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 high-quality 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.

1 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. A discussion on native trout and char and their values 2. Causes of declining populations and the need for restoration 3. Using the Conservation Success Index to assess status and trends 4. Protecting and restoring watersheds 5. 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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Credit: Nat Gillespie, TU; (inset) Mike Dean, CDFG

Credit: Nat Gillespie, TU; (inset) Rob Roberts, TU

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: Dan Doerner; (inset) Peter Rissler, Pyramid Lake Fisheries

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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 range-wide 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 stream habitat occupied

Best remaining trout populations occupy 50% or more of their historical habitat

Percent of historical subbasins occupied

This may be an important indicator for remaining genetic and life history diversity

Percent of historical subwatersheds occupied

This will indicate how well remaining habitat is distributed as compared to historical conditions

Percent of habitat occupied by stream orders

Ideally, there should be mixture of headwater habitat and larger stream habitat

Percent of historical lake habitat occupied

If lake habitats were important to fish 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

Population extent Larger populations are less vulnerable to loss from drought, flood or wildfire

Genetic purity Generally, genetic purity is critical; populations less than 90% pure are compromised

Disease vulnerability Non-native fish often are sources of new diseases or parasites

Life history diversity Most trouts have resident stream, lake and migratory habitat types – migratory and lake forms are highly vulnerable to disturbance

Habitat integrity

Land stewardship Amount of habitat in protected areas such as parks, refuges and wilderness areas

Watershed connectivity 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

Flow regime Includes daily and seasonal fluctuations

Vulnerability: future threats Land conversion Private lands and higher road densities may

indicate a higher likelihood of land conversion

Introduced species Likelihood of additional introduced species occurs with increasing access (e.g., roads along streams) and loss of fish barriers

Resource extraction Mineral resources, mining claims and oil and gas leases indicate higher likelihood for future activity

Flow modification Pending water rights applications and dam applications indicate future modifications

Climate change 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 Description Habitat diversity

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 species. Generally, <16

oC is needed for spawning, and

<18oC 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 watershed-scale 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 larger-scale 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. extirpation of populations, 2. loss of large numbers of individuals within existing populations, 3. mixing of populations by translocating individuals of one population to another, 4. introduction and subsequent hybridization with non-native fish, or 5. 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 non-native 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

Behavior Migration Distances

Example

Anadromous Born in freshwater, travel to ocean to feed and grow, return to freshwater to spawn

≤ 1,000’s of miles

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 long-term 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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