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Model code (R) to accompany the manuscript "How does habitat restoration influence resilience of salmon populations to climate change?", Ecosphere.

In the Pacific Northwest, widespread stream channel simplification has led to a loss of habitat area and diversity for rearing salmon. Subsequent efforts throughout the Columbia River basin (CRB) have attempted to restore habitats altered through land development to recover imperiled salmon populations. However, there is scant evidence for demographic change in salmon populations following restoration. We used a process-based approach to estimate the potential benefit of floodplain reconnection throughout the CRB to Chinook salmon (Oncorhynchus tshawytscha) parr. Using satellite imagery, we measured stream habitats at 2093 CRB stream reaches to construct random forest models of habitat based on geomorphic and regional characteristics. Connected floodplain width was the most important factor for determining side channel presence. We estimated a current CRB-wide decrease in side channel habitat area of 26% from historical conditions. Reconnection of historical floodplains currently used for agriculture could increase side channel habitat by 25% and spring Chinook salmon parr total rearing capacity by 9% over current estimates. Individual watersheds vary greatly in habitat factors that limit salmon recovery, and large-scale estimates of restoration potential like these are needed to make decisions about long-term restoration goals among imperiled populations.

Stream temperatures in the Pacific Northwest are projected to increase with climate change, placing additional stress on cold-water salmonids. We modeled the potential impact of increased stream temperatures on four anadromous salmonid populations in the Chehalis River Basin (spring-run and fall-run Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, and steelhead O. mykiss), as well as the potential for floodplain reconnection and stream shade restoration to offset the effects of future temperature increases. In the Chehalis River Basin, peak summer stream temperatures are predicted to increase by as much as 3°C by late-century, but restoration actions can locally decrease temperatures by as much as 6°C. On average, however, basin-wide average stream temperatures are expected to increase because most reaches have low temperature reduction potential for either restoration action relative to climate change. Results from the life cycle models indicated that, without restoration actions, increased summer temperatures are likely to produce significant declines in spawner abundance by late-century for coho (-29%), steelhead (-34%), and spring-run Chinook salmon (-95%), and smaller decreases for fall-run Chinook salmon (-17%). Restoration actions reduced these declines in all cases, although model results suggest that temperature restoration alone may not fully mitigate effects of future temperature increases. Notably, floodplain reconnection provided a greater benefit than riparian restoration for steelhead and both Chinook salmon populations, but riparian restoration provided a greater benefit for coho. This pattern emerged because coho salmon tend to spawn and rear in smaller streams where shade restoration has a larger effect on stream temperature, whereas Chinook and steelhead tend to occupy larger rivers where temperatures are more influenced by floodplain connectivity. Spring-run Chinook salmon are the only population for which peak temperatures affect adult prespawn survival in addition to rearing survival, making them the most sensitive species to increasing stream temperatures.

Successful restoration of riparian habitats and functions depends in part on selection of plant species that are suited to local geomorphic and climatic conditions, which often relies on contemporary reference sites to characterize target riparian vegetation communities. In heavily modified landscapes, a lack of undisturbed sites hinders the description of reference conditions to help guide planning efforts. In lieu of contemporary reference sites, we used historical Public Land Survey data from the late 1800s and early 1900s to document historical streamside vegetation at 1685 sites distributed throughout the Columbia River basin. We used those data to construct a random forest classification model using climatic and geomorphic variables to predict the probability of occurrence of riparian vegetation groups (conifer, deciduous, shrub, and willow) and individual taxa (fir, pine, cedar, cottonwood, alder, sagebrush) for all stream reaches with bankfull width >6 m in the interior Columbia River basin. The most common predictor variables included in the best models for vegetation groups or individual taxa were mean annual precipitation, minimum temperature, elevation, and bankfull width. For some taxa, temperature range and floodplain width were also important predictors. The probability maps indicate that riparian zones were likely dominated by willow species in semi‐desert regions and by conifer species in the humid mountain regions. Deciduous species dominated riparian areas in transition zones between conifer forests and semi‐deserts. Species distributions suggest that streams in the semi‐deserts were likely characterized by little shade and low wood abundance, whereas streams in the humid mountains would have been more heavily shaded with high wood abundance. The transitional deciduous areas were likely shaded with moderate wood abundance. Historical trends in air temperature and precipitation suggest relatively small changes in climate since the time of the surveys, indicating that current species ranges are likely similar to historical species ranges. Hence, these maps can be used to help identify suitable taxonomic groups and expected riparian functions for riparian restoration in the Columbia River basin, with appropriate adjustments made to site‐specific restoration designs to account for model uncertainty, future climate change, or land use constraints.

