A Guide to Native Trout Restoration:
Science to Protect and Restore Coldwater Fishes and their
Habitats
Trout Unlimited, Arlington, Virginia
April 2006
Our goal in producing this guidebook is to help the angler, landowner and interested
conservationist restore native coldwater fishes and their habitats. Healthy streams and
associated streamside riparian areas are important national assets that provide not only highquality fish habitat but also recreational opportunities and dependable sources of clean water.
Streams also serve as a source of natural beauty for eyes that are too often adjusted for the
clutter of our unnatural urban environments. We have condensed many years of stream
ecology research as well as trial-and-error lessons into a series of scientific principles to
guide successful trout and char restoration projects.
Our principles are designed to increase the long-term viability of fish populations and to
restore the health, integrity and productivity of streams. Our emphasis is on basic
conservation biology and restoration ecology principles, which equates to long-term and
large-scale approaches to restoration. We promote working with nature rather than
depending on highly engineered or artificial approaches that address short term issues.
Restoration of native trout and char is, of course, about more than simply applying the latest
scientific guidance. It is an opportunity to bring people together--the angler and landowner,
agency official and public citizen. It also enables us to engage school children in a better
understanding of the natural world. Barry Lopez described these broader ambitions of
restoration as “accepting abandoned responsibilities…as the joyful mending of biological
ties.” We hope this guidebook can assist in this effort.
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Prepared by Jack E. Williams, Warren Colyer, Nathaniel Gillespie, Amy Harig, Dana DeGraaf and Joe McGurrin.
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This guidebook is divided into the following topics:
1.
2.
3.
4.
5.
A discussion on native trout and char and their values
Causes of declining populations and the need for restoration
Using the Conservation Success Index to assess status and trends
Protecting and restoring watersheds
Protecting and restoring populations
At the end of this guidebook, we provide a short list of additional resources from printed
materials and the internet that will provide further guidance for restoring degraded habitats
and reduced populations.
Native trout and char of the United States
No other family of fishes generates as much interest as the Salmonidae, which includes at
least 66 species of trouts, chars, whitefish, grayling, steelhead and salmon in the Northern
Hemisphere. Scientists estimate that most species have been around for millions of years and
their distribution has been shaped by the ebb and flow of continental glaciers, uplift of
mountains, downcut of canyons, and changes in climate. Over this evolutionary history,
today’s salmonids successfully moved across vast distances and occupied new and expanding
habitats. The complex evolutionary history of the Salmonidae has sometimes confounded
taxonomists as they have attempted to categorize and name the various species and
subspecies.
Excluding salmon and whitefishes, there are about 30 species and subspecies of trout,
grayling and char that are native to the United States. Two of these, the yellowfin cutthroat
trout in Colorado and the Alvord cutthroat trout of Nevada and Oregon, are extinct. Some of
the remaining species are listed as endangered or threatened species according to federal and
state governments, while others are considered as “sensitive” or “rare” species. All have
substantially declined from their historic distribution.
In the western United States, native trout and char include bull trout, coastal cutthroat, golden
trout, redband trout, Apache trout, Gila trout, westslope cutthroat, Yellowstone cutthroat,
Bonneville cutthroat, Rio Grande cutthroat, Paiute cutthroat, Lahontan cutthroat, greenback
cutthroat, and Colorado River cutthroat. In the eastern and midwestern United States, brook
trout is the primary native salmonid. In addition, there are a number of genetically distinct
but undescribed subspecies or other population groupings that are worthy of specific
identification and management.
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Values of native salmonids
Native trout and salmon are vital resources to all Americans. They are adapted to a wide
variety of habitats and water conditions, and their natural diversity means they are more
likely to survive future environmental change. For example, native redband trout thrive in
small, seemingly inhospitable high desert streams. Redband in desert streams of southwest
Idaho have been documented in streams with temperatures of 80oF. Some native cutthroat
trout prefer turbulent mountain streams, while others thrive in low-elevation desert lakes. In
short, the native trout have adapted to local environments for many thousands of years and
are therefore more likely to survive periods of drought, flood, wildfire or other natural
catastrophes than are non-native or hatchery-reared fish.
Figure 1. Map on left showing native ranges of many western salmonids. Map on right
showing native range of brook trout in the United States.
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Figure 2. (upper left) Small desert
stream and redband trout; (lower left)
valley bottom river and westslope
cutthroat trout; (below) Pyramid Lake
and Lahontan cutthroat trout.
Credit: Nat Gillespie, TU; (inset) Mike Dean, CDFG
Credit: Dan Doerner; (inset) Peter Rissler, Pyramid
Lake Fisheries
Credit: Nat Gillespie, TU; (inset) Rob Roberts, TU
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Many trout species are important indicators of the health of our nation’s lakes and rivers.
Species such as Yellowstone cutthroat trout and bull trout are highly sensitive to chemical
pollutants and sedimentation, making them our “canaries in the coal mines” for lakes and
streams. As compared to hatchery-produced trout or other non-native species, native
cutthroat trout and bull trout have quite narrow tolerances for changes in the chemical or
physical conditions in their streams.
