This chapter summarizes information on presence, absence, current status, and probable historical distribution of steelhead Oncorhynchus mykiss and stream-type (age-1 migrant) and ocean type (age-0 migrant) chinook salmon O. tshawytscha in the interior Columbia River basin and portions of the Klamath River basin. Data were compiled from existing sources and via surveys completed by more than 150 biologists working in the region. We developed models to quantitatively explore relationships among fish status and distribution, the biophysical environment, and land management. Biophysical setting was an important determinant of species distributions and habitat suitability. We applied model results to predict fish presence in unsampled areas and mapped expected distributions in more than 3,700 subwatersheds. Chinook salmon and steelhead are extirpated from more than 50% of their potential historical ranges. Most remaining populations are severely depressed; less than 2% of the watersheds in the current range were classified as supporting strong populations of steelhead or stream-type chinook salmon. Wild, indigenous fish are rare; 22% of remaining steelhead stocks and less than 17% of chinook salmon stocks were judged to be genetically unaltered by hatchery-reared fish. Much of the historical production has been eliminated. However, a core for maintaining and rebuilding functional areas remains. Protection of core areas critical to stock persistence and restoration of a broader matrix of productive habitats will be necessary for productive and sustainable fisheries. This effort will require conservation and restoration of sufficient habitats to ensure the full expression of phenotypic and genotypic diversity in chinook salmon and steelhead.

Stream temperature thresholds used to delineate habitat quality for bull trout and rainbow trout.

Unpaved forest roads remain a pervasive disturbance on public lands and mitigating sediment from road networks remains a priority for management agencies. Restoring roaded landscapes is becoming increasingly important for many native coldwater fishes that disproportionately rely on public lands for persistence. However, effectively targeting restoration opportunities requires a comprehensive understanding of the effects of roads across different ecosystems. Here, we combine a review and a field study to evaluate the status of knowledge supporting the conceptual framework linking unpaved forest roads with streambed sediment. Through our review, we specifically focused on those studies linking measures of the density of forest roads or sediment delivery with empirical streambed sediment measures. Our field study provides an example of a targeted effort of linking spatially explicit estimates of sediment production with measures of streambed sediment. Surprisingly, our review uncovered few studies ( n = 8) that empirically tested the conceptual framework linking unpaved forest roads and streambed sediment, and the results varied considerably. Field results generally supported the conceptual model that unpaved forest roads can control streambed sediment quality, but demonstrated high‐spatial variability in the effects of forest roads on streambed sediment and the need to address hotspots of sediment sources. The importance of context in the effects of forest roads is apparent in both our review and field data, suggesting the need for in situ studies to avoid misdirected restoration actions.

The Columbia Basin once supported a diversity of native fishes and large runs of anadromous salmonids that sustained substantial fisheries and cultural values. Extensive land conversion, watershed disruptions, and subsequent fishery declines have led to one of the most ambitious restoration programs in the world. Progress has been made, but restoration is expensive (exceeding US$300M/year), and it remains unclear whether habitat actions, in particular, can be successful. A comprehensive approach is needed to guide cost-effective habitat restoration. Four elements that must be addressed simultaneously are (1) a scientific foundation from landscape ecology and the concept of resilience, (2) broad public support, (3) governance for collaboration and integration, and (4) a capacity for learning and adaptation. Realizing these in the Columbia Basin will require actions to rebalance restoration goals to include diversity, strengthen linkages between science and management, increase public engagement, work across traditional ecological and social boundaries, and learn from experience.

