mokelumne River anadromous salmonid
hatcheries.) The Nimbus Hatchery manager has a support staff of permanent and
seasonal staff that ranges from 8 to 19 people depending on the time of the year, with the
largest staff from September through June.
24
Director
Wildlife and Inland
Fisheries Division
Region 2
Land and
Facilities
Branch
Fisheries
Programs
Branch
Hatchery
Coordinator
Wild
Trout
Hatchery
Support
Heritage
Trout
Feather River H.
Region 1
Senior Hatchery
Supervisor
American River H.
Nimbus H.
Region 3
Mokelumne River H.
Region 4
Region 5
Figure 6. Nimbus Hatchery within the Department of Fish and Game prior to June 2006.
Organizationally within DFG, there is a hatchery coordinator located in the Land
and Facilities Branch of the Wildlife and Inland Fisheries Division. The Land and
Facilities Branch has a hatchery support person who coordinates stocking. Biological
input to Nimbus Hatchery operations comes from the area biologist located at the
Regional Fish and Game office in Rancho Cordova, adjacent to the Nimbus Hatchery as
well as biologists as appropriate. (Note that has of mid June 2006, the hatcheries are now
provisionally located in the Fisheries Branch. A new organization chart was not available
at the time this paper was released.)
Founder stock
The Nimbus Hatchery Chinook salmon founder stock was from the American
River. In 1955, Coleman Hatchery was the only other hatchery operating in the Central
Valley, thus it is likely that the majority of the salmon entering the Hatchery were from
the local run. Early on Coleman staff experimented with downstream (Delta) releases of
their production fish, which can cause increased straying, thus in all probability some
Battle Creek fall run were part of the founding stock.
25
Shortly after Nimbus Hatchery began operating, DFG managers decided to bring
in late fall green and eyed eggs from Coleman Hatchery in an attempt to establish a run
that spawned in the American River somewhat earlier than the local fall run. (This effort
was based on observations that temperature conditions in the river and Hatchery were
generally sub-optimum during the early fall and pre-spawning losses of fish in the
holding tanks was often severe.) As shown in Table __ (page ___) these efforts
continued for several years. There has not been sufficient evaluation conducted to
determine the effects of these attempts but the genetic information indicates that
American River fall Chinook are most closely aligned with other Central Valley fall
Chinook stocks, not with late fall Chinook (Banks et al. 2000)
Adult salmon entering the Nimbus Hatchery
Numbers: During the period 1955 through 2003, about 480,000 adult Chinook
salmon entered Nimbus Hatchery with the long-term being about 9560 per year. The
annual numbers are shown in Figure 7. During the past decade, the numbers of fish taken
in slightly exceeds the long-term average, or about 9,900 fish. There is no reliable record
of how of the fish were actually spawned or how many died before spawning. DFG
controls the numbers of fish entering the Hatchery based on production goals.
26
Figure . Total number fo Chinook salmon entering the Nimbus Hatchery, 1955-2003.
35000
30000
Numbers of salmon
25000
20000
15000
10000
5000
19
55
19
57
19
59
19
61
19
63
19
65
19
67
19
69
19
71
19
73
19
75
19
77
19
79
19
81
19
83
19
85
19
87
19
89
19
91
19
93
19
95
19
97
19
99
20
01
20
03
0
Years
Percent females: The long-term average percent females in the Hatchery fish was
about 44 percent, with annual distribution in percent females shown in Figure 8. The
data show considerable inter-annual variability with perhaps a decline in the percent
females in recent years. In fact, for the past decade the percent females has averaged
around 36 percent
27
Figure . Percent females entering the Nimbus Hatchery, 1955-2003.
0.7
0.6
Percent femaies
0.5
0.4
0.3
0.2
0.1
19
55
19
57
19
59
19
61
19
63
19
65
19
67
19
69
19
71
19
73
19
75
19
77
19
79
19
81
19
83
19
85
19
87
19
89
19
91
19
93
19
95
19
97
19
99
20
01
20
03
0
Years
Percent grilse - As shown in Figure 9, there is also considerable inter-annual
variability in the percent grilse in the Chinook entering the Hatchery, with the long-term
average of about 18 percent grilse. The average for the past decade has also been about
18 percent grilse, indicating that increasing percentages of grilse, almost all males, are
not responsible for the decline in percent females noted above. Note that grilse are
defined as those fish less than 60 centimeters fork length (23.6 inches) and all the fish
may not be two year olds. It is interesting to note than in some years several female
grilse were observed. Typically, between two and 20 female grilse were taken into the
Hatchery each year and were generally released back to the river.
28
Figure . Percent grilse entering Nimubs Hatchery, 1955-2003.
0.5
0.45
0.4
Percent grilse
0.35
0.3
0.25
0.2
0.15
0.1
0.05
19
55
19
57
19
59
19
61
19
63
19
65
19
67
19
69
19
71
19
73
19
75
19
77
19
79
19
81
19
83
19
85
19
87
19
89
19
91
19
93
19
95
19
97
19
99
20
01
20
03
0
Year
Spawning protocol
Nimbus Hatchery staff uses 1-to-1 mating as specified in the NOAA 1997
protocols. The annual goal is to have the 5.3 million eyed eggs, a goal that allows the
Hatchery to meet its target of releasing 4 million smolts. As needed, excess production is
reduced by removing a certain percentage of eyed eggs per female or spawning group.
Rearing
The young fish are generally moved to the outside raceways starting in February,
with fish at this time averaging 250 to 300 per pound. Ponding is complete in March.
The fish are fed six times per day, with the object of providing enough food to detect
uneaten food on the bottom of the raceways.
Release strategy for mitigation fish
The Nimbus (and other mitigation hatchery) managers generally release
production (mitigation) fish to maximize contribution to the fisheries and to assure that
29
sufficient numbers of adults return to the stream and hatchery to meet mitigation
requirements and hatchery spawning needs. Among the controllable factors in meeting
harvest and escapement goals are age and size at release, transport method, release
location, duration of the release season and manner of release. Variables beyond the
control of the hatchery manager that affect harvest and subsequent escapement include
conditions in stream or in the estuary in which the fish are released, amount of fishing
effort (both commercial and recreational), and conditions in the ocean itself. In reality all
of the environmental conditions vary seasonally, annually and over the long term thus
selecting the best release strategy involves an examination of the data from various
release strategies that have been attempted in the past (an ad hoc adaptive management
process – albeit with limited experimental data in the case of Nimbus Hatchery) and a
willingness to compromise on some objectives to achieve others. For example, off site
releases may increase straying but do increase contribution to the fisheries and to overall
escapement.
The juvenile Chinook salmon release strategy for Nimbus Hatchery specified in
the 1999 Operating Principles is deceptively simple:
4,000,000 smolts will be reared to at least 60 per pound. These fish will be
transported to the Carquinez Strait in the San Pablo Bay area for release in May-June.
Implicit in this strategy is a decision to accept any biological risks and adverse
impacts associated with off-site release (increased straying) in return for more fish in the
fisheries and in returns to the river and to the Hatchery. As is shown below, the decision
to release fish at the smolt stage and exclusively in the Carquinez Strait is relatively
recent.
To provide a historical perspective on how the release strategy has evolved over
time, below I comment on each of the components that a hatchery manager can control
when releasing the mitigation fish, namely: age and size at release, transport method,
duration of release season, release location and method of release. (Note that this only
pertains to release of mitigation fish. As described later, inland releases of nonmitigation fish has been more serendipity. Nimbus Hatchery juvenile Chinook salmon
have not been used extensively for survival research in the Delta, unlike fish from the
30
Feather River Hatchery (Brown et al. 2004) Coleman National Fish Hatchery (Brown and
Kimmerer 2006.)
Size and age at release
Nimbus Hatchery managers have tried releasing the mitigation fish at various
sizes during the Hatchery’s existence, Figure 10, plates A, B, C. Note in this figure I
break down the sizes into groups: fry and fingerlings, smolts and yearlings. The break
between fry and fingerlings and smolts occurs arbitrarily at 100 fish per pound and does
not actually pertain to the physiological state of smolting. The release data in the annual
reports are not always easy to interpret and compile and I think the overall picture in
Figure 10 is adequate for purposes of this report. (Note that in recent years the at-least60 per pound criterion and a sea water challenge for fish to be released help assure that
the fish are indeed smolting and ready to emigrate. There are other tests that could be
used to confirm the animals’ physiological state.) During the early years of Hatchery
operation, there were a few occasions when eyed eggs were buried in the American
River. For example, about 5.5 million eggs were buried in 1960 in the river above the
rack. Subsequent hatching was confirmed but there is no information to assess their
subsequent contribution to the fisheries or to escapement.
31
Plate A - fry and fingerling releases from Nimbus Hatchery, 1955-3003.
30,000,000
25,000,000
numbers of fish
20,000,000
15,000,000
Series1
10,000,000
5,000,000
19
55
19
57
19
59
19
61
19
63
19
65
19
67
19
69
19
71
19
73
19
75
19
77
19
79
19
81
19
83
19
85
19
87
19
89
19
91
19
93
19
95
19
97
0
year
7,000,000
6,000,000
5,000,000
4,000,000
3,000,000
2,000,000
1,000,000
0
19
67
19
70
19
73
19
76
19
79
19
82
19
85
19
88
19
91
19
94
19
97
20
00
20
03
number of fish
Plate B - smolt releases from the Nimbus
Hatchery
year
32
Plate C - Yearling releases from Nimbus Hatchery, 1955-2003
500,000
450,000
400,000
number of fish
350,000
300,000
250,000
Series1
200,000
150,000
100,000
50,000
19
55
19
56
19
57
19
58
19
59
19
60
19
61
19
62
19
63
19
64
19
65
19
66
19
67
19
68
19
69
19
70
19
71
19
72
19
73
19
74
19
75
19
76
19
77
19
78
19
79
0
year
Fry and fingerlings: Releases of this size fish, which occurred from as early as
January could be from swim up fry to fingerlings. Releases early in the brood year were
often made to reduce the Hatchery population to its rearing capability. Although there
was some tagging (fin clip combinations), it does not appear there was much analysis of
the contribution of these small fish to the subsequent spawning population. Fry and
fingerling releases were discontinued after the 1987 brood year.
Smolts: As mentioned above, the smolt data in Figure 10 are for fish that are 100
fish per pound or larger, many of which may not be actual smolts. Release of this size