Salmon, steelhead and trout are important to our nation’s economy and are highly valued as
recreational resources. Each year, many millions of dollars flow into local economies from
commercial and recreational fishers. In the U.S., trout anglers spend $6.4 billion annually on
fishing. As noted by the American Sportfishing Association, these expenditures are a
powerful engine in the broader economy of recreational angling, which generates $74.8
billion in economic outputs, $4.8 billion in tax revenues, and nearly 684,000 jobs. In
California alone, recreational angling accounts for nearly $3 billion in annual revenue and
more than 92,000 jobs. A recent study by IBM Business Consulting determined that the
value of wild steelhead in British Columbia’s Skeena River is nearly $110 million annually,
including recreational angling ($15 million), commercial fishing ($13.8 million), fish
processing ($32.8 million), tourism ($7.6 million), Native interests ($4.2 million) and other
values. Many anglers prefer wild fish for their fighting prowess compared to more
domesticated hatchery-produced fish.
Native trout and salmon are among the most beautiful creatures and are a priceless
connection to wild lands and wild rivers. Many anglers pursue native trout and steelhead, not
for food, but rather for the chance to experience some of our finest wildlands and to escape
from the stresses and hectic pace of urban life. Roadless and wilderness areas often are
among the last strongholds for native trout, salmon and steelhead.
The importance of protecting native species is reflected in national laws and policies. When
the Endangered Species Act was passed, virtually unanimously by members of the House and
Senate, there was a clear priority that native species were of significant scientific, ecologic
and economic value to our country and deserved protection. Similarly, laws from the Clean
Water Act to the National Wildlife Refuge System Improvement Act legislate the need to
restore the natural integrity of our lands and waters.
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Causes of decline and need for restoration
According to estimates from the American Fisheries Society and The Nature Conservancy,
nearly 37% of freshwater fishes in North America are greatly reduced in range or qualify for
threatened or endangered status. Many native trout and West Coast salmon are listed as
endangered or threatened species. What has caused these declines?
Figure 3. Percentage of animal groups at risk within the United States. Note that aquatic
groups have a much higher proportion of their species at risk of extinction compared to
terrestrial groups.
Historically, overfishing and habitat degradation were the principal causes of decline for
many trout and salmon species. For most species, overfishing is no longer a problem, but
loss of habitat and degradation of remaining habitat remains the primary cause of decline.
Introductions of non-native species have grown to be nearly as large a threat as habitat
decline. Non-native trout may hybridize with native trout, compete with them for limited
resources, prey on their young, or serve as vectors for new diseases and parasites. However,
non-native fishes are not the only concerns. Exotic invertebrates, such as the New Zealand
mud snail, can cause significant disruption among macroinvertebrate communities.
Habitat decline, often caused by a complex suite of problems, remains our most widespread
concern but one that can be addressed through restoration efforts. In many trout streams,
some combination of livestock grazing, road construction or timber harvest has accelerated
erosion rates and deposited fine sediments into spawning gravels. Riparian vegetation – the
critical streamside plant community – has been removed or seriously degraded in many areas.
As we lose trees along streams, shade decreases, water temperature rises, and the source of
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woody material for improving stream habitat disappears. Over time, deep pools fill in and
channels that were naturally narrow and deep become wide and shallow.
Credit: Nat Gillespie, TU
Figure 4. Common stressors for streams are shown clockwise below: channelization, double
box culvert impeding fish passage, road along stream bank causing sedimentation, and
livestock removing riparian vegetation and adding nutrients and sediment.
Perhaps the most disturbed stream systems are in urban areas and low-elevation agricultural
areas. If provided with suitable habitat including riparian vegetation, streams meandering
through urban areas can be cool and wet attractions for people on a hot summer day.
Unfortunately, most streams in and around our cities suffer a myriad of problems stemming
from plain neglect to use as wastewater drains. Urban streams often are channelized or
buried in culverts. Hydrocarbons from stormwater runoff as well as fertilizers and
insecticides from lawns contaminate streams and poison fish populations.
The Conservation Success Index: assessing status and trend
The status of our native trout and char provides a good indicator of the condition of the
streams and rivers they inhabit as well as broader watershed health. For this reason, trout and
char are often the focus of large-scale landscape assessments, such as those conducted in
recent years by federal land management agencies including the Forest Service and Bureau
of Land Management.
Native trout and char are good indicators of environmental conditions for the following
reasons. First, they typically are sensitive to degradation of habitats, reduced stream flows
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and poor water quality. Therefore, their presence is usually a good sign of the quality of the
habitats they occupy as well as those upstream areas that contribute to downstream habitat
quality. Second, native trout and char occur widely in a number of different river basins and
lake systems and they provide vast coverage across the country. Third, scientists know more
about trout and char than they do about other species. We have better information on their
historical ranges, their present habitats, and causes for changes in abundance and distribution.
Therefore, even when stream conditions and water quality cannot be measured directly over
large areas, the distribution of native trout and char provides information about broader
habitat conditions.
In 2004, Trout Unlimited launched a new effort aimed at developing a better understanding
of the conservation status of native coldwater fishes across the United States and the waters
they inhabit. This effort is called the Conservation Success Index (CSI). Simply put, the CSI
provides a framework to compare and report on the various conditions of our native trout and
char and to better understand the scope and complexity of threats they face. The CSI builds
upon a number of high-quality assessments of native trout in the West that have been
completed in recent years by state and federal agencies. In the East, the CSI utilizes a rangewide assessment of brook trout completed by the Eastern Brook Trout Joint Venture in 2006.
Part of the CSI includes a new generation of map products, focusing on the subwatershed
scale, that facilitate strategic approaches to restoration projects and priorities. The CSI uses a
variety of metrics under the four broad categories of historical versus current geographic
distribution, population integrity, habitat integrity, and future vulnerability as the basis for
evaluating the conservation status of native trout and char.