Context More than a century of forest and fire management of Inland Pacific landscapes has transformed their successional and disturbance dynamics. Regional connectivity of many terrestrial and aquatic habitats is fragmented, flows of some ecological and physical processes have been altered in space and time, and the frequency, size and intensity of many disturbances that configure these habitats have been altered. Current efforts to address these impacts yield a small footprint in comparison to wildfires and insect outbreaks. Moreover, many current projects emphasize thinning and fuels reduction within individual forest stands, while overlooking large-scale habitat connectivity and disturbance flow issues.Methods We provide a framework for landscape restoration, offering seven principles. We discuss their implication for management, and illustrate their application with examples.Results Historical forests were spatially heterogeneous at multiple scales. Heterogeneity was the result of variability and interactions among native ecological patterns and processes, including successional and disturbance processes regulated by climatic and topographic drivers. Native flora and fauna were adapted to these conditions, which conferred a measure of resilience to variability in climate and recurrent contagious disturbances.Conclusions To restore key characteristics of this resilience to current landscapes, planning and management are needed at ecoregion, local landscape, successional patch, and tree neighborhood scales. Restoration that works effectively across ownerships and allocations will require active thinking about landscapes as socio-ecological systems that provide services to people within the finite capacities of ecosystems. We focus attention on landscape-level prescriptions as foundational to restoration planning and execution.

Habitat fragmentation in aquatic systems has led to widespread isolation of stream fishes. Metapopulation theory predicts that persistence is directly related to local patch size and its characteristics, but because these relationships tend to be taxon-specific, empirical data are important. We assembled 246 observations of occurrence of westslope cutthroat trout (WCT), a taxon of concern in the western U.S. and Canada, in stream networks isolated for up to 100 years (median 40 years) above human-made barriers, mostly culverts, at road crossings within U.S. National Forests. We used logistic regression to analyse how WCT occurrence varied with patch size, isolation time and stream-level covariates. Occurrence was positively related to stream length and habitat quality within the isolated stream network and negatively related to elevation and channel gradient. Unexpectedly, the probability of occurrence was not related to how long a habitat patch had been isolated. At the median elevation (1354 m) and channel gradient (14%), and where habitat quality was poor, WCT were likely to occur (probability >0.5) if an isolated stream network was at least 1.7 km. If habitat quality was high, about 0.2 km of habitat produced the same probability. Although there are important limitations, this analysis provides the first empirical estimate for how patch size and patch-level characteristics influence persistence of WCT in isolated stream networks.

Fisheries professionals are increasingly tasked with incorporating climate change projections into their decisions. Here we demonstrate how a structured decision framework, coupled with analytical tools and spatial data sets, can help integrate climate and biological information to evaluate management alternatives. We present examples that link down-scaled climate change scenarios to fish populations for two common types of problems: (1) strategic spatial prioritization of limited conservation resources and (2) deciding whether removing migration barriers would benefit a native fish also threatened with invasion by a nonnative competitor. We used Bayesian networks (BNs) to translate each decision problem into a quantitative tool and implemented these models under historical and future climate projections. The spatial prioritization BN predicted a substantial loss of habitat for the target species by the 2080s and provided a means to map habitats and populations most likely to persist under future climate projections. The barrier BN applied to three streams predicted that barrier removal decisions-previously made assuming a stationary climate-were likely robust under the climate scenario considered. The examples demonstrate the benefit of structuring the decision-making process to clarify management objectives, formalize assumptions, synthesize current understanding about climate effects on fish populations, and identify key uncertainties requiring further investigation.

Forecasts of species distributions under future climates are inherently uncertain, but there have been few attempts to describe this uncertainty comprehensively in a probabilistic manner. We developed a Monte Carlo approach that accounts for uncertainty within generalized linear regression models (parameter uncertainty and residual error), uncertainty among competing models (model uncertainty), and uncertainty in future climate conditions (climate uncertainty) to produce site-specific frequency distributions of occurrence probabilities across a species' range. We illustrated the method by forecasting suitable habitat for bull trout (Salvelinus confluentus) in the Interior Columbia River Basin, USA, under recent and projected 2040s and 2080s climate conditions. The 95% interval of total suitable habitat under recent conditions was estimated at 30.1-42.5 thousand km; this was predicted to decline to 0.5-7.9 thousand km by the 2080s. Projections for the 2080s showed that the great majority of stream segments would be unsuitable with high certainty, regardless of the climate data set or bull trout model employed. The largest contributor to uncertainty in total suitable habitat was climate uncertainty, followed by parameter uncertainty and model uncertainty. Our approach makes it possible to calculate a full distribution of possible outcomes for a species, and permits ready graphical display of uncertainty for individual locations and of total habitat.

