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A common goal of biological adaptation planning is to identify and prioritize locations that remain suitably cool during the summer. This implicitly devalues areas that are ephemerally warm, even if they are suitable most of the year for mobile animals. Here we develop an alternative conceptual framework, the growth regime, which considers seasonal and landscape variation in physiological performance, focusing on riverine fish. Using temperature models for 14 river basins, we show that growth opportunities propagate up and down river networks on a seasonal basis, and that downstream habitats that are suboptimally warm in summer may actually provide the majority of growth potential expressed annually. We demonstrate with an agent-based simulation that the shoulder-season use of warmer downstream habitats can fuel annual fish production. Our work reveals a synergy between cold and warm habitats that could be fundamental to support cold-water fisheries, and highlights the risk in conservation strategies that underappreciate warm habitats. Modelling riverine fish growth across warm and cool sections of a river network, the authors demonstrate that habitats that are suboptimally warm in summer may actually provide the majority of growth potential. This highlights a risk in conservation strategies that devalue ephemerally warm habitats.

Partial migration, the phenomenon in which animal populations are composed of both migratory and nonmigratory individuals, is widespread among migrating animals. The proportion of migrants in these populations has direct influences on population genetics and dynamics, ecosystem dynamics, mating systems, evolution, and responses to environmental change, yet there are very few studies that measure the proportion of migrants. This is because existing methods to estimate the proportion of migrants are time-consuming and expensive. In this paper, we demonstrate a new method for estimating the proportion of migrants in a population based on sex ratio measurements. Many partially migratory taxa exhibit sex-biased migration or residency, and in these cases, the sex ratios of migrants and nonmigrants are fundamentally related to the proportion of migrants in the population. We define this relationship quantitatively and show how it can be used to infer the proportion of migrants in a population through a process we term “sex-ratio balancing”. We obtain Bayesian estimates of proportion of migrants and quantify the uncertainty in these estimates with highest posterior density intervals. Lastly, we validate the sex-ratio balancing approach with a Chinook salmon (Oncorhynchus tshawytscha Walbaum in Artedi, 1792) data set. Sex-ratio balancing holds promise as a tool for quantifying partial migration and filling a key data gap about partially migratory taxa.

This study examined how a suite of habitat and environmental variables relate to the ability of a stream surveyor to identify (observer efficiency) and distinguish (observer accuracy) steelhead (Oncorhynchus mykiss) redds from other stream features. Two existing spawning survey protocols that included one or two redd observers were used to develop models to estimate redd observer error. In most cases, steelhead redd abundances using raw redd counts were underestimated. Mean annual rates of observer efficiency ranged from 0.44 to 0.57, and observer accuracy ranged from 0.67 to 0.83. Regardless of the observer error model used, adjusted annual redd abundance estimates were generally unbiased (range 1.6–0.6 redds). A Gaussian area-under-the-curve methodology that incorporates redd count data and observer error rates was used to generate unbiased estimates of steelhead redd abundance in the Wenatchee (170 redds, coefficient of variation (CV) = 44%) and Methow (106 redds, CV = 41%) rivers. Unbiased estimates of redd abundance will help inform new population viability analyses to better prioritize those populations with the greatest conservation need.

In support of efforts to quantify relationships between juvenile salmonid habitat and population dynamics in the Pacific Northwest, over 2200 hydraulic models were generated at more than 900 individual reaches with unique bathymetry. Hydraulic models generated two dimensional field estimates of depth and velocity for each survey, providing a key linkage used to relate bathymetry and habitat data to juvenile salmonid population dynamics. Generating more than 2200 hydraulic models required development of an automated process to generate input files specifying bathymetry, computational grids, and boundary conditions for the Delft3D Flow software (which we run in 2D, and hereafter refer to as “Delft Flow” for clarity), enabling batch-processing of large numbers of hydraulic models, which is the novel advancement we present here. Hydraulic model inputs included digital elevation models (DEM) from topographic surveys, estimates of surface roughness based on pebble size distributions, and discharge. Outputs included velocity vector and depth fields estimated on a rectilinear grid of 10 cm spacing between grid points. Modeled velocities and depths were in reasonable agreement with field-collected velocities and depths. Certain topographic features, such as undercut banks and porous structures not represented in the DEM, resulted in modeled values that failed to reflect accurate velocities but were explained by the presence of these features. By utilizing a rectilinear grid, scaling grid spacing to computational resource limitations, leveraging a cloud computing system, and selecting simplified rules for discharge distribution for boundary conditions and model run times, we were able to successfully automate the hydraulic modeling process. Overall, automation of hydraulic model generation met precision and accuracy needs of habitat condition models, lowered labor costs, and standardized the modeling workflow, and enabled high survey volume processing needs.