fish began in 1967 and on average, about 3.3 million juvenile Chinook salmon in this size
range have been released each year since. Beginning in the mid-90s, most of these fish
have been in 50 to 60 fish per pound range and averaged about 4 million per year. After
1997 all production releases were in this size range and averaged near the 4 million/year
goal.
Yearlings: Averages of about 170,000 yearling Chinook salmon were released
each year from the Nimbus Hatchery from the 1955 to 1979 brood years. The yearling
program was discontinued in 1979 due to the high cost of holding (and feeding) fish over
33
the summer, as well as disease and other problems associated with rearing Chinook
salmon during the hot season.
Transport method
The fish have always been moved to the release sites by tanker truck. However,
for several years DFG has used specially designed large tanker trucks to minimize stress
and reduce the length of time between the first and last releases of the season. The
Nimbus Hatchery has two tanker trucks to haul the fish, one with a capacity of 2,800
gallons and the other 1,200 gallons. Water in the larger truck is oxygenated and this is
the primary transport vehicle. (The smaller truck may still be used on occasion.) The
large truck will handle approximately 2,800 pounds of fish per trip, or about 168,000
smolts at 60 fish per pound. Due to personnel safety and cost concerns, all transport and
release occurs during the daylight hours.
Seasonal duration of the release
In the early years of Nimbus Hatchery, fish from a single brood year were
released from January through October and at various life stages. With the current
program, all releases occur in May and June and at one life stage. Operationally this
release strategy makes sense, however there has been no quantitative analysis to
determine if releasing all fish as smolts reduces straying and increases survival.
Release location
If there is one clear trend in operation of the Nimbus Hatchery, it is the westward
migration of the release location. During the first years, production fish were often
released in the American River just below the Hatchery. Other release sites in the
American River were also used, as far down as Discovery Park. Then large numbers of
fish were released at Miller Park (on the Sacramento River in Sacramento, and in central
Delta locations such as Clarksburg and Rio Vista. After that releases were made in
Pittsburg and Benicia, locations below the Delta. The strategy now calls for releases to
be in the western end of Carquinez Strait, typically at the California Maritime Academy.
34
Moving the release site downstream is intended to reduce losses of fish in the Delta due
to operation of the State and Federal water projects.
The further downstream the release site, the more the fish are likely to stray when
returning to spawn. This hypothesis needs to be tested for Central Valley hatcheries that
do off-site releases of mitigation or enhancement production (that is FRH, NFH and
Mokelumne River Hatchery); however current marking and escapement and tag recovery
efforts are not adequate to provide data robust enough to test the straying hypothesis.
Brown et al. (2004) did not show significant straying of Bay released fish compared to inriver releases but the data base was relatively small.)
Release Method
Most of the releases have been made by driving a truck near the edge of the water
and releasing the fish down a chute into the water. Hatchery staff often noted that avian
and fish predators seemed to have a field day on the released fish. In an effort to reduce
the losses of Hatchery fish to predators, in 1994 DFG began using a net pen for Feather
River and Nimbus Hatchery releases. Under this procedure, the Hatchery truck driver
transfers the young salmon to a floating pen and then the pen is towed to near midchannel where the fish are released.
The Fishery Foundation conducted a three year study using FRH fish to assess the
benefits of the net pen release program. In this study, groups of coded wire tagged fish
were released directly from the transport truck or from the net pens. Recovery of the tags
in the ocean fisheries and the spawning surveys would then be used to determine if the
net pen released fish survived at a higher rate (as shown by recoveries of the tagged fish
in the fisheries and in the streams) than those released from the truck. The overall result
is that net pen released salmon were caught in the ocean at a rate of roughly 2.5 times
(range of 2.4 to 2.6) that of fish released directly from the trucks to the estuary (Table 3)
This effect was confirmed in freshwater where the ratio of recoveries was also 2.5.
Interestingly, more than 95 percent of the fish escaping the fisheries returned to the
Feather River or the Feather River Hatchery, with a few straying to the Nimbus and
Mokelumne River facilities
35
Table 3. Comparison of recoveries of tagged FRH juvenile Chinook salmon released from net
pens and transport trucks, 1994-1996. (From Brown et al., 2004)
Ocean Recoveries*
Numbers Released
Release Year1
Control
Experimental
Control
Experimental
1994
149,554
149,002
1057
2565
1995
139,443
147,816
716
1878
1996
149,440
150,089
1077
2595
*Recoveries through year 4 of the cohorts in ocean fisheries off CA, OR and WA.
The net pens were used through the 1990s; however this release method had to be
discontinued due to the deteriorating condition of both the floating pens and the boat
towing the nets to mid channel. If this release strategy is used again, I recommend the
original net pen evaluation study be repeated with Nimbus and/or Feather River fish.
Fecundity
When the Nimbus Hatchery was built, the designers assumed that the females
entering the Hatchery would have an average fecundity of 6,500 eggs per female. During
the spawning season, Hatchery personnel estimate fecundity by dividing the total egg
take (which is estimated from periodic counts of a known volume of eggs) divided by the
total numbers of females spawned. (It would be more informative to have actual egg
counts from a sub-sample of the females being spawned and Nimbus Hatchery staff is
beginning to collect this kind of data. Terry West, DFG, personal communication.)
Although average fecundity typically has been in the range of 5,000 to 6,000 eggs
per female (long-term average of 5,257 eggs per female) there were several instances of
much lower values. Only in one year did the values approach the assumed 6,500 eggs per
female.
1Adapted from DFG memo to Randall Brown dated 2/14/00.
36
Figure ___. Estimated average fecundity of female Chinook salmon
spawned at the Nimbus Hatchery - 1955-2003.
6,000
5,000
4,000
3,000
2,000
1,000
0
19
55
19
58
19
61
19
64
19
67
19
70
19
73
19
76
19
79
19
82
19
85
19
88
19
91
19
94
19
97
20
00
20
03
average number of eggs/female
7,000
year
From the data in Figure 11 it appears there may have been a decrease in average
fecundity during the almost 50 years of Hatchery operations. In Figure 12 the average
fecudity per decade has been plotted to show this trend more clearly, and the declining
trend is more apparent. The trend may be due to adults returning a a younger age,
although the information to support his hypothesis is not available. In addition, the
average fecundity data are themselves somewhat suspect in that they do not include
counts from a quantitatve sampling of the females spawned in the Hatchery.
37
Average number
of eggs per
female
Figure ___ Trends in Chinook
fecundity at Nimbus Hatchery,
1955-2003
8000
6000
4000
2000
0
0
2
4
6
Decade, 1955- 2003
Disease – problems and treatment
As described in Brown et al. (2004) there is a wide variety of viral and bacterial
diseases and parasites that can affect production in Central Valley salmonid hatcheries.
For those interested in a comprehensive treatment of the subject, Winton (2001) provides
an excellent reference source on fish health and disease.
Growing large numbers of fish in confined conditions can exacerbate disease
problems. Although many disease and parasite problems can be prevented, or controlled
by chemical and other treatments, the availability of treatment has become more limited
in recent years as concerns about the effects of the prophylactic agents on human health,
or the health of other animals have been raised ( Winton 2001). There are also concerns
that hatchery diseases may be transmitted to wild fish when the fish are released or if the
hatchery effluent reaches natural water bodies (Foott et al. 2006). Finally there are
concerns that the hatchery influent may contain disease vectors, thus hatchery intakes
often have filtration or disinfection systems such as the ozone system recently installed at
the Coleman National Fish Hatchery.
There is relatively little published information about disease problems at the
Nimbus Hatchery. The early annual Hatchery reports documented some of the vectors
causing problems, along with there control methods. DFG has a fish health laboratory
located near the Hatchery and routinely samples the fish for disease problems, most often
when the Hatchery manager reports unusual numbers of sick and dying fish. The fish
38
pathologists also work with the Hatchery manager to develop operational or chemical
control procedures.
As mentioned in the annual reports, diseases and parasites encountered at the
Nimbus Hatchery include:
Viral diseases – Sacramento River Chinook Disease, now called Infectious
Hematopoietic Necrosis Virus (IHNV).
Bacterial diseases
- Cytophaga columnaris
- Gill disease – Flavobacterium
- Fin rot
- Peduncle disease
- Furunculosis - Aeromonas
- PKD (proliferative kidney disease)
Parasites
- Gyrodactylus elegans
- Tricodina
- Ichthyophthirius multifilis
- Chilodon
- Hexamitus
- Epistylus
- Costia
For the most part, disease and parasite control at the Nimbus Hatchery seemed to
handle the problem effectively and efficiently. Generally, losses to disease did not seem
to be a significant impediment to meeting Chinook salmon production goals. (In reading
through the annual reports it did appear that steelhead suffered more disease problems.
This may in part be due to holding steelhead over summer.)
IHNV problems for juvenile Chinook salmon were the exception to the general
rule of no major untreatable disease concerns at Nimbus Hatchery. (IHNV is not a
concern for adult Chinook salmon.) IHNV is present throughout the Central Valley
(Foott et al., 2006) and has caused significant losses of Chinook salmon at the Coleman
National Fish Hatchery and the FRH. Although IHVV was likely present during the
early years of Nimbus Hatchery operations, it did not reach virulent conditions until the
1963 brood year when an estimated 70 percent of the Chinook production was lost due to
this untreatable viral disease. (The vector may be present and the fish are infected but do
not show symptoms of the disease. Stresses and other conditions may lead the juvenile
39
salmon to show symptoms and, in severe outbreaks, die.) Subsequent reported losses due
to IHNV by brood year were:











1964 – 25 percent
1965 – 17 percent
1967 – 1971 – no IHNV-related losses reported
1972 – 7.5 percent
1973 – 90 percent
1974 – 60 percent
1975 – 34 percent
1976 – 5 percent
1977-1982 – no IHNV-related losses reported
1982 – 15 percent
1983 – 2003 – no IHNV-related losses reported
Beginning in the early 1980s, IHNV control was obtained in Nimbus Hatchery by
treating all Chinook salmon and steelhead eggs with a weak iodine solution. Although
there is some concern that releasing juvenile fish infected with the IHNV could have
affected the progeny of naturally spawning salmon, Foott et al. (2006) have shown that
the chances of such lateral transmission are quite low.
Eliminating the yearling release program in 1980 also reduced Chinook salmon
disease problems at Nimbus Hatchery, in particular PKD.
Disposal of salmon carcasses
The 1999 Nimbus Hatchery operating protocol stipulates that edible carcasses will
be donated to non-profit organizations, with the Hatchery manager having the authority
to determine the allocation. Carcasses not deemed of sufficient quality to be used for
food were mostly rendered at a local plant. Until the 2001 spawning season, the
Hatchery manager dealt with the local non-profits with regard to allocation and to picking
up the carcasses. In 2001 the State contacted with the American Canadian Fisheries
Company in Washington State to process (fillet and freeze) the useable carcasses. The
frozen fillets are then sent to the California Emergency Foodlink in Sacramento for
distribution to nonprofits. This change not only resulted in a better product, but
alleviated Hatchery staff of the burden of coordinating the donation process.
The annual distribution of edible carcasses is shown in Figure 13. Over the past
50 years more than 2.8 million pounds of Chinook salmon were distributed to
Sacramento area non-profits, with an annual average of about 69,000 pounds. Note that
40
during much of this period this was carcass weight, head off and gutted. The recent
numbers are for filets. Although no economic value has been placed on these donations, it
would be significant.
Also note that no carcasses from the Hatchery are returned to the American River.
The Hatchery take is generally a relatively small proportion of the total Chinook salmon
run to the LAR and I assume (although I have seen no analyses on the subject) that
stream biologists believe that the number of fish that spawn and die in the American
River provides a sufficient nutrient contribution to maintain riverine productivity.
Figure . Number of pounds of edible salmon carasses distribured
to charitable organizations by Nimbus Hatchery staff.
160,000
140,000
120,000
100,000
80,000
60,000
40,000
20,000
0
19
63
19
65
19
67
19
69
19
71
19
73
19
75
19
77
19
79
19
81
19
83
19
85
19
87
19
89
19
91
19
93
19
95
19
97
19
99
20
01
Number of pounds of edible
Chinook salmon distributed
180,000
year
41
Visitors
Each year since it opened, Nimbus Hatchery staff has estimated the numbers of
people that have entered the Hatchery grounds to view salmon and steelhead ascend the
ladder, adult fish in the holding ponds, and juvenile salmon and steelhead growing in the
raceways. The estimated total number of visitors for the period of record exceeds 15
million. As shown in Figure 14, the number of visitors has increased considerably over
the past 50 years and for the past few years the number has consistently exceeded one
million visitors annually.
Figure ___. Estimated number of visitors to Nimbus Hatchery, 19552003
1,400,000
1,000,000
800,000
600,000
400,000
200,000
0
19
55
19
58
19
61
19
64
19
67
19
70
19
73
19
76
19
79
19
82
19
85
19
88
19
91
19
94
19
97
20
00
20
03
Number of visitors
1,200,000
year
42
By decade, or partial decade, the upwards trend is (numbers are rounded to nearest
thousand) is even more apparent:
Decade
1955-59
1960-69
1970-79
1980-89
1990-99
2000-03
Average annual number of visitors
70,000
65,000
140,000
343,000
595,000
1,000,000
The increased visitation is probably due to many factors but the increasing
urbanization of the area surrounding the Hatchery combined with the Hatchery’s location
in the American River Parkway and the chance for members of the public to see large
numbers of large fish up close may be the driving factors. DFG has made every attempt
to accommodate the visitors but after the first decade or so had to limit the numbers of
guided tours due to limitations of available personnel time. Since then Hatchery staff has
added extensive signage to make self-guided tours more informative.
Probably the most significant change in making the Hatchery more visitor
friendly, at least in a focused way, has been the American River Salmon Festival. The
Festival started in 1997 and annually attracts thousands of visitors to partake in a variety
of activities, ranging from educational exhibits to rafting – with everything centered on
Chinook salmon and the LAR. The 2005 Festival was held on October 8 and 9. DFG
calculates that approximately 75 percent of the estimated 20,000 people in attendance
were from the local area. Over 100 organizations and hundreds of volunteers help
organize and staff the festival.
The Nimbus Hatchery has provided the Sacramento metropolitan area with a
major environmental attraction. Visitation occurs year round, although it peaks during the
late fall when adult Chinook salmon are entering the Hatchery.
Transfer of genetic material to and from Nimbus Hatchery
Early on during Nimbus Hatchery operations, extensive amounts of genetic
material were transferred to and from the Hatchery. These transfers generally took the
form of green or eyed eggs but sometimes fry and fingerlings were transferred. The
43
objectives of these transfers were varied but generally involved attempts of change run
timing (e.g. bringing Coleman late fall Chinook to have a later run to the American – a
run that would be better able to handle American River fall water temperatures) or to help
other hatcheries when they did not meet their egg take goals or had serious fish losses
during incubation and or rearing.
The transfers of Chinook salmon genetic material in and out of Nimbus Hatchery
are shown in Tables 4 and 5. The data show that transfers of genetic material to Nimbus
Hatchery stopped in 1987 but transfers of eggs continued infrequently until the 1990s.
With the new hatchery protocols, there are essentially no more transfers. The effects of
large inter-basin transfers are unknown but have likely contributed to the low genetic
diversity observed by Banks et al (2000) and Williamson and May (2005) observed for
Central Valley fall Chinook.
Table 4. Genetic material transferred to Nimbus Hatchery from other Central Valley
hatcheries, 1955 through 2004 brood years
Brood year Life stage Run Number
Source
1957
Eggs
LF 1,014,000 CNFH
1958
Eggs
LF 1,482,000 CNFH
1959
Eggs
LF 1,118,000 CNFH
1982
Eggs
F*
2,559,000 FRH
1983
Eggs
F*
1,424,000 FRH**
1987
Eyed eggs F*
3,612,000 FRH
*Nominally fall but could contain FR springs
** All progeny planted in Central Valley streams including Bear River, CacheCreek,
Calaveras River, Cosumnes River, Mokelumne River and Putah Creek.
44
Table 5. Chinook salmon genetic material transferred from Nimbus Hatchery to other
Central Valley hatcheries, 1955 through 2004 brood years.
Brood year Life stage
1964
Eggs
Eyed eggs
1965
Eggs
1970
Adults
Eyed eggs
1971
Eyed eggs
Eyed eggs
1972
Eyed eggs
Eyed eggs
1973
Eggs
Eggs
1974
Eyed eggs
Eyed eggs
1975
Eyed eggs
Eyed eggs
1976
Eyed eggs
Eyed eggs
1977
Eyed eggs
Eyed eggs
1978
Eyed eggs
Eyed eggs
1985
Fingerlings
1996
Eyed eggs
Numbers
6,137,000
4,451,000
1,086,000
1126
2,334,000
10,433,000
2,108,000
2,499,000
5,320,000
6,557,000
172,000
3,419,000
102,000
8,247,000
104,000
2,427,000
501,000
1,111,000
200,000
4,010,000
1,655,000
126,000
504,000
To
CNFH
CNFH
CNFH
FRH
FRH
CNFH
FRH
CNFH
FRH
CNFH
MRFI
CNFH
MRFI
CNFH
MRFI
CNFH
MRFI
CNFH
MRFI
CNFH
MRFI
MRFI
MRFI
Chinook salmon run to the lower American River
The number of Chinook salmon entering the LAR to spawn is of interest to
resource managers and to the general public. This metric is often used to judge how well
we are doing in providing the amount and quality of habitat needed to maintain the run
and to meet AFRP doubling goals. Although the number of adult salmon is of prime
importance as an indicator, or performance measure in today’s parlance, the available
datas are difficult to assess and use.
The problems occur mainly because the quality of the estimates themselves is
variable and not well defined. Over the years different techniques have been used to
estimate escapement on the LAR, almost all of which are based on mark-recapture
studies. In addition, the size of the field crew used in the escapement surveys has varied
45
considerably from year to year – and crew size can affect the estimates (B.Cavallo,
DWR, personal communication). The overall result has been estimates that have wide,
but undefined (and unreported) error bars.
To use the number of escapees as a performance measure, one needs to know how
many of them are of direct hatchery origin that is they are returnees from hatchery
releases. There have not been enough tags applied and recovered to make reliable
estimates of the Hatchery contribution to harvest or to escapement, and to straying to
other Central Valley streams. Since there are four other Central Valley hatcheries
producing fall Chinook, and some of their releases may stray to the LAR, it is important
to know the source of all hatchery fish in the LAR.
Ocean conditions, including the recreational and commercial fisheries, affects
escapement but these effects can not be estimated with the available data.
In spite of the problems with using escapement as an indicator of how well we are
doing with regard to American River fall Chinook, the numbers are of interest. We do
have some data from the 2000 and 2001 brood years that provide useful qualitative
information about the runs and their fate. The discussion of run size is divided into the
following sections:

the historic run

factors that may be affecting escapement trends in LAR escapement

composition of the run to the LAR– natural and hatchery

fate of NFH fish – straying and harvest
Historic run: The historic run escapement estimates are available for all but two
years since 1944 (Figure 15). Although there has been considerable variation in the
estimates, three time related features seem to stand out – at least qualitatively.
1. A fairly stable population of from 25,000 to 60,000 fish between the 1960s and
1987.
2. A consistent decline in numbers from 1987 through 1992.
3. A remarkable increase in numbers from 1993 through 2004.
46
Figure ___. Estimated annual Chinook salmon run to the LAR,
including the hatchery component, 1944-2004
Estimated number of Chinook
salmon
200,000
180,000
160,000
140,000
120,000
100,000
80,000
60,000
40,000
20,000
19
44
19
47
19
50
19
53
19
56
10
59
19
62
19
65
19
68
19
71
19
74
19
77
19
80
19
83
19
86
19
89
19
92
19
95
19
98
20
01
20
04
0
year
Looking at the data in terms of decadal averages (Figure 16), one sees a slightly
different picture than shown by the year to year numbers. On average, escapement was
relatively stable at around 40,000 fish for four decades – from the 60s through the 90s –
and the averages during this period were about double those from the 40s and 50s. Since
the Hatchery came on line in 1955 and it took a few years to work out the kinks in
Hatchery operation, this doubling may be attributed to Hatchery operation. If this
assumption were true (and it is not possible to confirm it), it would seem that the
Hatchery had more than met its about 20,000 fish mitigation goal.
47
Figure ___. Estimated total Chinook salmon escapement to the LAR, by decade, 1944-2004
160,000
Estimated numbers of Chinook salmon
140,000
120,000
100,000
80,000
60,000
40,000
20,000
0
40
50
60
70
80
90
20
Decade
Factors That May Be Affecting Run Size
Environmental Conditions
The relatively steep decline from 1978 to 1992 may have been at least in part due
to an extended drought that affected environmental conditions in the Central Valley
and perhaps in the adjacent ocean. The recent large returns may be due to good
ocean conditions and most Sacramento Valley runs have done relatively well during
this period. For example, the 2005 winter run escapement of more than 15,000
adults was the largest for the past two decades. (NOAA Fisheries 2006.)
The Sacramento Valley fall run escapement goal is from 122,000 to 180,000
spawners and (as cited in Williams, in press) was not met for three consecutive years
(1990-1992) and triggered a review of potential factors by a subcommittee of the
Pacific Fisheries Management Council.
Ocean Harvest
As shown in Figure 17 there has been a significant decrease in the ocean harvest
index. The index is total ocean catch in the recreational and commercial fisheries
divided by the catch plus escapement. (Inland harvest is not included in this
calculation.) The declining percentage harvested is likely a combination of more fish
48
available to be harvested and harvest restrictions promulgated to protect weak stocks
such as listed species and Klamath River fall Chinook. These restrictions will be in
place till the stocks recover or meet escapement targets such as on the Klamath River.
The decrease in harvest index is also in least part due to decreased effort in the
commercial and recreational fleets (Figures 18 and 19 respectively.)
Central Valley Chinook Salmon Harvest Index
100
Harvest Index (%)
75
50
25
0
1970
1990
1980
2000
Year
Figure 17. Trend in Central Valley Salmon Harvest Index, 1970-2003. (Data from
PMFC, 2004.)
49
Vessels Landing Salmon
6000
Vessels Landing Salmon
5000
4000
3000
2000
1000
0
1960
1965
1970
1975
1980
1985
1990
1995
2000
2005
Year
Figure 18. Number of commercial trollers registered in California, 1960-2003.
(Adapted from data in PSMFC 2004)
50
Total Number of California Charter Boats Participating in the
Ocan Recreational Salmon Fishery
200
180
Number of Boats
160
140
120
100
80
60
40
20
19
87
19
88
19
89
19
90
19
91
19
92
19
93
19
94
19
95
19
96
19
97
19
98
19
99
20
00
20
01
20
02
20
03
0
Year
Figure 19. Total number of California charter boats participating in the ocean
recreational salmon fishery – 1987-2003. (Data from PMFC 2004)
Improved Hatchery Operations
New Hatchery procedures may have enhanced survival of planted fish. During
the 1990s Nimbus used the net pen release system to increase survival and settled on a
release size of 60 fish to the pound, basically smolts. A Fishery Foundation evaluation of
the net pen release system indicated that it resulted in a two to three fold increase in the
numbers of fish caught and returning to the river as compared to the previously used
direct release system. Planting all production in San Pablo as smolts may have helped as
well. Figure 20, historic runs to Battle Creek (mostly Coleman fish) shows dramatic
increases in run size during the same period. Coleman fall Chinook production has
always been released on site and operations have not changed appreciably in recent years
indicating that this may not be the primary factor behind the increased returns.
Freshwater Harvest
With the exception of a couple years in the 1990s, freshwater harvest is largely
unknown. Estimated harvest rates were on the order of 20-25 percent (DFG 2000).
Given the easy access to the LAR and large runs, it is unlikely that inland harvest rates
have decreased thus are not the cause of the increased escapement.
51
Improved Delta Conditions
Improved Delta conditions due to increased regulatory attempts to improve survival of
emigrating juvenile Chinook salmon, such as mandatory closures of the Delta Cross
Channel gates during the February through May period, may have enhanced survival.
Composition of Chinook Salmon to the American River
The basic question to be answered is what fraction of the adult salmon in the
annual spawning runs comes from the Nimbus Hatchery? Another question is how many
of the fish are strays from other hatcheries? The 2000 and 2001 tagging at the Nimbus
Hatchery, along with tagging from other Central Valley hatcheries, provides some
information that addresses these questions. The limited data and lack of a statistically
robust sampling program to recover the tags and estimate escapement makes any
conclusions very preliminary.
The information in Table 6 shows the expanded numbers and origin of tagged fish
recovered in the lower American River and Nimbus Hatchery in 2003 and 2004. The
information in the table needs some explanation to make its contribution apparent and to
emphasize the limitations of the data. Two important points to consider include:
1. The numbers of tag recoveries have been expanded for sampling effort. In the
Hatchery, it is assumed that all tags are collected and read. In the streams the raw
tag recoveries are expanded to account for the fact that all fish are not examined
for tags. The expansion factors vary by stream and by year and are found in the
PSMFC mark recovery data base.
2. The expansions do not account for the fact that not all fish from the originating
hatchery are tagged. For the Feather River, the expansion for percentage of fish
tagged will vary by year and by race. For example, in some years production fall
run that are planted in San Pablo Bay may have been tagged at a rate approaching
10 percent. For some of the fish, for example Coleman late falls; all the fish are
tagged for experimental purpose thus the expansion factor is one. The Merced
fish are also from experimental releases and are all tagged.
52
3. The age composition of the tagged fish must be considered since they may return
as 2, 3 or 4 year olds and you must look at the individual brood years in order to
calculate the expansion factors.
Tag origin by hatchery
2003
2004
CNFH
265
247
Feather River Hatchery
1506
160
Merced Fish Hatchery
351
305
Mokelumne Fish Hatchery
409
963
Nimbus Fish Hatchery
7149
3008
Table 6. Expanded numbers and origin of coded wire tags recovered in the lower
American River and Nimbus Hatchery in 2003 and 2004.
In spite of the caveats, the tag return data do provide some interesting insight into
the composition of Chinook salmon in the lower American River.
First, there are several sources for salmon in the spawning escapement and in
those fish entering Nimbus Hatchery. The mixing of runs from different streams is one
of the explanations of the lack of genetic diversity in Central Valley fall Chinook noted
by Banks et al.(2000) and Williamson and May (2005).
Although it can not be determined from the data in Table 6, the release locations
show the potential impacts of some of our hatchery and fish management practices: For
example:

All the CNFH are late falls from experimental releases in the Delta. All
production late falls are tagged and released on site and do not show up in
the American River. The late falls do not enter into the hatchery
propagation program (adipose fin clipped fish are not usually spawned)
but may be spawning in the American River.

The Merced fish are also part of experimental releases, probably mostly
for the Vernalis Adaptive Management Program studies with the releases
occurring in the lower San Joaquin River or in the Delta,
53