Table 1. Twenty metrics analyzed in CSI process.
Characteristic
Discussion
Comparisons between historical and current distribution
Percent of historical
Best remaining trout populations occupy 50% or
stream habitat occupied more of their historical habitat
Percent of historical
This may be an important indicator for
subbasins occupied
remaining genetic and life history diversity
Percent of historical
This will indicate how well remaining habitat is
subwatersheds
distributed as compared to historical conditions
occupied
Percent of habitat
Ideally, there should be mixture of headwater
occupied by stream
habitat and larger stream habitat
orders
Percent of historical
If lake habitats were important to fish
lake habitat occupied
historically, restoration efforts should include
these habitats
Population integrity
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Population density
Best adult trout populations are more than 400
fish/mile
Larger populations are less vulnerable to loss
from drought, flood or wildfire
Generally, genetic purity is critical; populations
less than 90% pure are compromised
Population extent
Genetic purity
Disease vulnerability
Non-native fish often are sources of new
diseases or parasites
Most trouts have resident stream, lake and
migratory habitat types – migratory and lake
forms are highly vulnerable to disturbance
Life history diversity
Land stewardship
Watershed connectivity
Habitat integrity
Amount of habitat in protected areas such as
parks, refuges and wilderness areas
Instream barriers, dams, and water diversions
fragment habitat and disconnect watersheds
Watershed condition
Condition indicators include road density,
riparian habitat quality, stream habitat diversity
Water quality
Quality indicators include number of water
quality limited streams, number of mines and
number of road crossings
Includes daily and seasonal fluctuations
Flow regime
Land conversion
Introduced species
Resource extraction
Flow modification
Climate change
Vulnerability: future threats
Private lands and higher road densities may
indicate a higher likelihood of land conversion
Likelihood of additional introduced species
occurs with increasing access (e.g., roads along
streams) and loss of fish barriers
Mineral resources, mining claims and oil and
gas leases indicate higher likelihood for future
activity
Pending water rights applications and dam
applications indicate future modifications
Larger, well-connected populations in high
quality habitat will be more resistant to future
climate change
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Many fish assessments provide information at various scales, including the stream reach,
subwatersheds, watersheds, or larger river basins. We recommend focusing on multiple
scales with special emphasis on the stream reach and subwatershed. Subwatersheds (defined
as 6th level hydrologic units across the country by the U.S. Geological Survey) range in size
from about 10,000 to 40,000 acres. This is an appropriate scale for many restoration efforts
because it is small enough to reflect local projects and stream conditions but also clearly
links to larger hydrologic units.
Figure 5. A hypothetical fish assessment showing subwatershed conditions and how local
population data facilitates status calls.
With the CSI process, local population data and a specific protocol designed for consistency
of analysis facilitates classifying the population status of individual subwatersheds. Green
subwatersheds are strongholds of larger fish populations, yellow subwatersheds contain
reduced fish populations, red subwatersheds contain greatly reduced fish populations, and
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gray subwatersheds indicate historical range from which the fish has been extirpated.
Subwatersheds with little or no quantitative data on population status are coded as well.
Maps are then produced that paint a color-coded picture of current population status across
the historical range of that fish.
PROTECTING AND RESTORING WATERSHEDS
The evaluation of native trout populations using the CSI demonstrates the inherent link
between the status of native salmonid species and the health of the watersheds that they
inhabit. The CSI can be very useful in identifying those watersheds that are a priority for
species conservation, but it is up to agency managers, scientists and local conservationists to
protect and restore those areas.
Knowing your stream: the watershed context
H.B.N. Hynes, a well-known stream ecologist, often said that we must not divorce the stream
from its valley. For the restorationist and land manager, Hynes was implying that
understanding the connections between streams and their surrounding lands is critical for
successful restoration. Water provides many of these connections as it flows from
headwaters to downstream reaches, and as rain or snow falls on slopes and percolates
downhill. Streams also connect to the landscape when floodwaters spill onto floodplains. In
many watersheds, human activities such as road construction, dams, water diversions and
channelization have severed these connections.
The first step in any successful native trout restoration effort is developing a solid
understanding of existing watershed conditions: what are the fundamental causes of any
problems, how the stream has changed over time, how the stream compares to undisturbed
streams of similar hydrology (reference conditions), how natural disturbances such as flood
or wildfire shape the stream, and how human-caused disturbances affect natural processes.
Many streams will have water quality plans, watershed analysis, or other assessments already
in existence that will provide a good start in understanding stream conditions.
Stream classifications systems also can assist the manager in understanding the inherent
capabilities of their stream. Perhaps the most widely used stream classification system was
devised by David Rosgen (see Recommended Reading and Information Sources section at
end of guidebook). By classifying a stream it is possible to predict a stream’s behavior and
understand hydraulic and sediment relationships for various stream channel types.
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We encourage a holistic approach to stream restoration with the following recommended
steps:
1. assess watershed condition and determine the primary factors affecting stream
habitats;
2. develop ecologically-sound project goals and quantifiable objectives;
3. design and implement a plan, in concert with partners and appropriate agencies, that
addresses the fundamental causes of stress; and
4. monitor and evaluate results and modify actions as needed.
Post-project monitoring and evaluation are just as important to success as is any other
element of the project--although they often are overlooked. There is no substitute for
monitoring a stream through the change of seasons and over multiple years to learn what will
work best to correct problems and limitations and how to design more effective management
in the future. This is the heart of adaptive management.