A geomorphic assessment of the Middle Fork John Day Watershed, Oregon, USA, was used to generate a hierarchical, map-based understanding of watershed impairments and potential opportunities for improvements. Specifically, we (1) assessed river diversity (character and behavior) and patterns of reach types (and their controls); (2) evaluated the geomorphic condition of the streams; (3) interpreted their geomorphic recovery potential; and (4) synthesized the above into a hypothetical, strategic management plan. Collectively, these maps can set bounds and provide realistic guidance for river rehabilitation, design and implementation efforts. Fifteen distinct reach types were identified, two-thirds of which are found along perennial streams. On the basis of a variety of geo-indicators, approximately two-thirds of all perennial stream reaches were found to be in ‘good’ geomorphic condition, whereas one-third had departed to ‘moderate’ and ‘poor’ condition. Departures from ‘good’ condition were primarily related to riparian vegetation removal, conversion of floodplain to agricultural land uses (farming and grazing), logging, and channel bed dredge mining for gold. Encouragingly, the majority of reaches classified as being in moderate geomorphic condition were found to have high recovery potential. While our geomorphic assessment has practical utility for informing physically realistic expectation management for efforts like salmonid habitat restoration, the maps themselves are the key vehicle for communicating and visualizing among stakeholders.

Species conservation is often informed by the use of models evaluating the effect of different management strategies on the status of at-risk populations. For Pacific salmon and steelhead (Oncorhynchus sp.), which have complex life cycles spanning diverse environments and jurisdictions, life-cycle models (LCMs) have proven particularly useful for this task. Yet, most salmonid LCM applications to date have not been able to tie projections of population performance to specific tributary habitat management actions, which is integral to many recovery plans. Here we describe a modelling framework that links reach-scale stream habitat models with a basin-scale LCM, bridged by statistical extrapolation models, to evaluate recovery opportunities for an imperiled population of steelhead (O. mykiss) in the Middle Fork John Day River, USA. We parameterized a LCM by leveraging results from (1) a large-scale environmental monitoring program that supports ecohydraulic modelling and characterizes habitat quality (with a salmonid emphasis) within individual stream reaches (ca. 100–600 m segments), and (2) detailed demographic studies that provide estimates of survival, age structure, fecundity, etc. relevant to the model population. We then applied the model to quantify population performance under current/base (status quo) conditions and under two classes of restoration that aim to increase survival for juvenile steelhead: riparian revegetation, which reduces (otherwise limiting) stream temperatures during the warm summer months; and woody structure addition, which increases in-stream hydraulic complexity and thus juvenile rearing capacity. Status quo simulations produced abundance dynamics consistent with recent population monitoring data and the population’s current threatened status. Our evaluation of these basic restoration scenarios revealed that while both strategies have the potential to improve the conservation status of steelhead, the benefits of woody structure addition were relatively minor compared to those resulting from stream temperature reductions. Together, our findings suggest that in thermally stressed systems the benefits of wood addition will be optimized if (1) structures are added at a considerably higher rate than is often done, focusing on reaches that are not thermally limited initially, and (2) these efforts are paired with extensive riparian planting (i.e., in reaches that have the highest potential for effective shading), which will address thermal limitations (if relevant) and offer a natural source for future wood recruitment. In addition to shedding light on effective strategies for recovering steelhead, our study illustrates the power of coordinated monitoring programs that can parameterize the relationships needed to integrate modelling possibilities across scales.

Despite substantial effort and resources being invested in habitat rehabilitation for stream fishes, mechanistic approaches to designing and evaluating how habitat actions influence the fish populations they are intended to benefit remain rare. We used a net rate of energy intake (NREI) model to examine expected and observed changes in energetic habitat quality and capacity from woody debris additions in a 40 m long study reach being treated as part of a restoration experiment in Asotin Creek, Washington. We simulated depths, velocities, and NREI values for pre-treatment, expected, and post-treatment habitat conditions, and we compared pre-treatment versus expected and pre-treatment versus post-treatment simulation results. The pre-treatment versus expected topography simulations suggested treatment would increase energetically favorable area, mean NREI, and capacity in the study reach. Pre-treatment versus post-treatment comparisons yielded similar predictions, though to smaller magnitudes, likely due to the short time span and single high-flow event between pre- and post-treatment data collection. We feel the NREI modelling approach is an important tool for improving the efficacy of habitat rehabilitation actions for stream fishes.

With high-resolution topography and imagery in fluvial environments, the potential to quantify physical fish habitat at the reach scale has never been better. Increased availability of hydraulic, temperature and food availability data and models have given rise to a host of species and life stage specific ecohydraulic fish habitat models ranging from simple, empirical habitat suitability curve driven models, to fuzzy inference systems to fully mechanistic bioenergetic models. However, few examples exist where such information has been upscaled appropriately to evaluate entire fish populations. We present a framework for applying such ecohydraulic models from over 905 sites in 12 sub-watersheds of the Columbia River Basin (USA), to assess status and trends in anadromous salmon populations. We automated the simulation of computational engines to drive the hydraulics, and subsequent ecohydraulic models using cloud computing for over 2075 visits from 2011 to 2015 at 905 sites. We also characterize each site's geomorphic reach type, habitat condition, geomorphic unit assemblage, primary production potential and thermal regime. We then independently produce drainage network-scale models to estimate these same parameters from coarser, remotely sensed data available across entire populations within the Columbia River Basin. These variables give us a basis for imputation of reach-scale capacity estimates across drainage networks. Combining capacity estimates with survival estimates from mark–recapture monitoring allows a more robust quantification of capacity for freshwater life stages (i.e. adult spawning, juvenile rearing) of the anadromous life cycle. We use these data to drive life cycle models of populations, which not only include the freshwater life stages but also the marine and migration life stages through the hydropower system. More fundamentally, we can begin to look at more realistic, spatially explicit, tributary habitat restoration scenarios to examine whether the enormous financial investment on such restoration actions can help recover these populations or prevent their extinction. Copyright © 2017 John Wiley & Sons, Ltd.