Most of the Mokelumne and Feather River fish come from Delta or San
Pablo Bay releases.
There appears to be considerable inter-annual variation, although one would have
to look at tag releases to make sure this is not an artifact of the tagging program.
These data along with information on the number of tags released, the total
number of fish, and the age composition of the fish themselves can be used to estimate
the fraction of the run that is a first generation hatchery fish. For 2003, preliminary
estimates were that first generation Nimbus Hatchery fish were about 50 percent of the
salmon spawning in the river and 70 percent of the fish that were spawned in the
hatchery. These percentages only apply to the 2 and 3 year old components of the run.
Similar estimates were not made for 2004, but the percentages would likely be lower.
These estimates are within the ranges reported earlier by Dettman and Kelley
(1987) of 87 percent hatchery fish for the period 1978 through 1984 and Cramer who
estimated that 29 percent during the period 1953 through 1987. In realty, the percent
hatchery fish in the runs probably varies from year to year and we don’t have a good
handle on the composition and its variation. As is discussed later, we need more tagged
fish and better tag recovery and escapement estimates to get this information. We can
make more sense of the data from 2000 and 2001 tagging efforts at Nimbus and three
other Central Valley hatcheries by using a cohort analysis to bring all the data together.
This is also discussed later.
Straying of Nimbus Hatchery Fish
All Chinook salmon stray when returning to spawn (Quinn 2005), however the
natural straying rate is accepted to be nominally low, generally on the order of a few
percent (see for example Quinn and Fresh 1984). In reality, as discussed by Healey 1991,
straying rates are complex and may depend on several factors including life history type
(ocean types may stray less than stream types) and early life history conditions. Hatchery
fish may stray more than wild salmon, and off station releases may increase straying. In
the Central Valley there are relatively few data on straying and no reliable data on
straying rates. This information gap is due mainly to the low numbers of coded wire tags
(or other marks) applied to hatchery fish and the lack of a statistically robust tag recovery
and escapement monitoring program in freshwater.
54
For the Nimbus Hatchery, we can obtain an idea of the straying of production fish
by looking at where the tagged fish appear when they return to freshwater to spawn.
(Note that we do not have data on straying of naturally spawning fish thus can not
compare hatchery versus natural straying.)
Table 8 shows the number of Nimbus
Hatchery tags recovered in the fall of 2003 at several Central Valley streams and
hatcheries. (Hatchery and stream recoveries have been combined for such streams as the
Feather and Mokelumne rivers and CNFH and Battle Creek.)
Tag recovery location - Yuba River
Tag Source CNFH
Raw number of tag recovered
1
FRH
47
Merced
1
Mokelumne
2
Nimbus
2
Tag recovery location - Feather R and FRH
Tag Source CNFH
FRH
5
1521
Merced
70
Mokelumne
7
Nimbus
2
Tag recovery location – Nimbus and LAR
Tag Source CNFH
90
FRH
161
Merced
52
Mokelumne
236
Nimbus
1131
Tag recovery location – Mok R. and
hatchery
Tag Source CNFH
FRH
32
43
55
Merced
44
Mokelumne
907
Nimbus
66
Tag recovery location – Butte Creek
Tag source FRH
35
Merced
15
Mokelumne
9
Nimbus
2
Table 8 Coded wire tag recoveries in Central Valley streams and hatcheries in 2003.
Note that only those locations where Nimbus Hatchery tags were recovered are shown,
Data from Regional Mark Information System data base.
The 2003 tag recovery data show that Nimbus Hatchery fish are straying
throughout the Sacramento Valley and into the Mokelumne River system. That being
said, the numbers of strays is relatively low in all recovery locations except the
Mokelumne River and its hatchery. As expected, by far the majority of the Nimbus tags
is recovered in the LAR and Nimbus Hatchery. The Mokelumne and American systems
have the largest variety of tag sources, which is probably an indication of the effects of
the complex pathway (involving coming through the Delta via the lower San Joaquin
River and back into the Sacramento River by way of the Delta Cross Channel. The LAR
is the first tributary on the Sacramento River system and some fish may be attracted to
the stream.
As mentioned previously, the presence of fair numbers of Coleman late falls and
Merced falls is of potential concern. These fish are all from Delta salmon survival
studies that have apparently increased propensity to stray. (Few if any of the Coleman
late falls and Merced falls that are released on station stray to other streams.) These
strays can exacerbate the already tenuous genetic integrity of Central Valley Chinook
runs.
56
Contribution of Nimbus Hatchery Fish to the Ocean Commercial and Sports
Fisheries
One of the goals of the Nimbus Hatchery is to produce Chinook that are harvested
in the ocean fisheries along the coast of California and, to a lesser extent, off the coasts of
Oregon and Washington. Harvest estimates are obtained by sampling about 20 percent of
the salmon landed in California and recovering the heads of adipose clipped fish. The
heads are transported to the DFG laboratory in Santa Rosa where the tags are recovered
and decoded. The information is checked and verified and then posted to the PSMFC
Regional Mark Information System, along with information on the tag source, release
location, number of tags and total releases. Most of the release data is from hatcheries
however there are programs on the Feather and Mokelumne rivers and Butte Creek where
the progeny of natural spawners are coded wire tagged and released in the streams.
The ocean tag recovery and total catch information is collected at several ports
and the results tabulated by general port area as follows:

NO – north Oregon

CO- Coos Bay Oregon

KO – Klamath Zone Oregon

KC - Klamath Zone California

FB – Fort Bragg

SF – San Francisco

MO – Monterey
The 2000 and 2001 brood year experimental tagging programs at Nimbus
Hatchery allowed us to obtain some information on the Nimbus Hatchery contribution to
the ocean fisheries. It must be kept in mind that in 2001, the numbers may overestimate
the contribution since all tagged fish were released in the Bay by use of a net pen,
whereas only a portion of the production was released in a similar manner. (As shown
earlier, the net pens have been shown to improve survival of hatchery released fish to the
ocean fisheries.)
The relative contributions of age 3 (the dominant age class) Nimbus Hatchery fish
to the ocean fisheries for the 2000 and 2001 brood years are shown in Figures 20 through
22. Note that the contribution varies between fisheries, ports and brood years.
57
Estimated commercial ocean catch
of age 3 NFH Chinook – 2000 by
Contribution to commercial catch Sep '02 - Aug '03
NimF Brdyr00 Age 3
250000
Other stocks
200000
150000
100000
50000
0
NO
CO
KO
KZ
FB
SF
MO