Fire will play an important role in shaping forest and stream ecosystems as the climate changes. Historic observations show increased dryness accompanying more widespread fire and forest die-off. These events punctuate gradual changes to ecosystems and sometimes generate stepwise changes in ecosystems. Climate vulnerability assessments need to account for fire in their calculus. The biophysical template of forest and stream ecosystems determines much of their response to fire. This report describes the framework of how fire and climate change work together to affect forest and fish communities. Learning how to adapt will come from testing, probing, and pushing that framework and then proposing new ideas. The western U.S. defies generalizations, and much learning must necessarily be local in implication. This report serves as a scaffold for that learning. It comprises three primary chapters on physical processes, biological interactions, and management decisions, accompanied by a special section with separately authored papers addressing interactions of fish populations with wildfire. Any one of these documents could stand on its own. Taken together, they serve as a useful reference with varying levels of detail for land managers and resource specialists. Readers looking for an executive summary are directed to the sections titled "Introduction" and "Next Steps."

Stream ecosystems are especially vulnerable to climate warming because most aquatic organisms are ectothermic and live in dendritic networks that are easily fragmented. Many bioclimatic models predict significant range contractions in stream biotas, but subsequent biological assessments have rarely been done to determine the accuracy of these predictions. Assessments are difficult because model predictions are either untestable or so imprecise that definitive answers may not be obtained within timespans relevant for effective conservation. Here, we develop the equations for calculating isotherm shift rates ( ISR s) in streams that can be used to represent historic or future warming scenarios and be calibrated to individual streams using local measurements of stream temperature and slope. A set of reference equations and formulas are provided for application to most streams. Example calculations for streams with lapse rates of 0.8 °C/100 m and long‐term warming rates of 0.1–0.2 °C decade −1 indicate that isotherms shift upstream at 0.13–1.3 km decade −1 in steep streams (2–10% slope) and 1.3–25 km decade −1 in flat streams (0.1–1% slope). Used more generally with global scenarios, the equations predict isotherms shifted 1.5–43 km in many streams during the 20th Century as air temperatures increased by 0.6 °C and would shift another 5–143 km in the first half of the 21st Century if midrange projections of a 2 °C air temperature increase occur. Variability analysis suggests that short‐term variation associated with interannual stream temperature changes will mask long‐term isotherm shifts for several decades in most locations, so extended biological monitoring efforts are required to document anticipated distribution shifts. Resampling of historical sites could yield estimates of biological responses in the short term and should be prioritized to validate bioclimatic models and develop a better understanding about the effects of temperature increases on stream biotas.

Well-functioning food webs are fundamental for sustaining rivers as ecosystems and maintaining associated aquatic and terrestrial communities. The current emphasis on restoring habitat structure-without explicitly considering food webs-has been less successful than hoped in terms of enhancing the status of targeted species and often overlooks important constraints on ecologically effective restoration. We identify three priority food web-related issues that potentially impede successful river restoration: uncertainty about habitat carrying capacity, proliferation of chemicals and contaminants, and emergence of hybrid food webs containing a mixture of native and invasive species. Additionally, there is the need to place these food web considerations in a broad temporal and spatial framework by understanding the consequences of altered nutrient, organic matter (energy), water, and thermal sources and flows, reconnecting critical habitats and their food webs, and restoring for changing environments. As an illustration, we discuss how the Columbia River Basin, site of one of the largest aquatic/riparian restoration programs in the United States, would benefit from implementing a food web perspective. A food web perspective for the Columbia River would complement ongoing approaches and enhance the ability to meet the vision and legal obligations of the US Endangered Species Act, the Northwest Power Act (Fish and Wildlife Program), and federal treaties with Northwest Indian Tribes while meeting fundamental needs for improved river management.