Across the Pacific Northwest, at least 17 intensively monitored watershed projects have been implemented to test the effectiveness of a broad range of stream restoration actions for increasing the freshwater production of salmon and steelhead and to better understand fish–habitat relationships. We assess the scope and status of these projects and report on challenges implementing them. We suggest that all intensively monitored watersheds should contain key elements based on sound experimental design concepts and be implemented within an adaptive management framework to maximize learning. The most significant challenges reported by groups were (1) improving coordination between funders, restoration groups, and researchers so that restoration and monitoring actions occur based on the project design and (2) maintaining consistent funding to conduct annual monitoring and evaluation of data. However, we conclude that despite these challenges, the intensively monitored watershed approach is the most reliable me...

Watershed assessments have become common for prioritizing restoration in river networks. These assessments primarily focus on geomorphic conditions of rivers but less frequently incorporate non-geomorphic abiotic factors such as water chemistry and temperature, and biotic factors such as the structure of food webs. Using a dynamic food web model that integrates physical and ecological environmental conditions of rivers, we simulated how juvenile salmon (Oncorhynchus spp.) biomass responded to restoration at twelve sites distributed across the Methow River (Washington, USA), ranging from headwater tributaries to mainstem reaches. We explored responses to three common river restoration strategies: (1) physical habitat modification, (2) nutrient supplementation, and (3) increased riparian vegetation cover. We also simulated how different food web configurations that exist in salmon-bearing streams, such as the presence of ‘non-target’ fishes and ‘armored’ predation resistant invertebrates, could mediate restoration outcomes. Some locations in the river network experienced relatively large increases in modeled fish biomass with restoration, whereas other locations were almost entirely unresponsive. Spatial variation in restoration outcomes was primarily controlled by non-geomorphic environmental conditions, such as nutrient availability, water temperature, and stream canopy cover. Restoration responses also varied significantly with different food web configurations, suggesting that as the structure of food webs varies across river networks, so too could the outcome of restoration. These findings illustrate that ecological responses to restoration may exhibit substantial spatial variation within river networks, resulting from heterogeneity in environmental conditions that are commonly overlooked—but which can and should be considered—in restoration planning and prioritization.

The goal of salmonid habitat monitoring programs is to measure habitat attributes linked to salmonid productivity based on protocols that have sufficient precision to detect environmental variation at relevant spatial and temporal scales. Benthic macroinvertebrate community composition often is evaluated as part of habitat monitoring and assessment protocols, despite a lack of direct relationships between benthic composition and salmonid production. Macroinvertebrate drift provides a direct measure of the food resources available to stream salmonids, but drift is rarely evaluated as part of habitat monitoring protocols. This reluctance may stem from the complex spatial and temporal variability inherent in macroinvertebrate drift abundances and an assumed inability to obtain precise estimates of drift abundance at relevant spatial and temporal scales. We evaluated an extensive set of paired drift and benthic macroinvertebrate samples to characterize variation in the biomass and density (i.e., counts) of macroinvertebrate samples across a hierarchy of spatial and temporal scales. Results suggest that estimates of total drift biomass may offer the most precise approach for detecting differences in salmonid food availability among stream reaches and, thus, may be more appropriate than benthic sampling for incorporation into salmonid habitat monitoring programs.

Beaver are an integral component of hydrologic, geomorphic, and biotic processes within North American stream systems, and their propensity to build dams alters stream and riparian structure and function to the benefit of many aquatic and terrestrial species. Recognizing this, beaver relocation efforts and/or application of structures designed to mimic the function of beaver dams are increasingly being utilized as effective and cost-efficient stream and riparian restoration approaches. Despite these verities, the notion that beaver dams negatively impact stream habitat remains common, specifically the assumption that beaver dams increase stream temperatures during summer to the detriment of sensitive biota such as salmonids. In this study, we tracked beaver dam distributions and monitored water temperature throughout 34 km of stream for an eight-year period between 2007 and 2014. During this time the number of natural beaver dams within the study area increased by an order of magnitude, and an additional 4 km of stream were subject to a restoration manipulation that included installing a high-density of Beaver Dam Analog (BDA) structures designed to mimic the function of natural beaver dams. Our observations reveal several mechanisms by which beaver dam development may influence stream temperature regimes; including longitudinal buffering of diel summer temperature extrema at the reach scale due to increased surface water storage, and creation of cool-water channel scale temperature refugia through enhanced groundwater-surface water connectivity. Our results suggest that creation of natural and/or artificial beaver dams could be used to mitigate the impact of human induced thermal degradation that may threaten sensitive species.