An age-structured life-cycle model of steelhead ( Oncorhynchus mykiss) for the Stillaguamish River in Puget Sound, Washington, USA, was employed to estimate the number of age-1 steelhead parr that could have produced the estimated adult return of 69 000 in 1895. We then divided the estimated parr numbers by the estimated area of steelhead rearing habitat in the Stillaguamish River basin in 1895 and under current conditions to estimate density of rearing steelhead then and now. Scaled to estimates of total wetted area of tributary and mainstem shallow shoreline habitat, our historic estimates averaged 0.39–0.49 parr·m−2, and ranged from 0.24 to 0.7 parr·m−2. These values are significantly greater than current densities in the Stillaguamish (mainstem average: 0.15 parr·m−2, tributaries: 0.07 parr·m−2), but well within the range of recent estimates of steelhead parr rearing densities in high-quality habitats. Our results indicate that modest improvement in the capacity of mainstem and tributary rearing habitat in Puget Sound rivers will yield large recovery benefits if realized in a large proportion of the area of river basins currently accessible to steelhead.

Identifying the relative contributions of physical and ecological processes to channel evolution remains a substantial challenge in fluvial geomorphology. We use a 74-year aerial photographic record of the Hoh, Queets, Quinault, and Elwha Rivers, Olympic National Park, Washington, USA, to investigate whether physical or trophic-cascade-driven ecological factors – excessive elk impacts after wolves were extirpated a century ago – are the dominant drivers of channel planform in these gravel-bed rivers. We find that channel width and braiding show strong relationships with recent flood history. All four rivers widened significantly after having been relatively narrow in the 1970s, consistent with increased flood activity since then. Channel planform also reflects sediment-supply changes, evident from landslide response on the Elwha River. We surmise that the Hoh River, which shows a multi-decadal trend toward greater braiding, is adjusting to increased sediment supply associated with rapid glacial retreat. These rivers demonstrate transmission of climatic signals through relatively short sediment-routing systems that lack substantial buffering by sediment storage. Legacy effects of anthropogenic modification likely also affect the Quinault River planform. We infer no correspondence between channel evolution and elk abundance, suggesting that trophic-cascade effects in this setting are subsidiary to physical controls on channel morphology. Our findings differ from previous interpretations of Olympic National Park fluvial dynamics and contrast with the classic example of Yellowstone National Park, where legacy effects of elk overuse are apparent in channel morphology; we attribute these differences to hydrologic regime and large-wood availability. Published 2016. This article is a U.S. Government work and is in the public domain in the USA

Prevailing theory suggests that stream temperature warms asymptotically in a downstream direction, beginning at the temperature of the source in the headwaters and levelling off downstream as it converges to match meteorological conditions. However, there have been few empirical examples of longitudinal patterns of temperature in large rivers due to a paucity of data. We constructed longitudinal thermal profiles (temperature vs distance) for 53 rivers in the Pacific Northwest (USA) using an extensive data set of remotely sensed summertime river temperatures and classified each profile into one of five patterns of downstream warming: asymptotic (increasing then flattening), linear (increasing steadily), uniform (not changing), parabolic (increasing then decreasing), or complex (not fitting other classes). We evaluated (1) how frequently profiles warmed asymptotically downstream as expected, and (2) whether relationships between river temperature and common hydroclimatic variables differed by profile class. We found considerable diversity in profile shape, with 47% of rivers warming asymptotically and 53% having alternative profile shapes. Water temperature did not warm substantially over the course of the river for coastal parabolic and uniform profiles, and for some linear and complex profiles. Profile classes showed no clear geographical trends. The degree of correlation between river temperature and hydroclimatic variables differed among profile classes, but there was overlap among classes. Water temperature in rivers with asymptotic or parabolic profiles was positively correlated with August air temperature, tributary temperature and velocity, and negatively correlated with elevation, August precipitation, gradient and distance upstream. Conversely, associations were less apparent in rivers with linear, uniform or complex profiles. Factors contributing to the unique shape of parabolic profiles differed for coastal and inland rivers, where downstream cooling was influenced locally by climate or cool water inputs, respectively. Potential drivers of shape for complex profiles were specific to each river. These thermal patterns indicate diverse thermal habitats that may promote resilience of aquatic biota to climate change. Without this spatial context, climate change models may incorrectly estimate loss of thermally suitable habitat. Copyright © 2015 John Wiley & Sons, Ltd.

Climate change and associated changes in streamflow may alter riparian habitats substantially in coming decades. Riparian restoration provides opportunities to respond proactively to projected climate change effects, increase riparian ecosystem resilience to climate change, and simultaneously address effects of both climate change and other human disturbances. However, climate change may alter which restoration methods are most effective and which restoration goals can be achieved. Incorporating climate change into riparian restoration planning and design is critical to long-term restoration of desired community composition and ecosystem services. In this review, we discuss and provide examples of how climate change might be incorporated into restoration planning at the key stages of assessing the project context, establishing restoration goals and design criteria, evaluating design alternatives, and monitoring restoration outcomes. Restoration planners have access to numerous tools to predict future climate, streamflow, and riparian ecology at restoration sites. Planners can use those predictions to assess which species or ecosystem services will be most vulnerable under future conditions, and which sites will be most suitable for restoration. To accommodate future climate and streamflow change, planners may need to adjust methods for planting, invasive species control, channel and floodplain reconstruction, and water management. Given the considerable uncertainty in future climate and streamflow projections, riparian ecological responses, and effects on restoration outcomes, planners will need to consider multiple potential future scenarios, implement a variety of restoration methods, design projects with flexibility to adjust to future conditions, and plan to respond adaptively to unexpected change. Copyright © 2015 John Wiley & Sons, Ltd.