Characteristics of healthy trout streams
More often than not, trout and char habitat has been incrementally degraded over time by
multiple factors. Often degradation has proceeded to the point that it is difficult to determine
natural conditions and the inherent capabilities of the stream. Although different streams will
vary in their potential, the following table provides general characteristics of healthy trout
and char streams. Conservation actions usually seek to protect or restore one or more of
these desired characteristics.
Characteristic
Habitat
diversity
Description
Roughly equal numbers of pools, riffles and runs should
be present. Complex braided channels are preferred over
simple, straight streams.
Large wood
Downed trees and other large woody debris functions to
create pools, store sediments, and act as a source of
needed organic matter.
Water quality
Cool, pollutant-free water is critical to spawning,
juvenile rearing and adult resting habitat for many fish
o
species. Generally, <16 C is needed for spawning, and
o
<18 C for rearing.
Flow regime
The hydrograph is similar in intensity and flow amounts
to historical conditions. Minimum flows are important
but high flows may be required at certain times to dig
pools and move sediment.
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Riparian
vegetation
Adequate riparian vegetation is needed to shade streams,
protect banks from severe erosion, and provide nutrients.
Deep pools
Sufficient deep pools are necessary as thermal refuges
and holding habitat for many fish species.
Width to depth
ratio
Generally, deeper and narrower streams provide better
habitat than shallower, wider streams
Bank stability
Banks should be 80-90% stable. Some erosion is
needed, but too much is detrimental.
Fine sediments
Stream substrates should not exceed 20% fine materials
(clay, silt and sand) in riffles. Most streams suffer from
high loads of sediment.
Table 2. Characteristics of healthy trout streams. Modified from Williams and Reeves
(2006). See References, Recommended Reading and Information Sources at end of
guidebook.
Work with natural processes
Understanding the context of a restoration site within its watershed and working with the
natural forces that define that watershed are critical to achieving long-term success. In the
past, many projects with good intentions failed to achieve their objectives because they
neglected to evaluate the underlying processes at work within the larger watershed. While
there is a strong temptation to dive right in and get the hands dirty, the wise approach is to
take a step back, assess the hydrologic, geomorphic and biologic functions within that
particular ecosystem, and determine the sources of stress to the project area that result from
various conditions in that watershed. Once the sources of stress are identified, a watershedscale approach to fixing problems from upstream to downstream will increase chances for
long-term success. Because a healthy stream system is the product of many complex
interactions of physical, chemical and biological factors, a focus beyond the target fish is
absolutely essential.
“Successful restoration usually has less to do with skillful manipulation
of ecosystems than it does with staying out of nature’s way. Most ecosystems
are resilient and natural restoration will occur if we allow it. To the extent
possible, restoration should promote and complement natural recovery
rather than attempt to repair undesired conditions.”
--Paul Angermeier, Virginia Tech
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Take a long-term, watershed-scale perspective to restoration
One of the more difficult exercises when trying to restore a section of stream or river is to
consciously expand one’s scope of vision. A section of stream may have its own name and
distinct personality, yet it is not an island unto itself. In reality, every section of stream is
part of a larger network of flowing waters that embody a connected, living system.
Chemically, if water quality becomes degraded in a tributary or in the headwaters, its impact
may resonate throughout the entire watershed. Physically, activities in one stream section
can cause widespread channel instability miles upstream or downstream of the disturbance.
Biologically, trout and char use all portions of the stream network, migrating to headwaters
to spawn, to deeper pools to overwinter, and to larger river environments to grow on
available foods. Impeding access to different components of the stream network within a
watershed consequently impacts trout and char populations. An ecologically-sound project
must examine the processes occurring across the broader watershed and recognize that
actions miles away may be affecting the project reach.
Changing our view of rivers demands an expansion of scope laterally as well, to the stream
banks, the floodplain and even the valley corridor. While people often think of a stream or
river as the low, summertime ribbon of water, a stream is more accurately visualized during
flood flow, where large portions of floodplain and at times the entire river valley serve as the
channel. The trees and vegetation that line the stream and the smoothed flats of the
floodplain are in fact a part of the stream. While they remain dry most of the year or even
several years in a row, they are important to the health of the stream and to trout and char,
just as the cobble and gravel lining the summertime low flow channel. The stream bank, its
vegetation, and the floodplain all provide functions that benefit water quality,
macroinvertebrate health, and fish habitat by absorbing nutrients, sediment and flood energy.
The streambank, floodplain and river valley are all components of the living organism of a
healthy river system and their health must be considered in any watershed restoration
strategy.
This concept of a range of natural variability applies directly to stream flows. The natural
hydrology of many rivers has been altered by dams, diversions and stormwater runoff. While
we enjoy fishing in lower summer flows, trout, char and the organisms they eat all have
evolved to deal with and to prosper from a range of natural flows, both high and low, with
different frequency and duration. While groundwater-fed spring systems have very little
natural fluctuation, most river systems vary in flow seasonally and annually. Many subtle
complexities have evolved among aquatic and riparian organisms that depend on seasonal
and annual variations in stream flow, many of which we do not fully understand or even
recognize. While floods are often viewed as destructive, they reshape new habitat and
distribute nutrients among the watershed. Restoring natural flows by reducing diversions,
removing unnecessary dams, modifying hydropower releases, and mitigating stormwater
impacts to hydrology represent key restoration strategies that will accrue various benefits
across the watershed.