Digital elevation models (DEMs) derived from ground-based topographic surveys have become ubiquitous in the field of fluvial geomorphology. Their wide application in spatially explicit analysis includes hydraulic modeling, habitat modeling, and morphological sediment budgeting. However, there is a lack of understanding regarding the repeatability and precision of DEMs derived from ground-based surveys conducted by different, and inherently subjective, observers. This is of particular concern when we consider the proportion of studies and monitoring programs that are implemented across multiple sites and over time by different observers. We used a case study from the Columbia Habitat Monitoring Program (CHaMP), where seven field crews sampled the same six sites, to quantify the magnitude and effect of observer variability on DEMs interpolated from total station surveys. We quantified the degree to which DEM-derived metrics and measured geomorphic change were repeatable. Across all six sites, we found an average elevation standard deviation of 0.05 m among surveys, and a mean total range of 0.16 m. A variance partition between site, crew, and unexplained errors for several topographically derived metrics showed that crew variability never accounted for > 1.5% of the total variability. We calculated minor geomorphic changes at one site following a relatively dry flow year between 2012 and 2011. Calculated changes were minimal (unthresholded net changes ±1–3 cm) with six crews detecting an indeterminate sediment budget and one crew detecting a minor net erosional sediment budget. While crew variability does influence the quality of topographic surveys, this study highlights that when consistent surveying methods are employed, the data sets are still sufficient to support derivation of topographic metrics and conduct basic geomorphic change detection. Copyright © 2014 John Wiley & Sons, Ltd.

Reproductive tactics and migratory strat- egies in Pacific and Atlantic salmonines are inextri- cably linked through the effects of migration (or lack thereof) on age and size at maturity. In this review, we focus on the ecological and evolutionary patterns of freshwater maturation in salmonines, a key process resulting in the diversification of their life histories. We demonstrate that the energetics of maturation and reproduction provides a unifying theme for under- standing both the proximate and ultimate causes of variation in reproductive schedules among species, populations, and the sexes. We use probabilistic maturation reaction norms to illustrate how variation in individual condition, in terms of body size, growth rate, and lipid storage, influences the timing of maturation. This useful framework integrates both genetic and environmental contributions to condi- tional strategies for maturation and, in doing so, demonstrates how flexible life histories can be both heritable and subject to strong environmental influ- ences. We review evidence that the propensity for freshwater maturation in partially anadromous species is predictable across environmental gradients at geo- graphic and local spatial scales. We note that growth is commonly associated with the propensity for fresh- water maturation, but that life-history responses to changes in growth caused by temperature may be strikingly different than changes caused by differences in food availability. We conclude by exploring how contemporary management actions can constrain or

Streams and rivers host a significant portion of Earth's biodiversity and provide important ecosystem services for human populations. Accurate information regarding the status and trends of stream resources is vital for their effective conservation and management. Most statistical techniques applied to data measured on stream networks were developed for terrestrial applications and are not optimized for streams. A new class of spatial statistical model, based on valid covariance structures for stream networks, can be used with many common types of stream data (e.g., water quality attributes, habitat conditions, biological surveys) through application of appropriate distributions (e.g., Gaussian, binomial, Poisson). The spatial statistical network models account for spatial autocorrelation (i.e., nonindependence) among measurements, which allows their application to databases with clustered measurement locations. Large amounts of stream data exist in many areas where spatial statistical analyses could be used to develop novel insights, improve predictions at unsampled sites, and aid in the design of efficient monitoring strategies at relatively low cost. We review the topic of spatial autocorrelation and its effects on statistical inference, demonstrate the use of spatial statistics with stream datasets relevant to common research and management questions, and discuss additional applications and development potential for spatial statistics on stream networks. Free software for implementing the spatial statistical network models has been developed that enables custom applications with many stream databases.