Despite decades of research on wood in rivers, the addition of wood as a river restoration technique remains controversial. We reviewed the literature on natural and placed wood to shed light on areas of continued debate. Research on river ecology demonstrates that large woody debris has always been a natural part of most rivers systems. Although a few studies have reported high structural failure rates (>50%) of placed instream wood structures, most studies have shown relatively low failure rates (

A substantial increase in fluvial sediment supply relative to transport capacity causes complex, large-magnitude changes in river and floodplain morphology downstream. Although sedimentary and geomorphic responses to sediment pulses are a fundamental part of landscape evolution, few opportunities exist to quantify those processes over field scales. We investigated the downstream effects of sediment released during the largest dam removal in history, on the Elwha River, Washington, USA, by measuring changes in riverbed elevation and topography, bed sediment grain size, and channel planform as two dams were removed in stages over two years. As 10.5 million t (7.1 million m3) of sediment was released from two former reservoirs, downstream dispersion of a sediment wave caused widespread bed aggradation of ~ 1 m (greater where pools filled), changed the river from pool–riffle to braided morphology, and decreased the slope of the lowermost river. The newly deposited sediment, which was finer than most of the pre-dam-removal bed, formed new bars (largely pebble, granule, and sand material), prompting aggradational channel avulsion that increased the channel braiding index by almost 50%. As a result of mainstem bed aggradation, floodplain channels received flow and accumulated new sediment even during low to moderate flow conditions. The river system showed a two- to tenfold greater geomorphic response to dam removal (in terms of bed elevation change magnitude) than it had to a 40-year flood event four years before dam removal. Two years after dam removal began, as the river had started to incise through deposits of the initial sediment wave, ~ 1.2 million t of new sediment (~ 10% of the amount released from the two reservoirs) was stored along 18 river km of the mainstem channel and 25 km of floodplain channels. The Elwha River thus was able to transport most of the released sediment to the river mouth. The geomorphic alterations and changing bed sediment grain size along the Elwha River have important ecological implications, affecting aquatic habitat structure, benthic fauna, salmonid fish spawning and rearing potential, and riparian vegetation. The response of the river to dam removal represents a unique opportunity to observe and quantify fundamental geomorphic processes associated with a massive sediment influx, and also provides important lessons for future river-restoration endeavors.

River restoration plans often propose multiple rehabilitation actions to address key habitat impairments, but they rarely attempt to quantify the potential benefits of alternative sets of actions for targeted biota. We use geomorphic and biological analyses to estimate restoration potential under three alternative scenarios for a 64-km section of the Trinity River, California, between the North Fork Trinity River and Lewiston Dam, which is the focus of habitat rehabilitation efforts under the Trinity River Restoration Program. The three scenarios are (1) increasing habitat quality by wood additions and alcove construction, (2) increasing habitat quantity by increasing sinuosity and side-channel length, and (3) increasing both habitat quality and quantity. For each scenario, we used existing stream habitat and juvenile salmonid data from previous studies to estimate potential improvements in fry or pre-smolt production. The potential increase in Oncorhynchus tshawytscha (Chinook salmon) and O. mykiss (steelhead) fry rearing capacity was 62 and 67%, respectively, for Scenario 1 (increasing habitat quality), and 36 and 44% for Scenario 2 (increasing habitat quantity). Only the most optimistic Scenario 3 (increasing both habitat quality and quantity) more than doubles potential juvenile salmonid production (112% increase in Chinook fry capacity and 107% increase in steelhead fry capacity). These quantitative predictions are useful in developing realistic restoration targets and evaluating whether proposed restoration actions can achieve the aims of a restoration program.

Intact riparian ecosystems are rich in biological diversity, but throughout the world, many have been degraded. Biodiversity declines, particularly of vertebrates, have led to experimental efforts to restore riparian forests by thinning young stands to accelerate creation of large diameter live trees. However, many vertebrates depend on large diameter deadwood that is standing as snags or fallen to the forest floor or fallen into streams. Therefore, we reviewed the sizes of deadwood and live trees used by different vertebrate species to understand which species are likely to benefit from different thinning treatments. We then examined how riparian thinning affects the long-term development of both large diameter live trees and deadwood. To this end, we used a forest growth model to examine how different forest thinning intensities might affect the long-term production and abundance of live trees and deadwood. Our results suggest that there are long-term habitat tradeoffs associated with different thinning intensities. Species that utilize large diameter live trees will benefit most from heavy thinning, whereas species that utilize large diameter deadwood will benefit most from light or no thinning. Because far more vertebrate species utilize large deadwood rather than large live trees, allowing riparian forests to naturally develop may result in the most rapid and sustained development of structural features important to most terrestrial and aquatic vertebrates.