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A challenge in identifying the specific forces at work in a watershed is recognizing the
difference between local (site-specific) variables and larger scale (watershed) variables.
Local variables include a segment of eroding streambank or a flat section of stream with little
adult trout habitat. Localized disturbances may result from larger scale processes at work
upstream or downstream of the project area. Larger scale variables tend to disrupt the natural
balances that maintain a watershed’s hydrology and geomorphology. For example, a large
clearcut or impervious development that alters flow regimes and the supply of sediment
upstream of the project site may be causing localized stream bank erosion and filling in
historically deep pools, yet any project focused solely on reducing erosion or rebuilding
habitat in that reach will ultimately fail because it is too narrow in scope.
After identifying both local and larger scale variables impacting the chemical, physical and
biological health of the watershed, it is imperative to differentiate between stresses and
sources of stress. For example, removing riparian vegetation from a stream results in warmer
water temperatures from increased solar radiation. Increased water temperatures are the
actual stress, while removal of trees along the streambank is the source of the stress.
Differentiating between the identifiable stress that is limiting water quality, aquatic habitat,
and trout populations and what is causing that limitation may take some discussion and some
detective work within the watershed. Consciously separating stresses from sources of stress
serves the crucial role of helping avoid the application of a “band-aid” fix to the symptom
instead of focusing on mitigating the root cause of the disturbance. Sources of stress are
often non-point source and cumulative by nature. A successful watershed
restoration effort therefore requires addressing the larger scale variables at work in the
watershed.
Organizationally, both planning and monitoring are key components to a successful project.
The inherent large scale and complexity of interactions among hydrology, geomorphology,
water chemistry and biology coupled with the political complexities of land ownership and
regulatory jurisdiction across a watershed encourages the development of broad, integrated
strategies. A more systematic, watershed-scale approach guided by a watershed plan is
necessary to successfully coordinate and implement restoration work at multiple sites.
Watershed-scale plans assure the broadening of perspective needed to help identify largerscale processes that influence site-specific projects, while also requiring the involvement of
many of the landowners and political entities that operate in that watershed. Building and
cultivating these relationships and incorporating the various needs of different partners
promote restoration goals while ensuring community support and funding over the long-term.
Where to start: priorities for protection, restoration, monitoring and reintroduction
Priorities for deciding where to work and what actions are needed can be determined by
comparing the quality (integrity) of habitats and populations versus their vulnerability to
future change. In general, we advocate following the principal “protect the best and restore
the rest.” However, monitoring may be nearly as important as protection and restoration
efforts for many populations and habitats.
Remaining population strongholds of high integrity and high quality habitats, including key
sources of cold water, should be a top priority for protection. High quality habitats can be
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important targets for protection even if they do not contain fish. It is more cost effective to
protect habitats that are in high quality condition than to attempt to restore them once they
are degraded. Within this framework, protection should focus on populations and habitats
that are most vulnerable to degradation.
The highest restoration priorities are the higher integrity habitats that are somewhat degraded
and therefore at risk of loss in the near future. Once the relatively strong, at-risk populations
and habitats are restored, the next tier of priorities is lower condition populations and
habitats. Restoration investments are more likely to be retained in areas that are less
vulnerable to additional outside stressors and future modification.
The highest priority for monitoring should be the best remaining populations and habitats. It
is critical to monitor populations and habitats at higher vulnerabilities and ensure they are not
degraded.
Table 3. Matrix for determining priorities for protection, restoration, monitoring and
reintroduction.
Areas with high integrity habitats and low to moderate vulnerability will be considered high
priorities for reintroduction even in the total absence of the target species. While different
threats may be responsible for extirpated fish populations, the combination of quality habitat
and a decreased risk of losing that habitat in the future suggests a greater likelihood of
successful reintroduction - if the specific threats or impacts can be mitigated or eliminated.
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PROTECTING AND RESTORING POPULATIONS
In addition to the basic principles for protecting and restoring stream, riparian and broader
watershed conditions, we need to bear in mind broader concepts for maintaining and
restoring population integrity over longer periods of time. Our intent in the following
sections is to focus on the need to protect genetic diversity, restore life history diversity, and
expand and reconnect fragmented populations.
Protect native diversity
The maintenance of remaining sources of genetic diversity should be a primary goal of all
species management plans. Genetic diversity is needed for species to survive future
environmental challenges caused by natural or human-caused disturbances as well as changes
caused by a warming planet. Rapid advances in genetic testing during the past 20 years have
demonstrated a much higher level of local genetic diversity within many salmonid species
than had been previously realized. According to Dr. Tim King with the U.S. Geological
Survey’s Biological Resources Division, microsatellite DNA analysis of brook trout
populations in the East has revealed a substantial pattern of genetic divergence among
populations. The differences are suspected to have evolved over thousands of generations in
response to specific conditions in local streams. This means that trout populations in
adjacent drainage basins may be genetically distinct from each other.
Thus, while it is important to protect the genetic purity of species or subspecies of trout from
hybridization with non-native trout, it also is important to protect sources of genetic diversity
within the species or subspecies. This requires a more cautious approach to management and
may dictate restrictions concerning translocation of populations. It also points out the
importance of maintaining good records of past translocations.
Genetic diversity in salmonid species may be lost through the following five distinct
mechanisms:
1.
2.
3.
4.