Major port area
Contribution to ocean recreational
catch by NFH age 3 Chinook – 00
by
Contribution to sport catch Sep '02 - Aug '03
100000
Nim F Brdyr00 Age 3
Other s tocks
75000
50000
25000
0
NO
CO
KO
KZ
FB
SF
MO
Major port area
58
Commercial catch of NFH age 3
Chinook – 2001 by
Contribution to commercial catch Sep '03 - Aug '04
NimF Brdyr01 Age 3
250000
Other stocks
200000
150000
100000
50000
0
NO
CO
KO
KZ
FB
SF
MO
Major port area
59
Contribution to sport catch Sep '03 - Aug '04
125000
NimF Brdyr01 Age 3
Other stocks
100000
75000
50000
25000
0
NO
CO
KO
KZ
FB
SF
MO
Major port area
The catch data indicate that the Nimbus Hatchery contributes to the ocean
fisheries, but perhaps at lower rates than estimated by Dettman and Kelley (1987) and
Cramer (1991). The actual contribution rates can only be determined by additional
tagging and recoveries and probably varies from year to year.
Nimbus Steelhead Production and the Lower American River.
Steelhead are endemic to the American River (Yoshiyama et al. 2001), probably
ascending to small tributaries below the large natural barriers. Construction of Nimbus
Dam restricted this typically high elevation, small stream fish to the Valley floor. There
may have been both summer and winter runs of steelhead in the American River but
evidence of a summer run is sparse. By the time Nimbus began operation, steelhead were
scarce in the American River and during the first two years of operation, only a hundred
or so adult steelhead entered the Hatchery. During the second year of operation, more
than 1 million green eggs were imported from an egg taking station on the Eel River and
more than 90 percent of these eggs successfully made it to the eyed stage.
60
The following summary of the early years of the Nimbus steelhead program is
from an undated and un-attributed short DFG report describing the history of the
Hatchery.
The contract did not provide mitigation goals for specific races of steelhead.
Nimbus Dam blocked access to the portion of the spawning area previously utilized by
100 percent of the steelhead run, therefore, both a summer and winter-run steelhead
program would be considered. The program began in April 1969 when eggs were
imported from Skamania Hatchery in Washougal, Washington for summer-run steelhead.
Creel census data indicated the summer-run fish were not successful in establishing a
summer fishery to the river. Other introduction attempts were, (fall-run Sacramento,
winter-run from the Russian, Mad and Eel rivers) were all introduced into the American
River. Our records indicate that the most successful have been the winter-run from the
Eel and Mad rivers. Currently, the winter-run from the Eel River has been established as
the American River steelhead which is considered to be an out-of-basin strain.
As indicated the LAR and Nimbus steelhead population is considered out of basin
and this stock is not part of the Central Valley steelhead Evolutionary Significant Unit
listed by NOAA Fisheries.
The current steelhead egg take goal at the Nimbus Hatchery is 800,000, with the
objective of rearing 430,000 yearling steelhead to be released in the LAR below
Discovery Park. (The egg take also allows for 250,000 eggs for transfer to Mokelumne
River Hatchery with the yearlings from these eggs to be released in the Mokelumne
River.
During the ten-year period between 1993-94 and 2003-04, an average of 1,820
(range of 649-3,805) spawners entered the Nimbus Hatchery to be spawned. Spawned
fish were returned to the river. More than 90 percent of these fish were adipose clipped,
thus were of hatchery origin (Terry West, DFG, personal communication.) Note that all
Central Valley hatchery steelhead are adipose clipped thus it is not possible to determine
the hatchery of origin.
As shown in Figure 21 American River steelhead are genetically distinct from
other Central Valley stocks and the hatchery and in-river runs are genetically similar.
61
Figure 21. Unrooted Neighbor-Joining tree based on Cavalli-Sforza and Edwards
chord distance for the Central Valley system derived from allelic variation at 11 micro
satellite loci. (From Neilsen et al. 2005)
It is difficult to determine the life history strategy of Central Valley steelhead.
The animals spawn during high winter flows; the juveniles migrate at a larger size and
may not be efficiently captured by typical netting techniques. There is some evidence
that the juveniles may remain in the streams instead of going to the ocean (reference) and
hatchery production appears to be driving the numbers of fish in such streams as the
American and Feather rivers.
62
Discussion
Fifty years ago, the role of the Nimbus Hatchery was probably quite clear to
agency decision makers. The U.S. Army Corps of Engineers had constructed a
permanent barrier to Chinook salmon moving upstream to spawning grounds on the
American River. Thus fall run spawning habitat would be covered by Nimbus and
Folsom reservoirs. (Note that the spring run was essentially eliminated before Nimbus
and Folsom dams were constructed.) DFG, USFWS and Reclamation agreed that a
Hatchery was the logical means of mitigating for the lost spawning habitat. The
Hatchery would only rear the one remaining Chinook salmon race, the fall run, and
steelhead rainbow trout as mitigation. Run size estimates and distribution of fall run
spawning indicated the Hatchery would need to replace about 19,000 spawners in order
to mitigate for the lost spawning habitat. The Hatchery spawning, incubating and rearing
facilities were sized to meet this mitigation responsibility, plus some extra capacity in
case things did not work our as planned.
For the past 50 years, the focus on Nimbus Hatchery has been mostly on
operations and facilities that would optimize production conditions (or to come as close
to optimization as the Hatchery location and water supply permitted) to produce large
numbers of Chinook salmon for the ocean fisheries, the inland recreational fishery and
spawning escapement. Hatchery staff dealt effectively with such problems as high water
temperatures, disease, bird depredation, size of fish to be released and release location.
During this period there was little emphasis by DFG and USBR management on the
biological implications of the Hatchery on naturally spawning Chinook salmon in the
American River or in other Central Valley streams. For example, the tagging rate for
Nimbus Hatchery production has been the lowest of any of other Central Valley
hatcheries and DFG has not attempted to determine seriously the contribution of Nimbus
Hatchery fish to the ocean fisheries, spawning escapement to the American River, or
straying of Nimbus Hatchery Chinook to other Central Valley streams.
Times have changed and hatcheries are no longer the straightforward answer to
mitigating for loss of salmonid spawning habitat. Practices that have been used by
Hatchery, and some biological staff over the years are either no longer acceptable or must
63
be examined in light of their potential biological impacts. A few examples of such
historic practices at the Nimbus Hatchery are:

Large transfers of genetic material (green eggs, eyed eggs, and juvenile fish
among Central Valley hatcheries.

Stocking Nimbus juvenile salmon in streams outside the American River
drainage.

Planting Hatchery production off site – for example, in San Pablo Bay.

Bringing fish in from other areas (for example, late fall run from Coleman) or
selecting later run fish at the Hatchery for spawning with the goal of changing
the run timing of Chinook salmon to the American River
With encouragement from NOAA Fisheries in 1999 DFG recognized the need to
get a better handle on some aspects of its hatchery system by issuing a draft Production
Goals and Constraints ((Operations Plans) for Nimbus, Feather River, Mokelumne and
Merced hatcheries. (Appendix 1 contains the revised operations plan for the Nimbus
Hatchery.) The Nimbus goals and constraints document (developed in coordination with
Reclamation) defined such operational features as broodstock collection, distribution of
egg allotment across the entire run, trapping and other Hatchery related activities. Many
of the these revised procedures had the intended effect of reducing the impacts of the
Nimbus Hatchery on Central Valley Chinook and steelhead. DFG took a second major
step towards incorporating biology in hatchery management by working with NOAA
Fisheries in reviewing the DFG hatchery programs. Among the considerations in their
joint report (DFG and NOAA Fisheries 2001) was rethinking the practice of releasing
hatchery production off site. The goals and constraints document was revised again in
2005.
In spite of these promising starts, in reality not much progress has been made
towards establishing the scientific information base needed to assess the impacts of the
Nimbus Hatchery on Central Valley Chinook salmon stocks. (I must emphasize that
Nimbus is not alone in this respect among Central Valley hatcheries but may be the most
information poor.)
64
Recommendations
Following are some suggestions as to the sorts of information needed to make
some critical decisions about Nimbus Hatchery operation over the next 50 years.
Following this annotated list of hatchery related studies I suggest some organizational
features that may help make use of the information gathered in the studies and the key
management questions that may be addressed. Many of these recommendations are
based on the Lichatowich et al. 2006 recommendation to treat hatchery production as an
experiment – and experiments require large amounts of data to carry them out. They also
require conceptual models and working hypotheses. Note that these are suggestions only
to start the serious discussions that are needed to sort out difficult hatchery issues. One
of my assumptions is that there will be a Nimbus Hatchery in the foreseeable future and
we need to figure how best it fits in the mix of fisheries management objectives.
1. Tag a Fraction of the Nimbus Production Fish With Coded Wire Tags
Biologists and managers must be able to identify the hatchery origin of fish
caught in the fisheries, spawning in the American River or entering the Nimbus Hatchery.
In my opinion the most efficient and cost effective means of identifying these fish is by
coded wire tagging (and clipping the adipose fins) of a constant fraction of the annual
production. Hankin and Newman (2005) have identified this fraction as 25 percent
needed to achieve statistically robust estimates of such parameters as contribution to the
fisheries and straying rate. In the case of Nimbus, that would mean tagging and marking
one million smolts at an annual estimated cost of $200,000. (This estimate is based on a
tag cost of 10 cents and another 10 cents per fish to apply the tag. The actual cost will
depend on when the program is started and the tagging procedures used to insert the tags
and clip the fins.)
The tagged fish must be mixed in with the production fish before release so that
the recoveries represent the release population.
Once the tags have been applied, the tagging information (individual tag codes,
numbers released per code, and release location, for example) is sent to DFG and then to
the Pacific States Marine Fisheries Commission for uploading into their Regional Mark
65
Information System data base. In the past there have been significant differences
between the hatchery tagging and release records and the information in the data base.
To make this work, the hatchery managers, the DFG data coordinator and the PSMFC
data managers must work closely together to ensure that the data base errors are
minimized.
It will be only of modest use if only Nimbus Hatchery tags and marks a constant
fraction of its production. All Central Valley hatcheries must also mark a constant
fraction of their production releases. This fraction would be on top of tagging for special
studies such as survival studies associated with the Vernalis Adaptive Management Plan
and the Interagency Ecological Program’s Delta juvenile salmon survival studies. DFG
staff and others are now developing a comprehensive constant fractional marking
proposal for all Central Valley hatcheries. Nimbus Hatchery will be included in this plan
but it will up to individual hatchery managers and the agencies with the mitigation
responsibilities to arrange for funding.
In spite of the lack of a comprehensive marking program, I recommend that
Nimbus Hatchery begin marking 25 percent of its production beginning with the 2006
brood year. Since it takes 2 years from release before most of the tagged fish are caught
in the fisheries or return to the river, getting an early start is critical to developing a better
understanding of the hatchery component of American River escapement. This
understanding is important when trying to assess the effects of new flow standards on
American River fall Chinook.
With respect to constant fractional marking, the CALFED Bay-Delta Program’s
Ecosystem Restoration Program will get the program jumpstarted. With A CALFED
grant, DFG is contracting to acquire automated tagging machines for use in tagging one
quarter the production of all Central Valley anadromous salmonid hatcheries. The goal is
to acquire the machines in 2006 and begin tagging in 2007. The CALFED grant will
cover all expenses associated with the tagging process, including the machines (and
trailers), supervision and the tags. Long-term funding for maintaining the machines,
moving the trailers between hatcheries, tag purchases and analyses of the results has not
been determined or acquired. Logically some combination of Reclamation, the Water
Forum and DFG would fund the long-term program.
66
2. Support a program to recover the coded wire tags in the ocean and estimating ocean
harvest
Recovering tags in the ocean consists of placing DFG staff in the major fishing
ports and sub-sampling the catch (both commercial and recreational) for tags and total
catch. This sampling effort is conducted out of the DFG office in Santa Rosa and has the
goal of sampling one fifth of the California ocean salmon catch. (Oregon, Washington
and British Columbia have similar sampling and reporting programs.) During sampling,
the heads from those fish with adipose clips are taken and sent to the laboratory in Santa
Rosa for extraction and decoding. The information is uploaded into the PSMFC’s
Regional Mark Information System, along with data on the releases themselves.
Currently DWR provides funding to Santa Rosa to partially support the ocean
salmon project’s sampling effort. If the amount of marking in Central Valley hatcheries
is increased significantly, the sampling and tag reading budget will have to been
increased. The draft Central Valley constant factional marking proposal addresses this
need. If Nimbus were to start tagging fish with the 2006 brood year, the USBR would
need to allocate some sampling/tag decoding funding to DFG Santa Rosa in the state 0607 fiscal year.
The move to a program that tags one quarter of the Central Valley fall Chinook
production may result in costs above and beyond what now occur. For example, typically
tags are recovered by taking the entire head and sending it to Santa Rosa for tag
extraction and decoding. This is not a significant problem with the sports fishery
recoveries but may pose an economic burden on the troll fishery. Troll-caught salmon
are normally sold as whole fish and taking the heads reduces the weight and the return to
the fisherman. The expanded marking program may result in a significant loss in
earnings and the industry may want to be reimbursed for this loss.
3. Support Annual Escapement Surveys and Recovery of Coded Wire Tags
To calculate the hatchery contribution to escapement (not only on the American
River but also strays to other streams) we need to know the total number of escapees, the
fraction of the escapement that is tagged and the source of those tags. Although this
67
sounds relatively simple, in reality there is no salmon stream in the Central Valley that
provides reliable information on fall run escapement and the fraction of fish that are
tagged. The sampling problems are important limitations but the most important
limitation seems to have been inadequate funding devoted to the field sampling
programs.
DFG, in cooperation with the Interagency Ecologial Program’s (IEP) Salmon
Escapement Project Work Team submitted a proposal to CALFED’s Ecosystem
Restoration Program to fund a project that is intended to result in a statistically reliable
escapement monitoring program for the Central Valley, including a tag recovery
component. This proposal has been funded and contracts are now being prepared to
implement the study. Results and conclusions are not expected before late 2007 or early
2008. Note that CALFED is also funding a similar effort to design a steelhead
monitoring effort.
The American River is part of the escapement study design proposal but in the
meantime, DFG must continue the annual escapement surveys at least at about the same
levels used in the 2003, 2004 and 2005 surveys. The past couple years have used a
combination of USBR, DFG and Water Forum funding.
4. Recover Tags at Nimbus and Other Hatcheries
Thus far this has been by far the strongest component of the tag recovery
program. Hatchery staff collects the heads from all adipose clipped salmon Chinook
salmon and forwards the heads to Santa Rosa for recovering and decoding the tags.
There is often a storage problem in that heads are collected and frozen until they can be
delivered to Santa Rosa. If Nimbus begins tagging with the 2006 brood year, hatchery
and ocean salmon staff will have to develop procedures (or facilities) for handling the
increased number of heads.
5. Reconsider the Nimbus Hatchery Goals and Release Strategy
One of the decisions facing DFG hatchery and biological staff will be moving the
production release site from San Pablo Bay, as per the recommendation in the 2001 DFG
NOAA Fisheries hatchery review. I recommend that an approach similar to that used on
68
the Feather be employed in American River. To this end, a significant number of smolts
would be tagged and released in the American River along with a comparable sized
release in San Pablo Bay. The technical committee, described later, would determine the
appropriate release numbers and release location. The released fish would be
subsequently recovered in trawl surveys near Sacramento and Chipps Island, the federal
and state salvage facilities in the South Delta, in the ocean fisheries and back in the
American River and other Central Valley streams and hatcheries.
The general objectives of these studies would be to assess the relative survival of
fish released in river as compared to those released in the Bay. The recovery data could
also be used to estimate relative straying rates of in-river and Bay releases. In addition,
the data would provide information as to the residence time of these fish in the system. If
they move downstream quickly, then there would be less concern that the hatchery
releases are competing with naturally produced fish for space and food.
DFG should consider reevaluating the net pen release strategy described earlier.
Fish from Feather, Nimbus or Mokelumne hatcheries could be used for these tests.
6. Consider a New Organizational Structure for Collecting, Analyzing and
Disseminating Hatchery and Stream Data
Collecting the above data, and data, will not be of much use unless there is a
substantial and consistent effort to tabulate, analyze and report the information to
managers and biologists. The American River Water Operations Group is a good start
but I believe there needs to be a small team dedicated to examining the technical data
coming out of both the Hatchery as well as the river. This team could be called
something like the American River technical team and would consist of at least the
Hatchery manager, the DFG area biologist responsible for the LAR, a representative of
the Water Forum, Reclamation, the USFWS and NOAA Fisheries. The team would meet
periodically to discuss data from the various studies and their implication to stream and
Hatchery management. One of the team outputs could be an annual state of the river
report presented to the American River Science Conference. The team’s objectives
would include addressing questions such as:
69