[1] Based on known relationships of slope, discharge, valley confinement, sediment supply, and sediment caliber in controlling channel patterns, we developed multivariate models to predict natural channel patterns across the 674,500 km2 Columbia River basin, USA. We used readily available geospatial data sets to calculate reach slopes, 2 year flood discharge, and valley confinement, as well as to develop hypothesized landscape-level surrogates for sediment load and caliber (relative slope, percent of drainage area in alpine terrain, and percent of drainage area in erosive fine-grained lithologies). Using a support vector machine (SVM) classifier, we found that the four channel patterns were best distinguished by a model including all variables except valley confinement (82% overall accuracy). We then used that model to predict channel pattern for the entire basin and found that the spatial distribution of straight, meandering, anabranching, and braided patterns were consistent with regional topography and geology. A simple slope-discharge model distinguished meandering channels from all other channel patterns, but did not clearly distinguish braided from straight channels (68% overall accuracy). Addition of one or more of the hypothesized sediment supply surrogates improved prediction accuracy by 4–14% over slope and discharge alone. Braided and straight channels were most clearly distinguished on an axis of relative slope, whereas braided and anabranching channels were most clearly distinguished by adding percent alpine area to the model.

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.

Summary Steelhead (Oncorhynchus mykiss) and other Pacific salmon are threatened by unsustainable levels of harvest, genetic introgression from hatchery stocks and degradation or loss of freshwater habitat. Projected climate change is expected to further stress salmon through increases in stream temperatures and altered stream flows. We demonstrate a spatially explicit method for assessing salmon vulnerability to projected climatic changes (scenario for the years 2030–2059), applied here to steelhead salmon across the entire Pacific Northwest (PNW). We considered steelhead exposure to increased temperatures and more extreme high and low flows during four of their primary freshwater life stages: adult migration, spawning, incubation and rearing. Steelhead sensitivity to climate change was estimated on the basis of their regulatory status and the condition of their habitat. We assessed combinations of exposure and sensitivity to suggest actions that may be most effective for reducing steelhead vulnerability to climate change. Our relative ranking of locations suggested that steelhead exposure to increases in temperature will be most widespread in the southern Pacific Northwest, whereas exposure to substantial flow changes will be most widespread in the interior and northern Pacific Northwest. There were few locations where we projected that steelhead had both relatively low exposure and sensitivity to climate change. Synthesis and applications. There are few areas where habitat protection alone is likely to be sufficient to conserve steelhead under the scenario of climate change considered here. Instead, our results suggest the need for coordinated, landscape-scale actions that both increase salmon resilience and ameliorate climate change impacts, such as restoring connectivity of floodplains and high-elevation habitats.

Ecological restoration is widely practiced as a means of rehabilitating ecosystems and habitats that have been degraded or impaired through human use or other causes. Restoration practices now are confronted by climate change, which has the potential to influence long-term restoration outcomes. Concepts and attributes from the resilience literature can help improve restoration and monitoring efforts under changing climate conditions. We systematically examined the published literature on ecological resilience to identify biological, chemical, and physical attributes that confer resilience to climate change. We identified 45 attributes explicitly related to climate change and classified them as individual- (9), population- (6), community- (7), ecosystem- (7), or process-level attributes (16). Individual studies defined resilience as resistance to change or recovery from disturbance, and only a few studies explicitly included both concepts in their definition of resilience. We found that individual and population attributes generally are suited to species- or habitat-specific restoration actions and applicable at the population scale. Community attributes are better suited to habitat-specific restoration at the site scale, or system-wide restoration at the ecosystem scale. Ecosystem and process attributes vary considerably in their type and applicability. We summarize these relationships in a decision support table and provide three example applications to illustrate how these classifications can be used to prioritize climate change resilience attributes for specific restoration actions. We suggest that (1) including resilience as an explicit planning objective could increase the success of restoration projects, (2) considering the ecological context and focal scale of a restoration action is essential in choosing appropriate resilience attributes, and (3) certain ecological attributes, such as diversity and connectivity, are more commonly considered to confer resilience because they apply to a wide variety of species and ecosystems. We propose that identifying sources of ecological resilience is a critical step in restoring ecosystems in a changing climate.

Stream classification provides a means to understand the diversity and distribution of channels and floodplains that occur across a landscape while identifying links between geomorphic form and process. Accordingly, stream classification is frequently employed as a watershed planning, management, and restoration tool. At the same time, there has been intense debate and criticism of particular frameworks, on the grounds that these frameworks classify stream reaches based largely on their physical form, rather than direct measurements of their component hydrogeomorphic processes. Despite this debate surrounding stream classifications, and their ongoing use in watershed management, direct comparisons of channel classification frameworks are rare. Here we implement four stream classification frameworks and explore the degree to which each make inferences about hydrogeomorphic process from channel form within the Middle Fork John Day Basin, a watershed of high conservation interest within the Columbia River Basin, U.S.A. We compare the results of the River Styles Framework, Natural Channel Classification, Rosgen Classification System, and a channel form-based statistical classification at 33 field-monitored sites. We found that the four frameworks consistently classified reach types into similar groups based on each reach or segment’s dominant hydrogeomorphic elements. Where classified channel types diverged, differences could be attributed to the (a) spatial scale of input data used, (b) the requisite metrics and their order in completing a framework’s decision tree and/or, (c) whether the framework attempts to classify current or historic channel form. Divergence in framework agreement was also observed at reaches where channel planform was decoupled from valley setting. Overall, the relative agreement between frameworks indicates that criticism of individual classifications for their use of form in grouping stream channels may be overstated. These form-based criticisms may also ignore the geomorphic tenet that channel form reflects formative hydrogeomorphic processes across a given landscape.