A warming climate may bring unprecedented changes to stream and river ecosystems, with temperature considerations being of utmost importance, given that most aquatic organisms are ectothermic. Previous broad-scale assessments of climate impacts to streams have been limited by inadequate stream temperature data and have often relied on imprecise air temperature-elevation relationships as surrogates. Large regional databases of stream temperature observations are becoming available for the northwest US and can be used to address a host of research and management issues associated with climate change. For example, regional temperature databases are being used with new spatial statistical methodologies to develop models that can accurately predict stream temperatures for all reaches of fish-bearing streams under a variety of climate scenarios. These temperature models will be valuable tools for performing climate vulnerability assessments and for providing spatially explicit maps of thermal habitats for different species. A regional stream temperature monitoring network is evolving that now consists of more than 1,500 sites where full-year data are being collected by numerous resource agencies. Data from these monitoring efforts can be applied to describe longterm trends, to understand short-term sensitivities of streams to climate forcing, to perform historical reconstructions that provide site-specific trend estimates, and to better define thermal criteria associated with species distributions, abundance, and developmental phenologies. In short, the ability to accurately measure and model stream temperature regimes across the region is rapidly improving and significant advancements in our understanding of stream thermal ecology are expected in future years. Snake Basin Hatchery and Harvest Management Coordination: Tools For Building Consensus Becky Johnson, Sam Sharr and John Cassinelli Nez Perce Tribe, Department of Fisheries Resources Management, Idaho Department Fish & Game Presenter: Becky Johnson, 208-621-4629 beckyj@nezperce.org The 31 extant wild populations of spring and summer Chinook salmon in the Snake River Basin experienced significant declines following construction of dams on the Columbia and Snake rivers and were listed as threatened under the federal Endangered Species Act. To mitigate for lost natural production, state, federal, and tribally operated hatchery programs in the Snake River Basin produce 12 million spring/summer Chinook smolts annually with many thousands of those PIT tagged for research and management purposes. Tribal, state, and federal interjurisdictional management of fisheries for conservation of natural populations, sharing of harvestable returns and ESA take, trapping of hatchery broodstocks, and distribution of fish trapped in excess of brood needs is extremely complex. In an effort to better coordinate hatchery and harvest management, agencies in the basin have implemented a structured pre-season planning, inseason coordination, post season review and evaluation process, and PIT tags play a key role in that process. Weekly inseason coordination teleconferences where run projections, harvest estimates, and hatchery trapping and broodstock collection data are exchanged are particularly important to successful resource management in the basin. This presentation describes the coordination effort that’s occurring through weekly information and planning, and internet-

Recent and projected climate warming trends have prompted interest in impacts on coldwater fishes. We examined the role of climate (temperature and flow regime) relative to geomorphology and land use in determining the observed distributions of three trout species in the interior Columbia River Basin, USA. We considered two native species, cutthroat trout ( Oncorhynchus clarkii ) and bull trout ( Salvelinus confluentus ), as well as nonnative brook trout ( Salvelinus fontinalis ). We also examined the response of the native species to the presence of brook trout. Analyses were conducted using multilevel logistic regression applied to a geographically broad database of 4165 fish surveys. The results indicated that bull trout distributions were strongly related to climatic factors, and more weakly related to the presence of brook trout and geomorphic variables. Cutthroat trout distributions were weakly related to climate but strongly related to the presence of brook trout. Brook trout distributions were related to both climate and geomorphic variables, including proximity to unconfined valley bottoms. We conclude that brook trout and bull trout are likely to be adversely affected by climate warming, whereas cutthroat trout may be less sensitive. The results illustrate the importance of considering species interactions and flow regime alongside temperature in understanding climate effects on fish.