5.
extirpation of populations,
loss of large numbers of individuals within existing populations,
mixing of populations by translocating individuals of one population to another,
introduction and subsequent hybridization with non-native fish, or
introduction of hatchery-reared fish.
Whenever possible, natural production should be encouraged over artificial propagation.
Even the best-designed hatchery program will result in domestication of fish and unintended
selection of certain genetic traits. Genetic material that encourages survival in the hatchery
environment may be counterproductive in the wild.
It is important to control non-native species, including not just non-native fish but also exotic
invertebrates, plants, diseases and parasites. Introduced species negatively affect more native
trout populations than any other factor except habitat degradation.
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In some situations, it may be prudent to protect populations with a relatively small amount of
non-native genes. All scientists will advocate protecting populations that are 99% or more
genetically pure but some scientists also advocate for protecting those populations that are
90% - 99% genetically pure. The argument for maintaining populations with slight levels of
non-native genes is that they may posses some important traits, such as a migratory life
history phase, that are underrepresented in other populations. Also, populations with slight
levels of introgression may contain pockets of genetically pure fish. Introgression of nonnative genes beyond 10% (that is, less than 90% genetically pure) usually places a population
beyond conservation value.
Proper genetic management often is complicated by a lack of recent genetic data. For
example, in a 2004 range-wide analysis of Bonneville cutthroat trout, only about 20% of
populations had been tested for genetic purity. The genetic status of a population may be
inferred by the presence of non-native trout or by general morphometric data, but we should
exercise caution in making conclusions without good scientific data. Populations of
unknown genetic status should be protected until definitive genetic data are available.
In some cases, populations at the edge of ranges may contain unique genetic data, as is now
accepted with the Southern Appalachian brook trout. Populations in close proximity
geographically that reside in separate river drainages may be genetically very different.
Populations with unknown genetic status should be saved pending the acquisition of more
detailed genetic data.
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Figure 6. GIS data showing various types of genetic information of different populations
within the historical range of a single species.
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Restore life history diversity
Life history diversity refers to the suite of alternative behaviors and adaptations (i.e.
strategies) within a population that help members to survive and successfully reproduce. As
they evolved, trout, salmon and char developed an incredible variety of life history strategies,
which allowed them to adapt to changing environmental conditions and expand their ranges
across several continents. Many of these strategies involved seasonal migrations among
different habitats within a watershed.
Unfortunately, human activities now interfere with the expression of many migratory life
history strategies. Dams, dewatered streams and poor water quality block migration
corridors between seasonal habitats, and, as a result, adaptations that evolved over the course
of thousands of years have all but disappeared.
The best known example of a unique migratory life history strategy is the migration pattern
of salmon and steelhead, which travel hundreds of miles to the ocean to feed and grow in the
ultra-productive marine environment before returning to their natal streams to spawn. As it
turns out, many inland native trout and char have evolved similarly complex migratory
strategies. For example, Bonneville cutthroat trout in the Bear River and bull trout in
Flathead Lake exhibit fluvial (river migratory) and adfluvial (lake migratory) life history
strategies, respectively. Fish spend most of the year in lower elevation large river or lake
habitats where water temperatures are relatively warm and food is plentiful. Adults must
then migrate long distances into tributaries to find the clean gravels and cool clear water they
require for spawning. By undertaking these seasonal migrations individuals can take
advantage of the best aspects of different habitats.
Credit: Warren Colyer, TU
Figure 7. The Bonneville cutthroat trout on the left is an adult fish typical of many resident
stream populations. The unique migratory life history adaptations of fluvial Bonneville
cutthroat in the Bear River system (pictured on the right) allow them to take advantage of
mainstem habitats and grow much larger.
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Most choices regarding life history strategies involve trade-offs. For instance, in the case of
inland cutthroat and bull trout, adopting a migratory life history strategy increases growth
potential, but also increases exposure to predators, dams, and irrigation ditches. As such, the
‘strategy’ has certain advantages and disadvantages. In some situations it might be a safer
bet to simply stay in the tributary where you were born (resident strategy), while in other
cases it might be worth the risk to move to more productive habitats (migratory strategy). A
population with individuals that express both strategies safeguards itself to some extent
against catastrophe. If a wildfire or flood destroys a resident population the migratory fish
can repopulate the habitat when they return to spawn in subsequent years. Conversely, if
predators or low water prevent migrants from returning to their natal stream, the resident
individuals in that stream can propagate the population. The more alternative strategies that
are expressed within a population, the more resilient that population is to catastrophic events
and changing environmental conditions.
Efforts to restore native trout should identify and protect existing life history diversity
strongholds and restore life history diversity where it has been reduced. Because life history
diversity is often correlated with habitat diversity, reestablishing migration corridors between
different habitat types, such as headwaters and mainstem rivers, encourages the development
of different life histories within a population. Reconnecting fragmented habitats by building
fish ladders, reestablishing flow in dewatered streams, and improving habitats and water
quality are often very effective ways to restore life history diversity within native fish
populations. Habitat restoration efforts should incorporate projects throughout the
watershed, from federally managed lands in upstream reaches to privately owned lands in
lower elevation, mainstem rivers. Restoring a habitat type that is used during one stage of a
fish’s life (e.g. spawning habitat in a tributary on a national forest) might not be enough to
recover a migratory population that faces habitat challenges during other stages of its life
(e.g. degraded overwintering habitat in mainstem reaches on private land).