An important question for salmon restoration efforts in the western USA is ‘How should habitat restoration plans be altered to accommodate climate change effects on stream flow and temperature?’ We developed a decision support process for adapting salmon recovery plans that incorporates (1) local habitat factors limiting salmon recovery, (2) scenarios of climate change effects on stream flow and temperature, (3) the ability of restoration actions to ameliorate climate change effects, and (4) the ability of restoration actions to increase habitat diversity and salmon population resilience. To facilitate the use of this decision support framework, we mapped scenarios of future stream flow and temperature in the Pacific Northwest region and reviewed literature on habitat restoration actions to determine whether they ameliorate a climate change effect or increase life history diversity and salmon resilience. Under the climate change scenarios considered here, summer low flows decrease by 35–75% west of the Cascade Mountains, maximum monthly flows increase by 10–60% across most of the region, and stream temperatures increase between 2 and 6°C by 2070–2099. On the basis of our literature review, we found that restoring floodplain connectivity, restoring stream flow regimes, and re-aggrading incised channels are most likely to ameliorate stream flow and temperature changes and increase habitat diversity and population resilience. By contrast, most restoration actions focused on in-stream rehabilitation are unlikely to ameliorate climate change effects. Finally, we illustrate how the decision support process can be used to evaluate whether climate change should alter the types or priority of restoration actions in a salmon habitat restoration plan. Copyright © 2012 John Wiley & Sons, Ltd.

As demand for fresh water increases in tandem with human population growth and a changing climate, the need to understand the ecological tradeoffs of flow regulation gains greater importance. Environmental classification is a first step towards quantifying these tradeoffs by creating the framework necessary for analysing the effects of flow variability on riverine biota. Our study presents a spatially explicit hydrogeomorphic classification of streams and rivers in Washington State, USA and investigates how projected climate change is likely to affect flow regimes in the future. We calculated 99 hydrologic metrics from 15 years of continuous daily discharge data for 64 gauges with negligible upstream impact, which were entered into a Bayesian mixture model to classify flow regimes into seven major classes described by their dominant flow source as follows: groundwater (GW), rainfall (RF), rain-with-snow (RS), snow-and-rain (SandR), snow-with-rain (SR), snowmelt (SM) and ultra-snowmelt (US). The largest class sizes were represented by the transitional RS and SandR classes (14 and 12 gauges, respectively), which are ubiquitous in temperate, mountainous landscapes found in Washington. We used a recursive partitioning algorithm and random forests to predict flow class based on a suite of environmental and climate variables. Overall classification success was 75%, and the model was used to predict normative flow classes at the reach scale for the entire state. Application of future climate change scenarios to the model inputs indicated shifts of varying magnitude from snow-dominated to rain-dominated flow classes. Lastly, a geomorphic classification was developed using a digital elevation model (DEM) and climatic data to assign stream segments as either dominantly able or unable to migrate, which was cross-tabulated with the flow types to produce a 14-tier hydrogeomorphic classification. The hydrogeomorphic classification provides a framework upon which empirical flow alteration–ecological response relationships can subsequently be developed using ecological information collected throughout the region. Copyright © 2011 John Wiley & Sons, Ltd.

Rivers and their associated floodplains are among the world's most highly altered ecosystems, resulting in billions of dollars in restoration expenditures. Successful restoration of these systems requires information at multiple spatial scales (from localized reaches to broader-scale watersheds), as well as information spanning long time frames. Here, we develop a suite of historical landscape indicators of riverine status, primarily from the perspective of salmonid management, using a case study in the Interior Columbia Basin, Washington, USA. We use a combination of historical and modern aerial photography to quantify changes in land cover and reach type, as well as potential fish habitat within channel and off-channel floodplain areas. As of 1949, 55% of the Wenatchee River floodplain had been converted to agriculture. By 2006, 62% had been modified by anthropogenic development, of which 20% was due to urban expansion. The historical percentage of agricultural land in the watershed and the contemporary percentage of urban area surpass thresholds in land cover associated with deleterious impacts on river systems. In addition, the abundance of reach types associated with the highest quality salmonid habitat (island braided and meandering reaches) has declined due to conversion to straight reach types. The area occupied by fish habitats associated with channel migration (slow/stagnant channels and dry channels) has declined approximately 25-30%. Along highly modified rivers, these habitats have also become increasingly fragmented. Caveats related to visual quality and seasonal timing of historical photographs were important considerations in the interpretation of changes witnessed for headwater island braided systems, as well as for floodplain ponds. Development of rigorous, long-term, multi-scale monitoring techniques is necessary to guide the management and restoration of river-floodplain systems for the diversity of ecosystem services they provide.