What are appropriate production numbers for Nimbus Hatchery in view of
escapement and mitigation goals?

What is a biologically and societal reasonable fall run escapement goal for the
LAR. The AFRP doubling goal would be a good starting point. In view of
more data obtained in the past several years, does this goal still seem
reasonable? If not, what is? What combination of natural and Hatchery
production is needed to meet the new goal? Consider changes in Hatchery
practices (for example, in-river releases) as a means to reduce the Hatchery
component?

What are relative benefits and detriments of releasing Nimbus production in
river versus in San Pablo Bay?

Are there additional Hatchery practices that could increase the fitness of
Hatchery fish and reduce adverse biological impacts of Hatchery production?

What additional questions should be answered regarding the Hatchery and its
impacts and what studies are needed to address these questions?

What sort of additional information is needed to complete a Hatchery and
Genetics Management Plan for the Nimbus Hatchery?

What hatchery related information should be contained in the annual DFG
Nimbus Hatchery reports? These reports should be continued (and kept up to
date) and could be more informative. I suggest looking at the Oregon
Department of Fisheries and Wildlife annual hatchery reports in that appear to
be present a variety of information in a useful format.

The work team should look closely at steelhead in the American River, and its
relation to hatchery production. The new CALFED-funded program to
develop a robust steelhead monitoring program should provide useful
information. The group might consider initial small steps like asking the local
angling club members to record and report the percent of steelhead they catch
with adipose clips. Although this will not tell us what hatchery the fish come
from, it can shed more light on the question of percent hatchery fish that
spawn in the LAR.
70
7. Consider The Long-Term (And Not So Long-Term) Effects Of Global Warming In
Planning For The Next Few Decades.
Temperature control is currently a problem at the Hatchery (and in the river) and
will likely be even more of a problem in the upcoming decades.
This team would not be a decision making body but would provide information to
managers and stakeholders. The team would be an essential part of the process of
formulating study plans, helping interpret results and discuss the results in terms of the
Hatchery and LAR salmon resources. With regard to specific analyses of Nimbus Fish
Hatchery releases, I would recommend that the DFG Ocean Salmon Project staff be
contacted to determine their interest in doing this work. Allen Grover and staff have
adapted the Klamath Basin cohort analyses software for the Central Valley (specifically
to examine the fate of Feather River Hatchery cohorts) and be able to handle similar data
from Nimbus and other Central Valley hatcheries. One or more representatives from the
Hatchery and the LAR biologists should become active members on the new IEP
Hatchery Project Work Team, in particular anyone working on the Nimbus HGMP.
Finally we should heed the Lichatowich et al. (2006) admonition that
consideration of hatcheries must be regional and include a fisheries perspective. There
are currently excellent study efforts underway at the Coleman, Livingston Stone, Feather
and Mokelumne hatcheries, including the supporting streams. These efforts, along with
this being proposed for Nimbus Hatchery, must be merged into a regional effort to
maximize their productivity and contribution to managing the fisheries. This is of
particular importance at this time since efforts to protect Klamath River stocks are
reducing the ocean fisheries and may lead to over-escapement to the streams and
hatcheries.
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