Fine-scale (submeter) resolution digital elevation models (DEMs) created from high precision (subcentimeter) instruments (e.g., total station, rtkGPS, and laser scanning) have become ubiquitous in the field of fluvial geomorphology. They permit a diverse range of spatially explicit analyses including hydraulic modeling, habitat modeling, and geomorphic change detection. While previous studies have assessed the quality of specific topographic survey methods at individual sites or across a limited number of sites, an intercomparison of survey technologies across a diverse range of wadeable streams could help clarify which techniques are feasible, as well as which work best under what circumstances and for what purposes. Although a wealth of existing studies and protocols explain how to undertake each individual technique, in this study we seek to provide guidance on what techniques to use in which circumstances. We quantified the relative quality and the amount of effort spent collecting data to derive bare earth topography from an array of ground-based and airborne survey techniques. We used topographic survey data collected over the summer of 2010 from six sample reaches of varying complexity in the Lemhi River basin, Idaho, USA. We attempted to conduct complete, replicate surveys at each site using total station (TS), real-time kinematic (rtk) GPS, discrete return terrestrial laser scanner (TLS), and airborne LiDaR surveys (ALS). We evaluated the precision and accuracy of derived bare earth DEMs relative to the higher precision total station point data. Discrepancies between pairwise techniques were calculated using propagated DEM errors thresholded at a 95% confidence interval. Mean discrepancies between total station and rtkGPS DEMs were relatively low (≤ 0.05 m), yet TS data collection time was up to 2.4 times longer than rtkGPS. The ALS DEMs had lower accuracy than TS or rtkGPS DEMs, but the aerial coverage and floodplain context of the ALS data set was superior to all other techniques. The TLS bare earth DEM accuracy and precision were lower than any other technique because of vegetation returns misinterpreted as ground returns. Our results are helpful for understanding the strengths and weaknesses of different approaches.

In partially migratory species, such as Oncorhynchus mykiss, the emergence of life history phenotypes is often attributed to fitness trade-offs associated with growth and survival. Fitness trade-offs can be linked to reproductive tactics that vary between the sexes, as well as the influence of environmental conditions. We found that O. mykiss outmigrants are more likely to be female in nine populations throughout western North America (grand mean 65% female), in support of the hypothesis that anadromy is more likely to benefit females. This bias was not related to migration distance or freshwater productivity, as indicated by latitude. Within one O. mykiss population we also measured the resident sex ratio and did not observe a male bias, despite a high female bias among outmigrants in that system. We provide a simulation to demonstrate the relationship between sex ratios and the proportion of anadromy and show how sex ratios could be a valuable tool for predicting the prevalence of life history types in a population.

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.

Beaver have been referred to as ecosystem engineers because of the large impacts their dam building activities have on the landscape; however, the benefits they may provide to fluvial fish species has been debated. We conducted a watershed-scale experiment to test how increasing beaver dam and colony persistence in a highly degraded incised stream affects the freshwater production of steelhead (Oncorhynchus mykiss). Following the installation of beaver dam analogs (BDAs), we observed significant increases in the density, survival and production of juvenile steelhead without impacting upstream and downstream migrations. The steelhead response occurred as the quantity and complexity of their habitat increased. This study is the first large-scale experiment to quantify the benefits of beavers and BDAs to a fish population and its habitat. Beaver mediated restoration may be a viable and efficient strategy to recover ecosystem function of previously incised streams and to increase the production of imperiled fish populations.

We described and predicted spatial varia- tion in marine migration (anadromy) of female Oncorhynchus mykiss in the John Day River water- shed, Oregon. We collected 149 juvenile O. mykiss across 72 sites and identified locations used by anadromous females by assigning maternal origin (anadromous versus non-anadromous) to each juve- nile. These assignments used comparisons of stron- tium to calcium ratios in otolith primordia and freshwater growth regions to indicate maternal origin. We used logistic regression to predict probability of anadromy in relation to mean annual stream runoff using data from a subset of individuals. This model correctly predicted anadromy in a second sample of individuals with a moderate level of accuracy (e.g., 68% correctly predicted with a 0.5 classification threshold). Residuals from the models were not spatially autocorrelated, suggesting that remaining variability in the expression of anadromy was due to localized influences, as opposed to broad-scale gra- dients unrelated to mean annual stream runoff. These results are important for the management of O. mykiss because anadromous individuals (steelhead) within the John Day River watershed are listed as a threatened species, and it is difficult to discern juvenile steelhead from non-anadromous individuals (rainbow trout) in the field. Our results provide a broad- scale description and prediction of locations supporting anadromy, and new insight for habitat restoration, monitoring, and research to better manage and under- stand the expression of anadromy in O. mykiss.

Alternative male phenotypes in salmonine fishes arise from individuals that mature as larger and older anadromous marine-migrants or as smaller and younger freshwater residents. To better understand the processes influencing the expression of these pheno- types we examined the influences of growth in length (fork length) and whole body lipid content in rainbow trout (Oncorhynchus mykiss). Fish were sampled from the John Day River basin in northeast Oregon where both anadromous ("steelhead") and freshwater resi- dent rainbow trout coexist. Larger males with higher lipid levels had a greater probability of maturing as a resident at age-1+. Among males, 38% were maturing overall, and the odds ratios of the logistic model indicated that the probability of a male maturing early as a resident at age-1+ increased 49% (95% confi- dence interval (CI)=23-81%) for every 5 mm in- crease in length and 33% (95% CI=10-61%) for every 0.5% increase in whole body lipid content. There was an inverse association between individual condition and water temperature as growth was greater in warmer streams while whole body lipid content was higher in cooler streams. Our results support predictions from life history theory and further suggest that relationships between individual condition, maturation, and environmental variables (e.g., water temperature) are shaped by complex developmental and evolutionary influences.