Using existing data from evaluations of habitat restoration, we estimated the average change in coho salmon Oncorhynchus kisutch and steelhead O. mykiss parr and smolt densities for common in-channel (culvert removal, large wood placement, boulder placement, and constructed logjams) and floodplain restoration techniques (constructed side channels and reconnected floodplain habitats). We then used these numbers and a Monte Carlo simulation to predict changes in fish numbers in a model watershed for two restoration scenarios: (1) restoration of all accessible habitat within the watershed and (2) restoration of the average amount historically implemented in Puget Sound watersheds (8% of total restorable areas). Mean increases in coho salmon parr or smolt density after restoration ranged from 0.19 to 2.32 parr/m for in-channel techniques and from 0.34 to 1.70 parr/m2 for floodplain techniques. Increases in steelhead parr or smolt density ranged from −0.06 to 0.71 fish/m and from 0.03 to 0.06 fish/m2 ...

Pollock, Michael M. and Timothy J. Beechie, 2010. Reply to Discussion –“Stream Temperature Relationships to Forest Harvest in Western Washington” by George Ice, George Brown, John Gravelle, C. Rhett Jackson, Jeff Light, Timothy Link, Douglas Martin, Dale McGreer, and Arne Skaugset. Journal of the American Water Resources Association (JAWRA) 46(4): 843-847. DOI: 10.1111/j.1752-1688.2010.00456.x

We compared summer stream temperature patterns in 40 small forested watersheds in the Hoh and Clearwater basins in the western Olympic Peninsula, Washington, to examine correlations between previ- ous riparian and basin-wide timber harvest activity and stream temperatures. Seven watersheds were unhar- vested, while the remaining 33 had between 25% and 100% of the total basin harvested, mostly within the last 40 years. Mean daily maximum temperatures were significantly different between the harvested and unhar- vested basins, averaging 14.5� C and 12.1� C, respectively. Diurnal fluctuations between harvested and unhar- vested basins were also significantly different, averaging 1.7� C and 0.9� C, respectively. Total basin harvest was correlated with average daily maximum temperature (r 2 = 0.39), as was total riparian harvest (r 2 = 0.32). The amount of recently clear-cut riparian forest ( 75% harvest met DOEs water quality standard. Many streams with extensive canopy closure, as estimated by the age of riparian trees, still had higher temperatures and greater diurnal fluctuations than the unharvested basins. This suggests that the impact of past forest harvest activities on stream temperatures cannot be entirely mitigated through the reestablishment of riparian buffers. (KEY TERMS: riparian ecology; fluvial processes; streamflow; land use ⁄land cover change; temperature; watershed management.)

The Elwha dam removal project presents an ideal opportunity to study how historic reduction and subsequent restoration of sediment supply alter river-floodplain dynamics in a large, forested river floodplain. We used remote sensing and onsite data collection to establish a historical record of floodplain dynamics and a baseline of current conditions. Analysis was based on four river reaches, three from the Elwha River and the fourth from the East Fork of the Quinault River. We found that the percentage of floodplain surfaces between 25 and 75 years old decreased and the percentage of surfaces >75 years increased in reaches below the Elwha dams. We also found that particle size decreased as downstream distance from dams increased. This trend was evident in both mainstem and side channels. Previous studies have found that removal of the two Elwha dams will initially release fine sediment stored in the reservoirs, then in subsequent decades gravel bed load supply will increase and gradually return to natural levels, aggrading river beds up to 1 m in some areas. We predict the release of fine sediments will initially create bi-modal grain size distributions in reaches downstream of the dams, and eventual recovery of natural sediment supply will significantly increase lateral channel migration and erosion of floodplain surfaces, gradually shifting floodplain age distributions towards younger age classes.

Ephemeral dams caused by landslides have been observed around the world, yet little is known about the effects of their failure on landforms and vegetation. In 1967, a landslide-dam-break flood in a pristine reach of the Elwha River valley filled the former channel and diverted the river. The reach is a reference site for restoration following the planned removal of dams on the river. We identified five surfaces on the 25 ha debris fan deposited by the flood. Based on tree ages and historic air photos, three of the surfaces formed in 1967, while two formed later. The surfaces varied in substrate (silt and sand, to boulders), and height above the river channel. Tree mortality resulted from tree removal and burial by sediment, the latter leaving snags and some surviving trees. Tree species composition was generally consistent within each surface. Dominant species included red alder (Alnus rubra) and Sitka willow (Salix sitchensis), alone or in combination, a combination of Douglas-fir (Pseudotsuga ...