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Table 4. Different migratory life history strategies of native trout, including: anadromous,
catadromous, fluvial, adfluvial, resident.
Life History
Strategy
Anadromous
Behavior
Born in freshwater,
travel to ocean to feed
and grow, return to
freshwater to spawn
Migration
Distances
≤ 1,000’s
of miles
Example
Salmon; Steelhead
trout
Catadromous
Born in the ocean, travel
into freshwater to feed
and grow, return to the
ocean to spawn
≤ 1,000’s
of miles
American eel
Fluvial
Born in tributaries,
travel to larger habitats
in mainstem rivers to
feed and grow, return to
tributaries to spawn
≤ 100’s of
miles
Many subspecies of
inland cutthroat
trout; bull trout
Adfluvial
Born in tributaries,
travel to lakes to feed
and grow, return to
tributaries to spawn
≤ 100’s of
miles
Pyramid Lake
Lahontan cutthroat
trout; Flathead Lake
bull trout
Resident
Born in tributaries, feed
and grow in tributaries,
spawn in tributaries
≤ 10’s of
miles
Present day
populations of
greenback cutthroat
trout and California
golden trout
Expand small, isolated populations at risk of extinction
The most common pattern of decline across native trout species has been a retreat of
populations towards the upstream fringes of their historic ranges. Today, many anglers
mistake current headwater distributions as evidence that native trout prefer those habitats.
That is not necessarily the case. In fact, native trout were historically distributed throughout
most of North America’s large rivers. Colorado River cutthroat trout and Rio Grande
cutthroat trout actually took their names from the very large rivers that they once occupied.
Today, both of those subspecies are found only in the most isolated headwater tributary
habitats within their respective ranges.
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Historical Distribution
Current Distribution
Figure 8. Hypothetical comparison between the historical range and current range of a
native trout species, showing the retreat of populations into isolated headwater habitats.
The reasons for the widespread decline of native trout are many and complicated, but most
relate in some way to the expansion of human civilization throughout the past century.
Settlements were most often located along large rivers which provided water, transportation
and waste disposal. Large river fish populations were the first to be subjected to habitat and
water quality degradation, water diversion, over-harvest, and non-native introductions.
More recently, the intentional isolation of small populations of native fish above barriers in
headwater streams has been used effectively by fisheries managers as a stop-gap measure to
slow precipitous slides towards extinction (greenback cutthroat trout and Little Kern golden
trout are examples of this). However, those methods are unlikely to save native trout species
in the long run. Several basic principles of conservation biology suggest that extinction is
much more likely to occur in small, isolated populations than in connected populations that
occupy larger habitats and contain more individuals. Small populations are much more
vulnerable to four primary factors that influence the likelihood of extinction: demographic
uncertainty, environmental uncertainty, genetic uncertainty, and natural catastrophes.
Environmental uncertainty and natural catastrophes include changes in weather, climate, food
availability, and competition, and catastrophic natural disasters like fire and flood. Genetic
uncertainty refers to the shrinkage of the gene pool results when only a small number of
reproductive individuals are present in a population. Demographic uncertainty includes
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random changes in population composition that affect survival and reproduction. For
instance, in a very small population chance might cause an unbalanced ratio of males to
females in a given year class. As an illustration of this the authors of Principles of
Conservation Biology note the example of one bird species that was doomed to extinction
when the remaining six known members of the population all turned out to be male.
Figure 9. Graph of extinction risk as a function of population size (from Groom et al. 2005).
The question of how big a population must be to ensure its survival into the future is a good
one. Scientists have attempted to answer it using a modeling tool called Population Viability
Analysis (PVA). PVA models take into account specific traits of a target population (i.e. age
of reproductive maturity, average life expectancy, number of offspring) and generate future
probabilities of extinction. Viability analyses yielded the 50/500 rule, whereby conservation
biologists argued that a population should contain 500 individuals to be considered viable,
and at least 50 individuals to survive in the short term. Use of that rule has fallen out of
favor, and ecologists now discourage the notion that there is some magic number that
guarantees a population’s survival. More recently, the focus of viability analysis has shifted
to habitat, and fisheries biologists have published studies showing that many of the habitats
that are currently occupied by resident populations of native trout are not large enough to
sustain those populations indefinitely. One study argues that tributary habitats that are less
than six miles long do not provide adequate habitat for resident populations. Maintaining a
minimum number of individuals and a minimum amount of habitat are both good rules of
thumb for species conservation, but it is important to realize that the ultimate survival of a
population will depend on complex interactions between environmental conditions and
biological traits.
One way to improve the odds of survival for native trout is to expand small populations into
larger habitats. Of course, these efforts must be balanced with protection from non-native
fishes that out compete or interbreed with native populations. Methods of expansion include
chemical treatments of streams to remove non-native species and reintroductions of native
fishes into the ‘reclaimed’ reaches. Care should be taken to ensure that the new stream
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reaches provide adequate habitat to support a large enough number of individuals to ensure
the long-term survival of the population.
KEYS TO SUCCESS
The following table summarizes many of the key elements for effective restoration programs
that have been discussed in this guidebook.
Table 5. Important considerations for a successful restoration program.
1. Recognize the inherent capabilities of your stream. Climate, geology
and plant communities shape the potential of each stream and watershed.
What were historic conditions? Are there high-quality reference streams
(benchmarks) to help understand potential?
2. Develop ecologically sound goals and objectives. Focus on processes
rather than structures.