Broad-scale studies of climate change effects on freshwater species have focused mainly on temperature, ignoring critical drivers such as flow regime and biotic interactions. We use downscaled outputs from general circulation models coupled with a hydrologic model to forecast the effects of altered flows and increased temperatures on four interacting species of trout across the interior western United States (1.01 million km(2)), based on empirical statistical models built from fish surveys at 9,890 sites. Projections under the 2080s A1B emissions scenario forecast a mean 47% decline in total suitable habitat for all trout, a group of fishes of major socioeconomic and ecological significance. We project that native cutthroat trout Oncorhynchus clarkii, already excluded from much of its potential range by nonnative species, will lose a further 58% of habitat due to an increase in temperatures beyond the species' physiological optima and continued negative biotic interactions. Habitat for nonnative brook trout Salvelinus fontinalis and brown trout Salmo trutta is predicted to decline by 77% and 48%, respectively, driven by increases in temperature and winter flood frequency caused by warmer, rainier winters. Habitat for rainbow trout, Oncorhynchus mykiss, is projected to decline the least (35%) because negative temperature effects are partly offset by flow regime shifts that benefit the species. These results illustrate how drivers other than temperature influence species response to climate change. Despite some uncertainty, large declines in trout habitat are likely, but our findings point to opportunities for strategic targeting of mitigation efforts to appropriate stressors and locations.