The Elwha River dams have disconnected the upper and lower Elwha watershed for over 94 years. This has disrupted salmon migration and reduced salmon habitat by 90%. Several historical salmonid populations have been extirpated, and remaining populations are dramatically smaller than estimated historical population size. Dam removal will reconnect upstream habitats which will increase salmonid carrying capacity, and allow the downstream movement of sediment and wood leading to long-term aquatic habitat improvements. We hypothesize that salmonids will respond to the dam removal by establishing persistent, self-sustaining populations above the dams within one to two generations. We collected data on the impacts of the Elwha River dams on salmonid populations and developed predictions of species-specific response dam removal. Coho (Oncorhynchus kisutch), Chinook (O. tshawytscha), and steelhead (O. mykiss) will exhibit the greatest spatial extent due to their initial population size, timing, ability to maneuver past natural barriers, and propensity to utilize the reopened alluvial valleys. Populations of pink (O. gorbuscha), chum (O. keta), and sockeye (O. nerka) salmon will follow in extent and timing because of smaller extant populations below the dams. The initially high sediment loads will increase stray rates from the Elwha and cause deleterious effects in the egg to outmigrant fry stage for all species. Dam removal impacts will likely cause a lag in recolonization and population rebuilding. These negative sediment effects will be locally buffered by the extent of functioning floodplain, and management attempts to minimize sediment impacts. Resident life forms of char (Salvelinus confluentus), rainbow trout (O. mykiss), and cutthroat (O. clarki) will positively interact with their anadromous counterparts resulting in a positive population level response.

We develop and illustrate the concept of ‘hydrologic spiralling’ using a high-resolution (2 × 2 m grid cell) simulation of hyporheic hydrology across a 1.7 km2 section of the sand, gravel and cobble floodplain aquifer of the upper Umatilla River of northeastern Oregon, USA. We parameterized the model using a continuous map of surface water stage derived from LIDAR remote sensing data. Model results reveal the presence of complex spatial patterns of hyporheic exchange across spatial scales. We use simulation results to describe streams as a collection of hierarchically organized, individual flow paths that spiral across ecotones within streams and knit together stream ecosystems. Such a view underscores the importance of: (1) gross hyporheic exchange rates in rivers, (2) the differing ecological roles of short and long hyporheic flow paths, and (3) the downstream movement of water and solutes outside of the stream channel (e.g. in the alluvial aquifer). Hydrologic spirals underscore important limitations of empirical measures of biotic solute uptake from streams and provide a needed hydrologic framework for emerging research foci in stream ecology such as hydrologic connectivity, spatial and temporal variation in biogeochemical cycling rates and the role of stream geomorphology as a dominant control on stream ecosystem dynamics. Copyright © 2008 John Wiley & Sons, Ltd.

Implicit in the question, “How should I prioritize restoration actions?” is often the unstated question, “What should I restore?” Distinguishing between these questions helps clarify the restoration planning process, which has four distinct steps: (1) identify the restoration goal, (2) select a project prioritization approach that is consistent with the goal, (3) use watershed assessments to identify restoration actions, and (4) prioritize the list of actions. A well-crafted restoration goal identifies the biological objective of restoration, addresses underlying causes of habitat change, and recognizes that social, economic, and land use objectives may constrain restoration options. Once restoration goals are identified, one of six general approaches can be selected for prioritizing restoration actions: project type, refugia, decision support systems, single-species analysis, multispecies analysis, and cost effectiveness. Prioritizing by project type, refugia, or a decision support system requir...

The degradation of inland aquatic habitats caused by decades of human activities has led to worldwide efforts to rehabilitate freshwater habitats for fisheries and aquatic resources. We reviewed published evaluations of stream rehabilitation techniques from throughout the world, including studies on road improvement, riparian rehabilitation, floodplain connectivity and rehabilitation, instream habitat improvement, nutrient addition, and other, less-common techniques. We summarize current knowledge about the effectiveness of these techniques for improving physical habitat and water quality and increasing fish and biotic production. Despite locating 345 studies on effectiveness of stream rehabilitation, firm conclusions about many specific techniques were difficult to make because of the limited information provided on physical habitat, water quality, and biota and because of the short duration and limited scope of most published evaluations. Reconnection of isolated habitats, floodplain rehabilita...

Large portions of anadromous salmonid habitat in the western United States has been lost because of dams and other blockages. This loss has the potential to affect salmonid evolution through natural selection if the loss is biased, affecting certain types of habitat differentially, and if phenotypic traits correlated with those habitat types are heritable. Habitat loss can also affect salmonid evolution indirectly, by reducing genetic variation and changing its distribution within and among populations. In this paper, we compare the characteristics of lost habitats with currently accessible habitats and review the heritability of traits which show correlations with habitat/environmental gradients. We find that although there is some regional variation, inaccessible habitats tend to be higher in elevation, wetter and both warmer in the summer and colder in the winter than habitats currently available to anadromous salmonids. We present several case studies that demonstrate either a change in phenotypic or life history expression or an apparent reduction in genetic variation associated with habitat blockages. These results suggest that loss of habitat will alter evolutionary trajectories in salmonid populations and Evolutionarily Significant Units. Changes in both selective regime and standing genetic diversity might affect the ability of these taxa to respond to subsequent environmental perturbations. Both natural and anthropogenic and should be considered seriously in developing management and conservation strategies.