Unfortunately, one of the co-author’s affiliations has been misspelled in the original article and the correct affiliation is ‘‘U.S. Geological Survey.’’ The ‘‘acknowledgment section’’ in the original publication should have included the following disclaimer: ‘‘Use of trade or firm names here is for reader information only and does not imply endorsement of any product or service by the U.S. Government.’’ Figures 1, 2, and 3 have been published incorrectly in the original publication of the article. The corrected version of these figures is provided below.

To comply with legal mandates, meet local management objectives, or both, many federal, state, and tribal organizations have monitoring groups that assess stream habitat at different scales. This myriad of groups has difficulty sharing data and scaling up stream habitat assessments to regional or national levels because of differences in their goals and data collection methods. To assess the performance of and potential for data sharing among monitoring groups, we compared measurements made by seven monitoring groups in 12 stream reaches in northeastern Oregon. We evaluated (1) the consistency (repeatability) of the measurements within each group, (2) the ability of the measurements to reveal environmental heterogeneity, (3) the compatibility of the measurements among monitoring groups, and (4) the relationships of the measurements to values determined from more intensive sampling (detailed measurements used as a standard for accuracy and precision in this study). Overall, we found that some stre...

There is a considerable body of research literature addressing questions surrounding the biomechanics, internal hydrodynamics, external fluid dynamics and neuronal control behind anguilliform swimming, or swimming with whole body undulations. This research spans experimental studies and a host of modelling efforts from the very simple to the enormously complex. In this paper we focus on models of anguilliform swimming at intermediate Reynolds number. The challenge inherent in these modelling efforts, is the unavoidable inextricability of the three components of the swim-system: neural control, muscle mechanics and fluid dynamics. These components all provide input and feedback one to each other in a nonlinear way. Thus, questions about the kinematics, dynamics or functioning of any part of the swim-system can only be truly answered if the entire swim-system is modeled. This is a formidable task, and so modelling efforts to date have restricted themselves to various aspects of the swim-system. We review current models of anguilliform swimming at intermediate Reynolds number and present a promising new modelling approach using the immersed boundary method. This computational method makes it possible to model the entire swim-system while keeping the computational load within manageable limits.

Channel incision is a widespread phenomenon throughout the dry interior Columbia River basin and other semi-arid regions of the world, which degrades stream habitat by fundamentally altering natural ecological, geomorphological and hydrological processes. We examined the extent of localized aggradation behind beaver dams on an incised stream in the interior Columbia River basin to assess the potential for using beaver, Castor canadensis, dams to restore such channels, and the effect of the aggradation on riparian habitat. We estimated aggradation rates behind 13 beaver dams between 1 and 6 years old on Bridge Creek, a tributary to the John Day River in eastern Oregon. Vertical aggradation rates are initially rapid, as high as 0·47 m yr−1, as the entrenched channel fills, then level off to 0·075 m yr−1 by year six, as the sediment begins accumulating on adjacent terraces. We found that a 0·5 m elevation contour above the stream channel approximately coincided with the extent of new riparian vegetation establishment. Therefore, we compared the area surrounding reaches upstream of beaver dams that were within 0·5 m elevation of the stream channel with adjacent reaches where no dams existed. We found that there was five times more area within 0·5 m elevation of the channel upstream of beaver dams, presumably because sediment accumulation had aggraded the channel. Our results suggest that restoration strategies that encourage the recolonization of streams by beaver can rapidly expand riparian habitat along incised streams. Copyright © 2007 John Wiley & Sons, Ltd.

Although water temperature is important to stream biota, it is difficult to collect in a spatially and temporally continuous fashion. We used remotely-sensed Land Surface Temperature (LST) data to estimate mean daily stream temperature for every confluence-to-confluence reach in the John Day River, OR, USA for a ten year period. Models were built at three spatial scales: site-specific, subwatershed, and basin-wide. Model quality was assessed using jackknife and cross-validation. Model metrics for linear regressions of the predicted vs. observed data across all sites and years: site-specific r2 = 0.95, Root Mean Squared Error (RMSE) = 1.25 °C, subwatershed r2 = 0.88, RMSE = 2.02 °C, and basin-wide r2 = 0.87, RMSE = 2.12 °C. Similar analyses were conducted using 2012 eight-day composite LST and eight-day mean stream temperature in five watersheds in the interior Columbia River basin. Mean model metrics across all basins: r2 = 0.91, RMSE = 1.29 °C. Sensitivity analyses indicated accurate basin-wide models can be parameterized using data from as few as four temperature logger sites. This approach generates robust estimates of stream temperature through time for broad spatial regions for which there is only spatially and temporally patchy observational data, and may be useful for managers and researchers interested in stream biota.