Fire will be the proverbial eye-of-the-needle through which many western U.S. mountain, forest, and stream ecosystems will pass as the climate changes. Historic observations show increased dryness and temperatures accompanying more widespread fire and forest die-off. These events may punctuate gradual changes to ecosystems, or may be a mechanism driving stepwise changes in ecosystems. Most western ecosystems are strongly tied to cycles of fire and recovery, and the changing nature of fire will have profound consequences. There is no question that vulnerability assessments of western U.S. ecosystems need to account for fire in their calculus. The biophysical template of the forest, riparian, and stream ecosystems determines much of the response to fire. The degree of forest adaptation to fire, including fuel loading, fuel continuity, and species mixes are clear determinants of fire spread, fire severity, and the forest’s response. For aquatic systems the relative spatial scales of fire and connected fish habitats form another critical factor in longterm population persistence. Terrain, climate, and geology all exert controls on the hydrology of both forests and streams which sets much of the stage. Land and water management alter these contexts, sometimes dramatically, particularly those associated with scales of fuel continuity and aquatic fragmentation. Intertwined are the roles of invasive terrestrial and aquatic species and their roles in changing the scales of events and the connectivity and size of populations. Adaptation to climate change in the combined context of fire and climate change takes on greater dimensionality than management for either alone. Conceptually the detrimental contributions of prior human interventions provide substantial fodder for corrective action in anticipation of future severe events. However, an equally strong conceptual argument notes that restoration to historical conditions is itself an unstable solution at best. Despite clear knowledge that resistance, for example in the form of fire suppression, has built an unsustainable legacy of risk, resistive techniques will necessarily play future roles because the contexts are changing so fast. Sustainable approaches will rely on activities encouraging resilience in forests, riparian habitats, and streams alike, as opposed to those benefiting one ecosystem component at the expense of another. We also need to understand how human activities, even seemingly nurturing ones, can interfere with basic dynamic processes that form the foundation of resilience in fire adapted ecosystems. By understanding the processes reducing vulnerability to both severe disturbance and climate change, we can begin to envision many ways to facilitate more reliable positive outcomes for fire and related ecological dynamics. The future will likely require an increasing number of rapid decisions with a great deal of uncertainty about what will happen in the future, which would suggest that a present focus on reducing uncertainty about current resource conditions and limitations would be a wise investment. Adaptation taken in its most commonly used sense is about evolving, which is to say it is about learning; learning what works best. A principal goal of this GTR is to describe the framework of how we think that fire and climate change work together to affect fish communities. Learning will come from testing, probing, and pushing that framework to understand how it doesn’t work and then proposing new ideas. The western U.S. is a big place, with many diverse landscapes, defying generalizations and much learning must necessarily be local in implication. We present what we hope serves as a scaffold for that learning. This GTR comprises 2 parts: An overview document speaking to the breadth of processes interlinked by forests, fish, fire, and climate change, and a brief series of more specific and scholarly papers describing the biological interactions of fish, fire, and land management in more detail. Any one of these documents could stand on its own. Taken together they serve as a useful reference with varying levels of detail for land managers and resource specialists. Background and Purpose Managing the balance between aquatic resources, wildfire, and fuel conditions has always been difficult, and is becoming further complicated by changes in climate that alter both aquatic ecosystems and wildfire characteristics. An important question is how we expect the changing nature of fire in the landscape and our shifting management responses to interact with the changing hydrologic and aquatic systems. Multiple federal agencies face this challenge and are looking for solutions. Several summaries of the effects of fire on aquatic ecosystems exist (Minshall et al., 1997, Gresswell, 1999, Rieman et al, 2003, Luce, 2005, Shakesby and Doerr, 2006). Since the last major summary, many results have come from National Fire Plan and Joint Fire Sciences Program funded studies. In addition a great deal has been recognized about the nature of climate change, how it affects fire, and how it directly affects aquatic systems. Finally, the fire management community has made dramatic changes in their approach to wildfire using Appropriate Management Response, giving fire a much larger role in landscape-scale vegetation management. Within hours of weather updates, decisions are now made that affect thousands to tens of thousands of acres. The stakes are higher and the decisions more complex. There is a need for an updated review and synthesis of how fire affects aquatic ecosystems, how it interacts with land, fuel, and fire management decisions, and how this all fits into the context of a changing climate. We prepared a synthesis and several focused papers highlighting recent research on fish and wildfire. We also conducted a workshop with line officers and specialists to to provide updated information and syntheses supporting management policies and decisions incorporating the best available science. Study description and location The project had two components: (1) a workshop with land and aquatic managers, (2) a synthesis of current research for managers. The purpose of the workshop was to gather insights about what was helpful from previous synthesis efforts, and what was needed from new synthetic work. Presentations from the workshop are included as deliverables. The written synthesis comprises four principle parts: (1) An overview and discussion of the different management concerns that come into play for managing for changing fire, (2) a multidisciplinary technical review of concepts and recent papers providing information about climate, fire, forests, riparian areas, hydrology, geomorphology, and fish, (3) several detailed papers on aspects of fish and fire interactions, and (4) management concepts including easily applied next steps. The more technical portions are intended to be relatively accessible outside of the disciplines and are meant to provide entry to the literature for specialists who may need more detailed information. The Endnote citation file is also included as a deliverable to assist in preparing NEPA specialist reports. Conceptual and technical figures will be made available separately to assist with public meetings. Key findings with one-two paragraph discussion of each From the workshop, it was clear that managers from all disciplines and line officers had a relatively clear understanding of the complexity of the issues facing them in managing for fish and fire in a changing climate. They had few questions about how to achieve results on the landscape, even where the fish, forests, and riparian areas were particularly sensitive. The managers were all familiar with the existing literature on fish and fire, and their purposes, goals, methods, and reasoning for their projects were largely in concordance with the recommendations from the synthesis team. They did express some concern and uncertainty about what changes in climate might mean for the success of the projects. The managers agreed that their primary problem was a lack of time and materials for explaining the complexity of the issues to the public (with varying levels of education) and being able to explain the technical reasons for the design choices made for projects. There was also interest in improving communications about technical issues across disciplines for similar reasons. They were interested in access to figures, references, and a brief summary of scientific results that could be brought to meetings or provided to the public to help explain why they were proposing the various projects. They were less interested in advice on how to proceed or design projects than in materials that would help them Generating the summary and synthesis of new research and further interaction with managers produced a few new ideas that were not covered at the workshop. Among these was the notion that many climate change projections have substantial uncertainty, and what that means for both forests and stream habitats is a great deal of uncertainty about how different threats may manifest. Another was that many managers were spending more of their time responding to fires, insect attacks, and other mortality events than actually planning and preparing. They noticed that the bottlenecks were preparing NEPA reports and reconciling emergency response actions with an outlook for the longerterm. The synthesis portion of the GTR addresses this apparent conflict and should help bolster and guide policy changes already occurring in the Forest Service, BLM, and Fish and Wildlife Service to provide decision support information for managers both responding to and planning for the consequences of climate change. Specifically, managers wanted faster access to information about conditions in their streams and forests and the known and projected vulnerabilities. They wanted to be able to summarize and display information about