Contemporary evolution of Pacific salmon (Oncorhynchus spp.) is best viewed in the context of the evolutionary history of the species and the dynamic ecosystems they inhabit. Speciation was complete by the late Miocene, leaving c. six million years for intraspecific diversification. Following the most recent glacial maximum, large areas became available for recolonization. Current intraspecific diversity is thus the product of recent evolution overlaid onto divergent historical lineages forged during recurrent episodes of Pleistocene glaciation. In northwestern North America, dominant habitat features have been relatively stable for the past 5000 years, but salmon ecosystems remain dynamic because of disturbance regimes (volcanic eruptions, landslides, wildfires, floods, variations in marine and freshwater productivity) that occur on a variety of temporal and spatial scales. These disturbances both create selective pressures for adaptive responses by salmon and inhibit long-term divergence by periodically extirpating local populations and creating episodic dispersal events that erode emerging differences. Recent anthropogenic changes are replicated pervasively across the landscape and interrupt processes that allow natural habitat recovery. If anthropogenic changes can be shaped to produce disturbance regimes that more closely mimic (in both space and time) those under which the species evolved, Pacific salmon should be well-equipped to deal with future challenges, just as they have throughout their evolutionary history.

We evaluated controls on locations of channel incision, variation in channel evolution pathways and the time required to reconnect incised channels to their historical floodplains in the Walla Walla and Tucannon River basins, northwestern USA. Controls on incision locations are hierarchically nested. A first-order geological control defines locations of channels prone to incision, and a second-order control determines which of these channels are incised. Channels prone to incision are reaches with silt-dominated valley fills, which have sediment source areas dominated by loess deposits and channel slopes less than 0·1(area)−0·45. Among channels prone to incision, channels below a second slope–area threshold (slope = 0·15(area)−0·8) did not incise. Once incised, channels follow two different evolution models. Small, deeply incised channels follow Model I, which is characterized by the absence of a significant widening phase following incision. Widening is limited by accumulation of bank failure deposits at the base of banks, which reduces lateral channel migration. Larger channels follow Model II, in which widening is followed by development of an inset floodplain and aggradation. In contrast to patterns observed elsewhere, we found the widest incised channels upstream of narrower reaches, which reflects a downstream decrease in bed load supply. Based on literature values of floodplain aggradation rates, we estimate recovery times for incised channels (the time required to reconnect to the historical floodplain) between 60 and 275 years. Restoration actions such as allowing modest beaver recolonization can decrease recovery time by 17–33 per cent. Published in 2007 by John Wiley & Sons, Ltd.

Endangered and threatened populations of Pacific salmon (Oncorhynchus spp.) in the United States span major freshwater and marine ecosystems from southern California to northern Washington, Their wide-ranging habits and anadromous life history exposes them to a variety of risk factors and influences, including hydropower operations, ocean and freshwater harvest, habitat degradation, releases of hatchery-reared salmon, variable ocean productivity, toxic contaminants, density-dependent effects, and a suite of native and non-native predators and competitors. We review the range of analyses that form the scientific backbone of recovery plans being developed for Pacific salmon listed under the U.S. Endangered Species Act. This process involves: identifying the appropriate conservation units (demographically independent Evolutionarily Significant Units [ESUs] and their populations), developing viability criteria for Pacific salmon populations and overall ESUs, and using coarse-resolution habitat analys...

In this article, we describe a method for predicting floodplain locations and potential lateral channel migration across 82,900 km (491km 2 by bankfull area) of streams in the Columbia River basin. Predictions are based on channel confinement, channel slope, bankfull width, and bankfull depth derived from digital elevation and precipitation data. Half of the 367 km 2 (47,900 km by length) of low-gradient channels (≤ 4% channel slope) were classified as floodplain channels with a high likelihood of lateral channel migration (182 km 2 , 50%). Classification agreement between modeled and field-measured floodplain confinement was 85% (K = 0.46, p < 0.001) with the largest source of error being the misclassification of unconfined channels as confined (55% omission error). Classification agreement between predicted channel migration and lateral migration determined from aerial photographs was 76% (κ = 0.53, p < 0.001) with the largest source of error being the misclassification of laterally migrating channels as non-migrating (35% omission error). On average, more salmon populations were associated with laterally migrating channels and floodplains than with confined or nonmigrating channels. These data are useful for many river basin planning applications, including identification of land use impacts to floodplain habitats and locations with restoration potential for listed salmonids or other species of concern.

Mapping stream channels and their geomorphic attributes is an important step in many watershed research and management projects. Often insufficient field data exist to map hydromorphologic attributes across entire drainage basins, necessitating the application of hydrologic modeling tools to digital elevation models (DEMs) via a geographic information system (GIS). In this article, we demonstrate methods for deriving synthetic stream networks via GIS across large and diverse basins using drainage-enforced DEMs, along with techniques for estimating channel widths and gradient on the reach scale. The two-step drainage enforcement method we used produced synthetic stream networks that displayed a high degree of positional accuracy relative to the input streams. The accuracies of our estimated channel parameters were assessed with field data, and predictions of bankfull width, wetted width and gradient were strongly correlated with measured values (r 2 = 0.92, r 2 = 0.95, r 2 = 0.88, respectively). Classification accuracies of binned channel attributes were also high. Our methodology allows for the relatively rapid mapping of stream channels and associated morphological attributes across large geographic areas. Although initially developed to provide salmon recovery planners with important salmon habitat information, we suggest these methodologies are relevant to a variety of research and management questions.