In ecology, as in other research fields, efficient sampling for population estimation often drives sample designs toward unequal probability sampling, such as in stratified sampling. Design based statistical analysis tools are appropriate for seamless integration of sample design into the statistical analysis. However, it is also common and necessary, after a sampling design has been implemented, to use datasets to address questions that, in many cases, were not considered during the sampling design phase. Questions may arise requiring the use of model based statistical tools such as multiple regression, quantile regression, or regression tree analysis. However, such model based tools may require, for ensuring unbiased estimation, data from simple random samples, which can be problematic when analyzing data from unequal probability designs. Despite numerous method specific tools available to properly account for sampling design, too often in the analysis of ecological data, sample design is ignored and consequences are not properly considered. We demonstrate here that violation of this assumption can lead to biased parameter estimates in ecological research. In addition, to the set of tools available for researchers to properly account for sampling design in model based analysis, we introduce inverse probability bootstrapping (IPB). Inverse probability bootstrapping is an easily implemented method for obtaining equal probability re-samples from a probability sample, from which unbiased model based estimates can be made. We demonstrate the potential for bias in model-based analyses that ignore sample inclusion probabilities, and the effectiveness of IPB sampling in eliminating this bias, using both simulated and actual ecological data. For illustration, we considered three model based analysis tools--linear regression, quantile regression, and boosted regression tree analysis. In all models, using both simulated and actual ecological data, we found inferences to be biased, sometimes severely, when sample inclusion probabilities were ignored, while IPB sampling effectively produced unbiased parameter estimates.

Twelve salmonid evolutionarily significant units (ESUs) throughout the Columbia River Basin are currently listed as threatened or endangered under the Endangered Species Act; these ESUs are affected differentially by a variety of human activities. We present a standardized quantitative status and risk assessment for 152 listed salmonid stocks in these ESUs and 24 nonlisted stocks. Using data from 1980–2000, which represents a time of stable conditions in the Columbia River hydropower system and a period of ocean conditions generally regarded as poor for Columbia Basin salmonids, we estimated the status of these stocks under two different assumptions: that hatchery-reared spawners were not reproducing during the period of the censuses, or that hatchery-reared spawners were reproducing and thus that reproduction from hatchery inputs was masking population trends. We repeated the analyses using a longer time period containing both “good” and “bad” ocean conditions (1965–2000) as a first step toward determini...

Slender-bodied organisms swimming with whole-body undulations exhibit what appears to be a high degree of kinematic parameter conservation, which is independent of body size. However, organisms of very different sizes swim in fundamentally different physical realms, owing to the relative scaling of viscous and inertial fluid stresses as a function of size and speed. In light of the size-dependent fluid forces, the kinematic constancy suggests three hypotheses: (1) swimming organisms adopt a single "ideal" swimming mode requiring the modification of muscle forces or motor patterns through ontogeny, (2) swimming kinematics are determined predominantly by the passive mechanical interaction of the body and the fluid, resulting in a single swimming mode independent of absolute body size, or (3) while undulatory swimming kinematics may be similar between organisms, there are important size-dependent kinematic differences. In this study, I address this issue by examining the swimming kinematics and dynamics of the medicinal leech Hirudo medicinalis L. as a function of body size. Over a 5-fold increase in body length, the relative amplitude of body undulations during swimming did not change; however, swimming speed, propulsive wave speed, and propulsive wave frequency all decreased, while propulsive wave number increased slightly, strongly supporting hypothesis 2. To determine the source of the observed size-dependent swimming kinematics, I manipulated the dynamic viscosity of the organism's fluid environment to alter the constraints placed on swimming behavior by the physical surroundings. In the elevated-viscosity treatment, all kinematic parameters changed in the opposite direction to that predicted by hypothesis 2, rejecting both the idea that swimming kinematics are simply determined by passive mechanical interactions and that leeches have a target swimming mode under active control.

The biological world is full of systems whose component parts interact in a coupled non—linear fashion. As a result, studying any component of the system in isolation may not be representative of its natural behavior due to the coupling, and predicting the behavior of the entire system as a function of variation in any one parameter may be quite difficult due to the non—linear nature of the interactions. Swimming with whole body undulations is just such a system. The component parts of the swimming-system (muscle, skeleton, soft—tissue, and the surrounding fluid), are mechanically and physiologically coupled in a strongly nonlinear manner. Therefore, to predict the outcome of the entire system, i.e., swimming behavior, or to understand the role any one component plays as a determinant of the outcome, a mechanistic approach encompassing the form of the component's interactions is required. This approach is essential for developing scaling arguments, or discussing the consequences of morphological and physiological variation on behavioral and evolutionary “performance.” Below I outline an example of this method: a simplistic model of the mechanical interactions between the swimming system components of a leech. The model is based on in vitro characterizations of these components and first principle descriptions of their interactions. Solving the model's governing equations generates swimming behavior in the model organism. In addition, the model can predict the behavior of the swimming-system's component parts, allowing calculations of swimming performance and parameter variation not possible with other approaches.