3. Measure progress in terms of native species and communities. Native
trout often are sensitive to habitat disturbances and are good indicators of
stream conditions. Macroinvertebrate species richness and relative
densities of EPT species (mayflies, stoneflies, and caddisflies) indicate
healthy stream conditions.
4. Eliminate the causes of problems rather than just treating symptoms.
Often the primary cause of stream erosion may be found upstream or
upslope. Solve for pattern and context.
5. Be skeptical of engineered fixes. Enhancing natural recovery
processes, or at least not inhibiting them, is more likely to lead to longterm success.
6. Remember the inherent relationship between a stream and its valley.
Consider the watershed context to any problems observed along the
stream.
7. Reconnect severed linkages. Much successful restoration deals with
reconnecting fragmented populations and habitats. This may include
reconnecting a river with its floodplain or reconnecting headwaters with
downstream rivers.
8. Riparian habitats are critical to proper stream function. Adequate
riparian vegetation should be present to buffer against sediments from
upstream problems, shade streams, provide nutrients, provide large woody
materials into streams, and filter sediment during high flows.
9. Restore habitat diversity. Providing diverse habitats, including riffles,
runs, deep pools, and braided channels will increase opportunities for fish
to adapt to changing environmental conditions and multiple stressors.
10. Monitor, evaluate and adapt. Streams and fish communities are the
result of complex interactions between natural disturbances and human
modifications. We should expect to learn as we proceed and incorporate
our learning experiences into future project modifications.
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Organizationally, both planning and monitoring are key components to a successful native
trout restoration program. Tools such as the Conservation Success Index will help identify
key watersheds that are the primary focus for our actions. The inherent large scale and
complexity of interactions between native trout populations and their watersheds, coupled
with the political complexities of species recovery and regulatory jurisdictions, lends itself
the importance of developing broad, integrated strategies to address these concerns. Such
complexities also illustrate the importance of monitoring and adaptive management.
Monitoring project effectiveness is essential to sorting out the complexities of natural
systems and likelihood of increasing environmental change in the future. Restoration
projects then become our tools to learn from and develop even better projects in the future.
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RECOMMENDED READING AND INFORMATION SOURCES
References
Allan, J.D. 1995. Stream ecology: structure and function of running waters. Chapman and
Hall, New York.
Behnke, R.J. 1992. Native trout of western North America. American Fisheries Society
Monograph 6, Bethesda, Maryland. Available at www.fisheries.org
Behnke, R.J. 2002. Trout and salmon of North America. The Free Press, Simon and
Shuster, New York.
Groom, M.J., G.K. Meffe, and C.R. Carroll. 2005. Principles of conservation biology, third
edition. Sinauer Associates, Inc., Sunderland, Massachusetts.
Hilderbrand, R.H., and J.L. Kershner. 2000. Conserving inland cutthroat trout in small
streams: how much stream is enough? North American Journal of Fisheries Management
20:513-520.
Leopold, L.B. 1994. A view of the river. Harvard University Press, Cambridge,
Massachusetts. Available at www.hup.harvard.edu
Montgomery, D.R., S. Bolton, D.B. Booth and L. Wall (editors). 2003. Restoration of Puget
Sound rivers. University of Washington Press, Seattle. Available at
www.washington.edu/uwpress/
Newbury, R.W., and M.N. Gaboury. 1993. Stream analysis and fish habitat design: a field
manual. Newbury Hydraulics Ltd., Gibsons, British Columbia.
Newbury, R., M. Gaboury, C. Watson and Nonpoint Pollution Control Program, Illinois State
Water Survey. 1999. Field manual of urban stream restoration. U.S. Environmental
Protection Agency Region 5 and Illinois Environmental Protection Agency, Champaign.
Richter, B.D., J.V. Baumgartner, R. Wigington and D.P. Baun. 1997. How much water does
a river need? Freshwater Biology 37:231-249.
Rosgen, D.L. 1996. Applied river morphology. Wildland Hydrology Books, Pagosa
Springs, Colorado. Available at www.wildlandhydrology.com
Walters, T.F. 1995. Sediment in streams: sources, biological effects and control. American
Fisheries Society Monograph 7, Bethesda, Maryland. Available at www.fisheries.org
Wiley, M.J. and P.W. Seelbach. 1997. An introduction to rivers – the conceptual basis for
the Michigan Rivers Inventory (MRI) Project. Fisheries Special Report 20. State of
Michigan Department of Natural Resources. Available at www.michigan.gov/dnr
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Williams, J.E., and G. H. Reeves. 2006. Stream restoration. Island Press, Washington, D.C.
(in press) Available at www.islandpress.com
Williams, J.E., C.A. Wood, and M.P. Dombeck (editors). 1997. Watershed restoration:
principles and practices. American Fisheries Society, Bethesda, Maryland. Available at
www.fisheries.org
Websites
Center for Watershed Protection www.cwp.org
North Carolina Stream Restoration Institute: www.ncsu.edu/sri/ Stream restoration
guidebook produced by North Carolina Stream Restoration Institute and North Carolina Sea
Grant. Undated. Stream restoration: a natural channel design handbook. Available through
North Carolina Stream Restoration Institute
U.S. Environmental Protection Agency, Office of Water, River Corridor and Wetland
Restoration: www.epa.gov/owow/wetlands/restore/
Wildland Hydrology: www.wildlandhydrology.com
The Xerces Society: www.xerces.org for information on macroinvertebrate sampling and
water quality indicators
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