International audience; Dendritic ecological networks (DENs) are a unique form of ecological networks that exhibit a dendritic network topology (e.g. stream and cave networks or plant architecture). DENs have a dual spatial representation; as points within the network and as points in geographical space. Consequently, some analytical methods used to quantify relationships in other types of ecological networks, or in 2-D space, may be inadequate for studying the influence of structure and connectivity on ecological processes within DENs. We propose a conceptual taxonomy of network analysis methods that account for DEN characteristics to varying degrees and provide a synthesis of the different approaches within the context of stream ecology. Within this context, we summarise the key innovations of a new family of spatial statistical models that describe spatial relationships in DENs. Finally, we discuss how different network analyses may be combined to address more complex and novel research questions. While our main focus is streams, the taxonomy of network analyses is also relevant anywhere spatial patterns in both network and 2-D space can be used to explore the influence of multi-scale processes on biota and their habitat (e.g. plant morphology and pest infestation, or preferential migration along stream or road corridors).

Degradation of dryland riparian ecosystems has been linked to the lowering of alluvial groundwater tables and reduced floodplain connectivity. Establishing riparian plants in dryland ecosystems with high water-stress and herbivore pressure presents major challenges for restoration practitioners. By planting at sufficient depths to reach lowered water tables, deep-planting provides direct access to water and encourages root development within hydrated soils. While deep-planting is a promising alternative to traditional supplemental irrigation in dryland areas affected by lowered water tables, few studies have evaluated deep-planting where planting depths must exceed one-meter to reach water tables and where herbivore protection is required. To evaluate deep-planting as an irrigation alternative where lowered water tables present a challenge to riparian restoration, we conducted experimental plantings along an incised stream within a semiarid watershed using deep-planting without supplemental irrigation in ...

Conservation and recovery plans for endangered species around the world, including the US Endangered Species Act (ESA), rely on habitat assessments for data, conclusions and planning of short and long-term management strategies. In the Pacific Northwest of the United States, hundreds of millions of dollars ($US) per year are spent on thousands of restoration projects across the extent of ESA-listed Pacific salmon—often without clearly connecting restoration actions to ecosystem and population needs. Numerous decentralized administrative units select and fund projects based on agency/organization needs or availability of funds with little or no centralized planning nor post-project monitoring. The need therefore arises for metrics to identify whether ecosystem and species level restoration needs are being met by the assemblage of implemented projects. We reviewed habitat assessments and recovery plans to identify ecological needs and statistically compared these to the distribution of co-located restoratio...

Processes that influence habitat selection in landscapes involve the interaction of habitat composition and configuration and are particularly important for species with complex life cycles. We assessed the relative influence of landscape spatial processes and local habitat characteristics on patterns in the distribution and abundance of spawning steelhead (Oncorhynchus mykiss), a threatened salmonid fish, across ∼15,000 stream km in the John Day River basin, Oregon, USA. We used hurdle regression and a multi-model information theoretic approach to identify the relative importance of covariates representing key aspects of the steelhead life cycle (e.g., site access, spawning habitat quality, juvenile survival) at two spatial scales: within 2-km long survey reaches (local sites) and ecological neighborhoods (5 km) surrounding the local sites. Based on Akaike's Information Criterion, models that included covariates describing ecological neighborhoods provided the best description of the distribution and abundance of steelhead spawning given the data. Among these covariates, our representation of offspring survival (growing-season-degree-days, °C) had the strongest effect size (7x) relative to other predictors. Predictive performances of model-averaged composite and neighborhood-only models were better than a site-only model based on both occurrence (percentage of sites correctly classified = 0.80±0.03 SD, 0.78±0.02 vs. 0.62±0.05, respectively) and counts (root mean square error = 3.37, 3.93 vs. 5.57, respectively). The importance of both temperature and stream flow for steelhead spawning suggest this species may be highly sensitive to impacts of land and water uses, and to projected climate impacts in the region and that landscape context, complementation, and connectivity will drive how this species responds to future environments.

Before-after-control-impact (BACI) designs are an effective method to evaluate natural and human-induced perturbations on ecological variables when treatment sites cannot be randomly chosen. While effect sizes of interest can be tested with frequentist methods, using Bayesian Markov chain Monte Carlo (MCMC) sampling methods, probabilities of effect sizes, such as a ≥20 % increase in density after restoration, can be directly estimated. Although BACI and Bayesian methods are used widely for assessing natural and human-induced impacts for field experiments, the application of hierarchal Bayesian modeling with MCMC sampling to BACI designs is less common. Here, we combine these approaches and extend the typical presentation of results with an easy to interpret ratio, which provides an answer to the main study question—“How much impact did a management action or natural perturbation have?” As an example of this approach, we evaluate the impact of a restoration project, which implemented beaver dam analogs, on survival and density of juvenile steelhead. Results indicated the probabilities of a ≥30 % increase were high for survival and density after the dams were installed, 0.88 and 0.99, respectively, while probabilities for a higher increase of ≥50 % were variable, 0.17 and 0.82, respectively. This approach demonstrates a useful extension of Bayesian methods that can easily be generalized to other study designs from simple (e.g., single factor ANOVA, paired t test) to more complicated block designs (e.g., crossover, split-plot). This approach is valuable for estimating the probabilities of restoration impacts or other management actions. Electronic supplementary material The online version of this article (doi:10.1007/s10661-016-5526-6) contains supplementary material, which is available to authorized users.